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authorAllen Byrne <50328838+byrnHDF@users.noreply.github.com>2021-08-23 18:50:17 (GMT)
committerGitHub <noreply@github.com>2021-08-23 18:50:17 (GMT)
commitf8ecdf846c7e054d874ea92baf5c9b6c2b47e836 (patch)
treeeb33b014a18e87bf9df4dfa21b532af5c288c225 /tools/src
parent0a9099807a127a74b35ecf2c4ad98d6571f2e753 (diff)
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1.12 Tools merges from develop (#949)
* Tools merges from develop Brings the tools getopt(3) replacement into the main library (#803) Perform option arg variables (#834) Removes unused commented-out code from h5jamgentest.c (#851) Reorg tools perform to provide h5perf for installation (#884) * Fix missing files * Remove empty files * Remove empty file * Resync defines * Fix endif typo * Add Makfile to list * Fix typo * Remove H5_GCC_DIAG_ON line to match removal of H5_GCC_DIAG_OFF line in sio_engine.c/ Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com> Co-authored-by: Larry Knox <lrknox@hdfgroup.org>
Diffstat (limited to 'tools/src')
-rw-r--r--tools/src/CMakeLists.txt5
-rw-r--r--tools/src/Makefile.am2
-rw-r--r--tools/src/h5copy/h5copy.c48
-rw-r--r--tools/src/h5diff/h5diff_common.c108
-rw-r--r--tools/src/h5dump/h5dump.c262
-rw-r--r--tools/src/h5dump/h5dump_xml.c39
-rw-r--r--tools/src/h5format_convert/h5format_convert.c43
-rw-r--r--tools/src/h5import/h5import.c162
-rw-r--r--tools/src/h5jam/h5jam.c20
-rw-r--r--tools/src/h5jam/h5unjam.c20
-rw-r--r--tools/src/h5perf/CMakeLists.txt103
-rw-r--r--tools/src/h5perf/Makefile.am63
-rw-r--r--tools/src/h5perf/perf.c802
-rw-r--r--tools/src/h5perf/pio_engine.c2747
-rw-r--r--tools/src/h5perf/pio_perf.c1718
-rw-r--r--tools/src/h5perf/pio_perf.h109
-rw-r--r--tools/src/h5perf/sio_engine.c1330
-rw-r--r--tools/src/h5perf/sio_perf.c1301
-rw-r--r--tools/src/h5perf/sio_perf.h104
-rw-r--r--tools/src/h5repack/h5repack_main.c162
-rw-r--r--tools/src/h5stat/h5stat.c141
-rw-r--r--tools/src/misc/h5clear.c51
-rw-r--r--tools/src/misc/h5mkgrp.c28
23 files changed, 8729 insertions, 639 deletions
diff --git a/tools/src/CMakeLists.txt b/tools/src/CMakeLists.txt
index 8c3e361..e291f61 100644
--- a/tools/src/CMakeLists.txt
+++ b/tools/src/CMakeLists.txt
@@ -13,7 +13,7 @@ add_subdirectory (misc)
#-- Add the h5import and test executables
add_subdirectory (h5import)
-#-- h5Repack executables
+#-- h5repack executables
add_subdirectory (h5repack)
#-- Add the h5dump and test executables
@@ -30,3 +30,6 @@ add_subdirectory (h5dump)
#-- Add the h5format_convert and test executables
add_subdirectory (h5format_convert)
+
+#-- h5perf executables
+add_subdirectory (h5perf)
diff --git a/tools/src/Makefile.am b/tools/src/Makefile.am
index 397bd31..5af7d06 100644
--- a/tools/src/Makefile.am
+++ b/tools/src/Makefile.am
@@ -23,6 +23,6 @@ CONFIG=ordered
# All subdirectories
SUBDIRS=h5diff h5ls h5dump misc h5import h5repack h5jam h5copy \
- h5format_convert h5stat
+ h5format_convert h5stat h5perf
include $(top_srcdir)/config/conclude.am
diff --git a/tools/src/h5copy/h5copy.c b/tools/src/h5copy/h5copy.c
index f618914..4e9a25e 100644
--- a/tools/src/h5copy/h5copy.c
+++ b/tools/src/h5copy/h5copy.c
@@ -19,23 +19,23 @@
#define PROGRAMNAME "h5copy"
/* command-line options: short and long-named parameters */
-static const char * s_opts = "d:f:hi:o:ps:vVE";
-static struct long_options l_opts[] = {{"destination", require_arg, 'd'},
- {"flag", require_arg, 'f'},
- {"help", no_arg, 'h'},
- {"input", require_arg, 'i'},
- {"output", require_arg, 'o'},
- {"parents", no_arg, 'p'},
- {"source", require_arg, 's'},
- {"verbose", no_arg, 'v'},
- {"version", no_arg, 'V'},
- {"enable-error-stack", no_arg, 'E'},
- {NULL, 0, '\0'}};
-char * fname_src = NULL;
-char * fname_dst = NULL;
-char * oname_src = NULL;
-char * oname_dst = NULL;
-char * str_flag = NULL;
+static const char * s_opts = "d:f:hi:o:ps:vVE";
+static struct h5_long_options l_opts[] = {{"destination", require_arg, 'd'},
+ {"flag", require_arg, 'f'},
+ {"help", no_arg, 'h'},
+ {"input", require_arg, 'i'},
+ {"output", require_arg, 'o'},
+ {"parents", no_arg, 'p'},
+ {"source", require_arg, 's'},
+ {"verbose", no_arg, 'v'},
+ {"version", no_arg, 'V'},
+ {"enable-error-stack", no_arg, 'E'},
+ {NULL, 0, '\0'}};
+char * fname_src = NULL;
+char * fname_dst = NULL;
+char * oname_src = NULL;
+char * oname_dst = NULL;
+char * str_flag = NULL;
/*-------------------------------------------------------------------------
* Function: leave
@@ -242,19 +242,19 @@ main(int argc, const char *argv[])
} /* end if */
/* parse command line options */
- while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+ while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
switch ((char)opt) {
case 'd':
- oname_dst = HDstrdup(opt_arg);
+ oname_dst = HDstrdup(H5_optarg);
break;
case 'f':
/* validate flag */
- if (parse_flag(opt_arg, &flag) < 0) {
+ if (parse_flag(H5_optarg, &flag) < 0) {
usage();
leave(EXIT_FAILURE);
}
- str_flag = HDstrdup(opt_arg);
+ str_flag = HDstrdup(H5_optarg);
break;
case 'h':
@@ -263,11 +263,11 @@ main(int argc, const char *argv[])
break;
case 'i':
- fname_src = HDstrdup(opt_arg);
+ fname_src = HDstrdup(H5_optarg);
break;
case 'o':
- fname_dst = HDstrdup(opt_arg);
+ fname_dst = HDstrdup(H5_optarg);
break;
case 'p':
@@ -275,7 +275,7 @@ main(int argc, const char *argv[])
break;
case 's':
- oname_src = HDstrdup(opt_arg);
+ oname_src = HDstrdup(H5_optarg);
break;
case 'V':
diff --git a/tools/src/h5diff/h5diff_common.c b/tools/src/h5diff/h5diff_common.c
index 1b81824..b669087 100644
--- a/tools/src/h5diff/h5diff_common.c
+++ b/tools/src/h5diff/h5diff_common.c
@@ -25,30 +25,30 @@ static int check_d_input(const char *);
* Command-line options: The user can specify short or long-named
* parameters.
*/
-static const char * s_opts = "hVrv*qn:d:p:NcelxE:A:S";
-static struct long_options l_opts[] = {{"help", no_arg, 'h'},
- {"version", no_arg, 'V'},
- {"report", no_arg, 'r'},
- {"verbose", optional_arg, 'v'},
- {"quiet", no_arg, 'q'},
- {"count", require_arg, 'n'},
- {"delta", require_arg, 'd'},
- {"relative", require_arg, 'p'},
- {"nan", no_arg, 'N'},
- {"compare", no_arg, 'c'},
- {"use-system-epsilon", no_arg, 'e'},
- {"follow-symlinks", no_arg, 'l'},
- {"no-dangling-links", no_arg, 'x'},
- {"exclude-path", require_arg, 'E'},
- {"exclude-attribute", require_arg, 'A'},
- {"enable-error-stack", no_arg, 'S'},
- {"vol-value-1", require_arg, '1'},
- {"vol-name-1", require_arg, '2'},
- {"vol-info-1", require_arg, '3'},
- {"vol-value-2", require_arg, '4'},
- {"vol-name-2", require_arg, '5'},
- {"vol-info-2", require_arg, '6'},
- {NULL, 0, '\0'}};
+static const char * s_opts = "hVrv*qn:d:p:NcelxE:A:S";
+static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'},
+ {"version", no_arg, 'V'},
+ {"report", no_arg, 'r'},
+ {"verbose", optional_arg, 'v'},
+ {"quiet", no_arg, 'q'},
+ {"count", require_arg, 'n'},
+ {"delta", require_arg, 'd'},
+ {"relative", require_arg, 'p'},
+ {"nan", no_arg, 'N'},
+ {"compare", no_arg, 'c'},
+ {"use-system-epsilon", no_arg, 'e'},
+ {"follow-symlinks", no_arg, 'l'},
+ {"no-dangling-links", no_arg, 'x'},
+ {"exclude-path", require_arg, 'E'},
+ {"exclude-attribute", require_arg, 'A'},
+ {"enable-error-stack", no_arg, 'S'},
+ {"vol-value-1", require_arg, '1'},
+ {"vol-name-1", require_arg, '2'},
+ {"vol-info-1", require_arg, '3'},
+ {"vol-value-2", require_arg, '4'},
+ {"vol-name-2", require_arg, '5'},
+ {"vol-info-2", require_arg, '6'},
+ {NULL, 0, '\0'}};
/*-------------------------------------------------------------------------
* Function: check_options
@@ -232,7 +232,7 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
exclude_attr_head = NULL;
/* parse command line options */
- while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+ while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
switch ((char)opt) {
default:
usage();
@@ -256,20 +256,20 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
* special check for short opt
*/
if (!strcmp(argv[i], "-v")) {
- if (opt_arg != NULL)
- opt_ind--;
+ if (H5_optarg != NULL)
+ H5_optind--;
opts->mode_verbose_level = 0;
break;
}
else if (!strncmp(argv[i], "-v", (size_t)2)) {
- if (opt_arg != NULL)
- opt_ind--;
+ if (H5_optarg != NULL)
+ H5_optind--;
opts->mode_verbose_level = atoi(&argv[i][2]);
break;
}
else {
- if (opt_arg != NULL)
- opts->mode_verbose_level = HDatoi(opt_arg);
+ if (H5_optarg != NULL)
+ opts->mode_verbose_level = HDatoi(H5_optarg);
else
opts->mode_verbose_level = 0;
}
@@ -308,7 +308,7 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
}
/* init */
- exclude_node->obj_path = opt_arg;
+ exclude_node->obj_path = H5_optarg;
exclude_node->obj_type = H5TRAV_TYPE_UNKNOWN;
exclude_prev = exclude_head;
@@ -336,7 +336,7 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
}
/* init */
- exclude_attr_node->obj_path = opt_arg;
+ exclude_attr_node->obj_path = H5_optarg;
exclude_attr_node->obj_type = H5TRAV_TYPE_UNKNOWN;
exclude_attr_prev = exclude_attr_head;
@@ -356,23 +356,23 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
case 'd':
opts->delta_bool = 1;
- if (check_d_input(opt_arg) == -1) {
- HDprintf("<-d %s> is not a valid option\n", opt_arg);
+ if (check_d_input(H5_optarg) == -1) {
+ HDprintf("<-d %s> is not a valid option\n", H5_optarg);
usage();
h5diff_exit(EXIT_FAILURE);
}
- opts->delta = HDatof(opt_arg);
+ opts->delta = HDatof(H5_optarg);
/* do not check against default, the DBL_EPSILON is being replaced by user */
break;
case 'p':
opts->percent_bool = 1;
- if (check_p_input(opt_arg) == -1) {
- HDprintf("<-p %s> is not a valid option\n", opt_arg);
+ if (check_p_input(H5_optarg) == -1) {
+ HDprintf("<-p %s> is not a valid option\n", H5_optarg);
usage();
h5diff_exit(EXIT_FAILURE);
}
- opts->percent = HDatof(opt_arg);
+ opts->percent = HDatof(H5_optarg);
/* -p 0 is the same as default */
if (H5_DBL_ABS_EQUAL(opts->percent, 0.0))
@@ -381,12 +381,12 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
case 'n':
opts->count_bool = 1;
- if (check_n_input(opt_arg) == -1) {
- HDprintf("<-n %s> is not a valid option\n", opt_arg);
+ if (check_n_input(H5_optarg) == -1) {
+ HDprintf("<-n %s> is not a valid option\n", H5_optarg);
usage();
h5diff_exit(EXIT_FAILURE);
}
- opts->count = HDstrtoull(opt_arg, NULL, 0);
+ opts->count = HDstrtoull(H5_optarg, NULL, 0);
break;
case 'N':
@@ -403,34 +403,34 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
case '1':
opts->vol_info[0].type = VOL_BY_VALUE;
- opts->vol_info[0].u.value = (H5VL_class_value_t)HDatoi(opt_arg);
+ opts->vol_info[0].u.value = (H5VL_class_value_t)HDatoi(H5_optarg);
opts->custom_vol[0] = TRUE;
break;
case '2':
opts->vol_info[0].type = VOL_BY_NAME;
- opts->vol_info[0].u.name = opt_arg;
+ opts->vol_info[0].u.name = H5_optarg;
opts->custom_vol[0] = TRUE;
break;
case '3':
- opts->vol_info[0].info_string = opt_arg;
+ opts->vol_info[0].info_string = H5_optarg;
break;
case '4':
opts->vol_info[1].type = VOL_BY_VALUE;
- opts->vol_info[1].u.value = (H5VL_class_value_t)HDatoi(opt_arg);
+ opts->vol_info[1].u.value = (H5VL_class_value_t)HDatoi(H5_optarg);
opts->custom_vol[1] = TRUE;
break;
case '5':
opts->vol_info[1].type = VOL_BY_NAME;
- opts->vol_info[1].u.name = opt_arg;
+ opts->vol_info[1].u.name = H5_optarg;
opts->custom_vol[1] = TRUE;
break;
case '6':
- opts->vol_info[1].info_string = opt_arg;
+ opts->vol_info[1].info_string = H5_optarg;
break;
}
}
@@ -447,15 +447,15 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
opts->exclude_attr = exclude_attr_head;
/* check for file names to be processed */
- if (argc <= opt_ind || argv[opt_ind + 1] == NULL) {
+ if (argc <= H5_optind || argv[H5_optind + 1] == NULL) {
error_msg("missing file names\n");
usage();
h5diff_exit(EXIT_FAILURE);
}
- *fname1 = argv[opt_ind];
- *fname2 = argv[opt_ind + 1];
- *objname1 = argv[opt_ind + 2];
+ *fname1 = argv[H5_optind];
+ *fname2 = argv[H5_optind + 1];
+ *objname1 = argv[H5_optind + 2];
H5TOOLS_DEBUG("file1 = %s", *fname1);
H5TOOLS_DEBUG("file2 = %s", *fname2);
@@ -466,8 +466,8 @@ parse_command_line(int argc, const char *argv[], const char **fname1, const char
}
H5TOOLS_DEBUG("objname1 = %s", *objname1);
- if (argv[opt_ind + 3] != NULL) {
- *objname2 = argv[opt_ind + 3];
+ if (argv[H5_optind + 3] != NULL) {
+ *objname2 = argv[H5_optind + 3];
}
else {
*objname2 = *objname1;
diff --git a/tools/src/h5dump/h5dump.c b/tools/src/h5dump/h5dump.c
index c9c8185..cab340d 100644
--- a/tools/src/h5dump/h5dump.c
+++ b/tools/src/h5dump/h5dump.c
@@ -80,132 +80,54 @@ struct handler_t {
*/
/* The following initialization makes use of C language concatenating */
/* "xxx" "yyy" into "xxxyyy". */
-static const char * s_opts = "a:b*c:d:ef:g:hik:l:m:n*o*pq:rs:t:uvw:xyz:A*BCD:E*F:G:HM:N:O*RS:VX:";
-static struct long_options l_opts[] = {{"attribute", require_arg, 'a'},
- {"attribut", require_arg, 'a'},
- {"attribu", require_arg, 'a'},
- {"attrib", require_arg, 'a'},
- {"attri", require_arg, 'a'},
- {"attr", require_arg, 'a'},
- {"att", require_arg, 'a'},
- {"at", require_arg, 'a'},
- {"binary", optional_arg, 'b'},
- {"count", require_arg, 'c'},
- {"coun", require_arg, 'c'},
- {"cou", require_arg, 'c'},
- {"co", require_arg, 'c'},
- {"dataset", require_arg, 'd'},
- {"datase", require_arg, 'd'},
- {"datas", require_arg, 'd'},
- {"escape", no_arg, 'e'},
- {"filedriver", require_arg, 'f'},
- {"filedrive", require_arg, 'f'},
- {"filedriv", require_arg, 'f'},
- {"filedri", require_arg, 'f'},
- {"filedr", require_arg, 'f'},
- {"filed", require_arg, 'f'},
- {"file", require_arg, 'f'},
- {"fil", require_arg, 'f'},
- {"fi", require_arg, 'f'},
- {"group", require_arg, 'g'},
- {"grou", require_arg, 'g'},
- {"gro", require_arg, 'g'},
- {"gr", require_arg, 'g'},
- {"help", no_arg, 'h'},
- {"hel", no_arg, 'h'},
- {"object-ids", no_arg, 'i'},
- {"object-id", no_arg, 'i'},
- {"object-i", no_arg, 'i'},
- {"object", no_arg, 'i'},
- {"objec", no_arg, 'i'},
- {"obje", no_arg, 'i'},
- {"obj", no_arg, 'i'},
- {"ob", no_arg, 'i'},
- {"block", require_arg, 'k'},
- {"bloc", require_arg, 'k'},
- {"blo", require_arg, 'k'},
- {"bl", require_arg, 'k'},
- {"soft-link", require_arg, 'l'},
- {"soft-lin", require_arg, 'l'},
- {"soft-li", require_arg, 'l'},
- {"soft-l", require_arg, 'l'},
- {"soft", require_arg, 'l'},
- {"sof", require_arg, 'l'},
- {"format", require_arg, 'm'},
- {"contents", optional_arg, 'n'},
- {"output", optional_arg, 'o'},
- {"outpu", optional_arg, 'o'},
- {"outp", optional_arg, 'o'},
- {"out", optional_arg, 'o'},
- {"ou", optional_arg, 'o'},
- {"properties", no_arg, 'p'},
- {"sort_by", require_arg, 'q'},
- {"string", no_arg, 'r'},
- {"strin", no_arg, 'r'},
- {"start", require_arg, 's'},
- {"star", require_arg, 's'},
- {"sta", require_arg, 's'},
- {"datatype", require_arg, 't'},
- {"datatyp", require_arg, 't'},
- {"dataty", require_arg, 't'},
- {"datat", require_arg, 't'},
- {"use-dtd", no_arg, 'u'},
- {"use-dt", no_arg, 'u'},
- {"use-d", no_arg, 'u'},
- {"use-", no_arg, 'u'},
- {"use", no_arg, 'u'},
- {"us", no_arg, 'u'},
- {"u", no_arg, 'u'},
- {"vds-view-first-missing", no_arg, 'v'},
- {"width", require_arg, 'w'},
- {"widt", require_arg, 'w'},
- {"wid", require_arg, 'w'},
- {"wi", require_arg, 'w'},
- {"xml", no_arg, 'x'},
- {"xm", no_arg, 'x'},
- {"noindex", no_arg, 'y'},
- {"sort_order", require_arg, 'z'},
- {"onlyattr", optional_arg, 'A'},
- {"superblock", no_arg, 'B'},
- {"boot-block", no_arg, 'B'},
- {"boot-bloc", no_arg, 'B'},
- {"boot-blo", no_arg, 'B'},
- {"boot-bl", no_arg, 'B'},
- {"boot-b", no_arg, 'B'},
- {"boot", no_arg, 'B'},
- {"boo", no_arg, 'B'},
- {"bo", no_arg, 'B'},
- {"no-compact-subset", no_arg, 'C'},
- {"xml-dtd", require_arg, 'D'},
- {"xml-dt", require_arg, 'D'},
- {"xml-d", require_arg, 'D'},
- {"enable-error-stack", optional_arg, 'E'},
- {"form", require_arg, 'F'},
- {"vds-gap-size", require_arg, 'G'},
- {"header", no_arg, 'H'},
- {"heade", no_arg, 'H'},
- {"head", no_arg, 'H'},
- {"hea", no_arg, 'H'},
- {"packed-bits", require_arg, 'M'},
- {"any_path", require_arg, 'N'},
- {"ddl", optional_arg, 'O'},
- {"region", no_arg, 'R'},
- {"stride", require_arg, 'S'},
- {"strid", require_arg, 'S'},
- {"version", no_arg, 'V'},
- {"versio", no_arg, 'V'},
- {"versi", no_arg, 'V'},
- {"vers", no_arg, 'V'},
- {"ver", no_arg, 'V'},
- {"ve", no_arg, 'V'},
- {"xml-ns", require_arg, 'X'},
- {"xml-n", require_arg, 'X'},
- {"s3-cred", require_arg, '$'},
- {"hdfs-attrs", require_arg, '#'},
- {"vol-value", require_arg, '1'},
- {"vol-name", require_arg, '2'},
- {"vol-info", require_arg, '3'},
- {NULL, 0, '\0'}};
+static const char * s_opts = "a:b*c:d:ef:g:hik:l:m:n*o*pq:rs:t:uvw:xyz:A*BCD:E*F:G:HM:N:O*RS:VX:";
+static struct h5_long_options l_opts[] = {{"attribute", require_arg, 'a'},
+ {"binary", optional_arg, 'b'},
+ {"count", require_arg, 'c'},
+ {"dataset", require_arg, 'd'},
+ {"escape", no_arg, 'e'},
+ {"filedriver", require_arg, 'f'},
+ {"group", require_arg, 'g'},
+ {"help", no_arg, 'h'},
+ {"object-ids", no_arg, 'i'},
+ {"block", require_arg, 'k'},
+ {"soft-link", require_arg, 'l'},
+ {"format", require_arg, 'm'},
+ {"contents", optional_arg, 'n'},
+ {"output", optional_arg, 'o'},
+ {"properties", no_arg, 'p'},
+ {"sort_by", require_arg, 'q'},
+ {"string", no_arg, 'r'},
+ {"start", require_arg, 's'},
+ {"datatype", require_arg, 't'},
+ {"use-dtd", no_arg, 'u'},
+ {"vds-view-first-missing", no_arg, 'v'},
+ {"width", require_arg, 'w'},
+ {"xml", no_arg, 'x'},
+ {"noindex", no_arg, 'y'},
+ {"sort_order", require_arg, 'z'},
+ {"onlyattr", optional_arg, 'A'},
+ {"superblock", no_arg, 'B'},
+ {"boot-block", no_arg, 'B'},
+ {"no-compact-subset", no_arg, 'C'},
+ {"xml-dtd", require_arg, 'D'},
+ {"enable-error-stack", optional_arg, 'E'},
+ {"form", require_arg, 'F'},
+ {"vds-gap-size", require_arg, 'G'},
+ {"header", no_arg, 'H'},
+ {"packed-bits", require_arg, 'M'},
+ {"any_path", require_arg, 'N'},
+ {"ddl", optional_arg, 'O'},
+ {"region", no_arg, 'R'},
+ {"stride", require_arg, 'S'},
+ {"version", no_arg, 'V'},
+ {"xml-ns", require_arg, 'X'},
+ {"s3-cred", require_arg, '$'},
+ {"hdfs-attrs", require_arg, '#'},
+ {"vol-value", require_arg, '1'},
+ {"vol-name", require_arg, '2'},
+ {"vol-info", require_arg, '3'},
+ {NULL, 0, '\0'}};
/*-------------------------------------------------------------------------
* Function: leave
@@ -917,7 +839,7 @@ parse_command_line(int argc, const char *argv[])
}
/* parse command line options */
- while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+ while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
parse_start:
switch ((char)opt) {
case 'R':
@@ -931,8 +853,8 @@ parse_start:
case 'n':
dump_opts.display_fi = TRUE;
last_was_dset = FALSE;
- if (opt_arg != NULL)
- h5trav_set_verbose(HDatoi(opt_arg));
+ if (H5_optarg != NULL)
+ h5trav_set_verbose(HDatoi(H5_optarg));
break;
case 'p':
dump_opts.display_dcpl = TRUE;
@@ -949,8 +871,8 @@ parse_start:
last_was_dset = FALSE;
break;
case 'A':
- if (opt_arg != NULL) {
- if (0 == HDatoi(opt_arg))
+ if (H5_optarg != NULL) {
+ if (0 == HDatoi(H5_optarg))
dump_opts.include_attrs = FALSE;
}
else {
@@ -974,7 +896,7 @@ parse_start:
goto done;
break;
case 'w': {
- int sh5tools_nCols = HDatoi(opt_arg);
+ int sh5tools_nCols = HDatoi(H5_optarg);
if (sh5tools_nCols <= 0)
h5tools_nCols = 65535;
@@ -988,7 +910,7 @@ parse_start:
for (i = 0; i < argc; i++)
if (!hand[i].func) {
hand[i].func = handle_paths;
- hand[i].obj = HDstrdup(opt_arg);
+ hand[i].obj = HDstrdup(H5_optarg);
break;
}
@@ -1000,7 +922,7 @@ parse_start:
for (i = 0; i < argc; i++)
if (!hand[i].func) {
hand[i].func = handle_attributes;
- hand[i].obj = HDstrdup(opt_arg);
+ hand[i].obj = HDstrdup(H5_optarg);
break;
}
@@ -1012,7 +934,7 @@ parse_start:
for (i = 0; i < argc; i++)
if (!hand[i].func) {
hand[i].func = handle_datasets;
- hand[i].obj = HDstrdup(opt_arg);
+ hand[i].obj = HDstrdup(H5_optarg);
hand[i].subset_info = parse_subset_params(hand[i].obj);
last_dset = &hand[i];
break;
@@ -1021,7 +943,7 @@ parse_start:
last_was_dset = TRUE;
break;
case 'f':
- driver_name_g = opt_arg;
+ driver_name_g = H5_optarg;
break;
case 'g':
dump_opts.display_all = 0;
@@ -1029,7 +951,7 @@ parse_start:
for (i = 0; i < argc; i++)
if (!hand[i].func) {
hand[i].func = handle_groups;
- hand[i].obj = HDstrdup(opt_arg);
+ hand[i].obj = HDstrdup(H5_optarg);
break;
}
@@ -1041,7 +963,7 @@ parse_start:
for (i = 0; i < argc; i++)
if (!hand[i].func) {
hand[i].func = handle_links;
- hand[i].obj = HDstrdup(opt_arg);
+ hand[i].obj = HDstrdup(H5_optarg);
break;
}
@@ -1053,7 +975,7 @@ parse_start:
for (i = 0; i < argc; i++)
if (!hand[i].func) {
hand[i].func = handle_datatypes;
- hand[i].obj = HDstrdup(opt_arg);
+ hand[i].obj = HDstrdup(H5_optarg);
break;
}
@@ -1061,7 +983,7 @@ parse_start:
break;
case 'O':
- if (h5tools_set_output_file(opt_arg, 0) < 0) {
+ if (h5tools_set_output_file(H5_optarg, 0) < 0) {
usage(h5tools_getprogname());
goto error;
}
@@ -1069,20 +991,20 @@ parse_start:
case 'o':
if (bin_output) {
- if (h5tools_set_data_output_file(opt_arg, 1) < 0) {
+ if (h5tools_set_data_output_file(H5_optarg, 1) < 0) {
usage(h5tools_getprogname());
goto error;
}
}
else {
if (dump_opts.display_attr_data && !dump_opts.display_data) {
- if (h5tools_set_attr_output_file(opt_arg, 0) < 0) {
+ if (h5tools_set_attr_output_file(H5_optarg, 0) < 0) {
usage(h5tools_getprogname());
goto error;
}
}
if (dump_opts.display_data || dump_opts.display_all) {
- if (h5tools_set_data_output_file(opt_arg, 0) < 0) {
+ if (h5tools_set_data_output_file(H5_optarg, 0) < 0) {
usage(h5tools_getprogname());
goto error;
}
@@ -1091,12 +1013,12 @@ parse_start:
dump_opts.usingdasho = TRUE;
last_was_dset = FALSE;
- outfname_g = opt_arg;
+ outfname_g = H5_optarg;
break;
case 'b':
- if (opt_arg != NULL) {
- if ((bin_form = set_binary_form(opt_arg)) < 0) {
+ if (H5_optarg != NULL) {
+ if ((bin_form = set_binary_form(H5_optarg)) < 0) {
/* failed to set binary form */
usage(h5tools_getprogname());
goto error;
@@ -1115,7 +1037,7 @@ parse_start:
break;
case 'q':
- if ((sort_by = set_sort_by(opt_arg)) < 0) {
+ if ((sort_by = set_sort_by(H5_optarg)) < 0) {
/* failed to set "sort by" form */
usage(h5tools_getprogname());
goto error;
@@ -1123,7 +1045,7 @@ parse_start:
break;
case 'z':
- if ((sort_order = set_sort_order(opt_arg)) < 0) {
+ if ((sort_order = set_sort_order(H5_optarg)) < 0) {
/* failed to set "sort order" form */
usage(h5tools_getprogname());
goto error;
@@ -1135,7 +1057,7 @@ parse_start:
error_msg("option \"-%c\" can only be used after --dataset option\n", opt);
goto error;
}
- if (parse_mask_list(opt_arg) != SUCCEED) {
+ if (parse_mask_list(H5_optarg) != SUCCEED) {
usage(h5tools_getprogname());
goto error;
}
@@ -1145,7 +1067,7 @@ parse_start:
dump_opts.display_vds_first = TRUE;
break;
case 'G':
- dump_opts.vds_gap_size = HDatoi(opt_arg);
+ dump_opts.vds_gap_size = HDatoi(H5_optarg);
if (dump_opts.vds_gap_size < 0) {
usage(h5tools_getprogname());
goto error;
@@ -1172,13 +1094,13 @@ parse_start:
case 'D':
/* specify alternative XML DTD or schema */
/* To Do: check format of this value? */
- xml_dtd_uri_g = opt_arg;
+ xml_dtd_uri_g = H5_optarg;
h5tools_nCols = 0;
break;
case 'm':
/* specify alternative floating point printing format */
- fp_format = opt_arg;
+ fp_format = H5_optarg;
h5tools_nCols = 0;
break;
@@ -1189,10 +1111,10 @@ parse_start:
usage(h5tools_getprogname());
goto error;
}
- if (HDstrcmp(opt_arg, ":") == 0)
+ if (HDstrcmp(H5_optarg, ":") == 0)
xmlnsprefix = "";
else
- xmlnsprefix = opt_arg;
+ xmlnsprefix = H5_optarg;
h5tools_nCols = 0;
break;
/** end XML parameters **/
@@ -1238,33 +1160,33 @@ parse_start:
HDfree(s->start.data);
s->start.data = NULL;
}
- parse_hsize_list(opt_arg, &s->start);
+ parse_hsize_list(H5_optarg, &s->start);
break;
case 'S':
if (s->stride.data) {
HDfree(s->stride.data);
s->stride.data = NULL;
}
- parse_hsize_list(opt_arg, &s->stride);
+ parse_hsize_list(H5_optarg, &s->stride);
break;
case 'c':
if (s->count.data) {
HDfree(s->count.data);
s->count.data = NULL;
}
- parse_hsize_list(opt_arg, &s->count);
+ parse_hsize_list(H5_optarg, &s->count);
break;
case 'k':
if (s->block.data) {
HDfree(s->block.data);
s->block.data = NULL;
}
- parse_hsize_list(opt_arg, &s->block);
+ parse_hsize_list(H5_optarg, &s->block);
break;
default:
goto end_collect;
}
- } while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF);
+ } while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF);
end_collect:
last_was_dset = FALSE;
@@ -1277,8 +1199,8 @@ end_collect:
/** end subsetting parameters **/
case 'E':
- if (opt_arg != NULL)
- enable_error_stack = HDatoi(opt_arg);
+ if (H5_optarg != NULL)
+ enable_error_stack = HDatoi(H5_optarg);
else
enable_error_stack = 1;
break;
@@ -1294,7 +1216,7 @@ end_collect:
case '$':
#ifdef H5_HAVE_ROS3_VFD
- if (h5tools_parse_ros3_fapl_tuple(opt_arg, ',', &ros3_fa_g) < 0) {
+ if (h5tools_parse_ros3_fapl_tuple(H5_optarg, ',', &ros3_fa_g) < 0) {
error_msg("failed to parse S3 VFD credential info\n");
usage(h5tools_getprogname());
free_handler(hand, argc);
@@ -1311,7 +1233,7 @@ end_collect:
case '#':
#ifdef H5_HAVE_LIBHDFS
- if (h5tools_parse_hdfs_fapl_tuple(opt_arg, ',', &hdfs_fa_g) < 0) {
+ if (h5tools_parse_hdfs_fapl_tuple(H5_optarg, ',', &hdfs_fa_g) < 0) {
error_msg("failed to parse HDFS VFD configuration info\n");
usage(h5tools_getprogname());
free_handler(hand, argc);
@@ -1328,18 +1250,18 @@ end_collect:
case '1':
vol_info_g.type = VOL_BY_VALUE;
- vol_info_g.u.value = (H5VL_class_value_t)HDatoi(opt_arg);
+ vol_info_g.u.value = (H5VL_class_value_t)HDatoi(H5_optarg);
use_custom_vol_g = TRUE;
break;
case '2':
vol_info_g.type = VOL_BY_NAME;
- vol_info_g.u.name = opt_arg;
+ vol_info_g.u.name = H5_optarg;
use_custom_vol_g = TRUE;
break;
case '3':
- vol_info_g.info_string = opt_arg;
+ vol_info_g.info_string = H5_optarg;
break;
case '?':
@@ -1351,7 +1273,7 @@ end_collect:
parse_end:
/* check for file name to be processed */
- if (argc <= opt_ind) {
+ if (argc <= H5_optind) {
error_msg("missing file name\n");
usage(h5tools_getprogname());
goto error;
@@ -1443,7 +1365,7 @@ main(int argc, const char *argv[])
}
}
- if (argc <= opt_ind) {
+ if (argc <= H5_optind) {
error_msg("missing file name\n");
usage(h5tools_getprogname());
h5tools_setstatus(EXIT_FAILURE);
@@ -1496,8 +1418,8 @@ main(int argc, const char *argv[])
}
}
- while (opt_ind < argc) {
- fname = HDstrdup(argv[opt_ind++]);
+ while (H5_optind < argc) {
+ fname = HDstrdup(argv[H5_optind++]);
fid = h5tools_fopen(fname, H5F_ACC_RDONLY, fapl_id, (fapl_id == H5P_DEFAULT) ? FALSE : TRUE, NULL, 0);
diff --git a/tools/src/h5dump/h5dump_xml.c b/tools/src/h5dump/h5dump_xml.c
index 5507dcc..0e881df 100644
--- a/tools/src/h5dump/h5dump_xml.c
+++ b/tools/src/h5dump/h5dump_xml.c
@@ -2365,14 +2365,21 @@ xml_dump_named_datatype(hid_t type, const char *name)
h5tools_context_t ctx; /* print context */
h5tool_format_t * outputformat = &xml_dataformat;
h5tool_format_t string_dataformat;
- char * tmp;
- char * dtxid;
- char * parentxid;
- char * t_tmp;
- char * t_prefix;
- char * t_name;
+ char * tmp = NULL;
+ char * dtxid = NULL;
+ char * parentxid = NULL;
+ char * t_tmp = NULL;
+ char * t_prefix = NULL;
+ char * t_name = NULL;
tmp = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2);
+ if (tmp == NULL) {
+ indentation(dump_indent);
+ error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__);
+ h5tools_setstatus(EXIT_FAILURE);
+ goto done;
+ }
+
HDstrcpy(tmp, prefix);
HDstrcat(tmp, "/");
HDstrcat(tmp, name);
@@ -2627,6 +2634,13 @@ xml_dump_group(hid_t gid, const char *name)
}
else {
tmp = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2);
+ if (tmp == NULL) {
+ indentation(dump_indent);
+ error_msg("internal error (file %s:line %d)\n", __FILE__, __LINE__);
+ h5tools_setstatus(EXIT_FAILURE);
+ return;
+ }
+
HDstrcpy(tmp, prefix);
par = HDstrdup(tmp);
cp = HDstrrchr(par, '/');
@@ -3146,8 +3160,11 @@ xml_print_strs(hid_t did, int source)
}
bp = (char *)buf;
- if (!is_vlstr)
+ if (!is_vlstr) {
onestring = (char *)HDcalloc(tsiz, sizeof(char));
+ if (onestring == NULL)
+ goto error;
+ }
/* setup */
HDmemset(&buffer, 0, sizeof(h5tools_str_t));
@@ -3768,6 +3785,14 @@ xml_dump_dataset(hid_t did, const char *name, struct subset_t H5_ATTR_UNUSED *ss
char *pstr = (char *)HDmalloc((size_t)100);
tmp = (char *)HDmalloc(HDstrlen(prefix) + HDstrlen(name) + 2);
+ if (tmp == NULL) {
+ error_msg("buffer allocation failed\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ HDfree(rstr);
+ HDfree(pstr);
+ return;
+ }
+
HDstrcpy(tmp, prefix);
HDstrcat(tmp, "/");
HDstrcat(tmp, name);
diff --git a/tools/src/h5format_convert/h5format_convert.c b/tools/src/h5format_convert/h5format_convert.c
index 321f274..ddf129c 100644
--- a/tools/src/h5format_convert/h5format_convert.c
+++ b/tools/src/h5format_convert/h5format_convert.c
@@ -38,28 +38,11 @@ static int verbose_g = 0;
* Command-line options: The user can specify short or long-named
* parameters.
*/
-static const char * s_opts = "hVvd:n";
-static struct long_options l_opts[] = {{"help", no_arg, 'h'},
- {"hel", no_arg, 'h'},
- {"he", no_arg, 'h'},
- {"version", no_arg, 'V'},
- {"version", no_arg, 'V'},
- {"versio", no_arg, 'V'},
- {"versi", no_arg, 'V'},
- {"vers", no_arg, 'V'},
- {"verbose", no_arg, 'v'},
- {"verbos", no_arg, 'v'},
- {"verbo", no_arg, 'v'},
- {"verb", no_arg, 'v'},
- {"dname", require_arg, 'd'},
- {"dnam", require_arg, 'd'},
- {"dna", require_arg, 'd'},
- {"dn", require_arg, 'd'},
- {"noop", no_arg, 'n'},
- {"noo", no_arg, 'n'},
- {"no", no_arg, 'n'},
- {"enable-error-stack", no_arg, 'E'},
- {NULL, 0, '\0'}};
+static const char * s_opts = "hVvd:n";
+static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'}, {"version", no_arg, 'V'},
+ {"verbose", no_arg, 'v'}, {"dname", require_arg, 'd'},
+ {"noop", no_arg, 'n'}, {"enable-error-stack", no_arg, 'E'},
+ {NULL, 0, '\0'}};
/*-------------------------------------------------------------------------
* Function: usage
@@ -123,7 +106,7 @@ parse_command_line(int argc, const char **argv)
}
/* parse command line options */
- while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+ while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
switch ((char)opt) {
case 'h':
usage(h5tools_getprogname());
@@ -140,11 +123,11 @@ parse_command_line(int argc, const char **argv)
break;
case 'd': /* -d dname */
- if (opt_arg != NULL && *opt_arg)
- dname_g = HDstrdup(opt_arg);
+ if (H5_optarg != NULL && *H5_optarg)
+ dname_g = HDstrdup(H5_optarg);
if (dname_g == NULL) {
h5tools_setstatus(EXIT_FAILURE);
- error_msg("No dataset name\n", opt_arg);
+ error_msg("No dataset name\n", H5_optarg);
usage(h5tools_getprogname());
goto error;
}
@@ -167,19 +150,19 @@ parse_command_line(int argc, const char **argv)
} /* switch */
} /* while */
- if (argc <= opt_ind) {
+ if (argc <= H5_optind) {
error_msg("missing file name\n");
usage(h5tools_getprogname());
h5tools_setstatus(EXIT_FAILURE);
goto error;
}
- fname_g = HDstrdup(argv[opt_ind]);
+ fname_g = HDstrdup(argv[H5_optind]);
- return (0);
+ return 0;
error:
- return (-1);
+ return -1;
;
} /* parse_command_line() */
diff --git a/tools/src/h5import/h5import.c b/tools/src/h5import/h5import.c
index 2a65591..04e1c35 100644
--- a/tools/src/h5import/h5import.c
+++ b/tools/src/h5import/h5import.c
@@ -489,7 +489,7 @@ readIntegerData(FILE *strm, struct Input *in)
case 0: /* TEXTIN */
in08 = (H5DT_INT8 *)in->data;
for (i = 0; i < len; i++, in08++) {
- if (fscanf(strm, "%hd", &temp16) != 1) {
+ if (HDfscanf(strm, "%hd", &temp16) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -521,7 +521,7 @@ readIntegerData(FILE *strm, struct Input *in)
switch (in->inputClass) {
case 0: /* TEXTIN */
for (i = 0; i < len; i++, in16++) {
- if (fscanf(strm, "%hd", in16) != 1) {
+ if (HDfscanf(strm, "%hd", in16) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -558,7 +558,7 @@ readIntegerData(FILE *strm, struct Input *in)
switch (in->inputClass) {
case 0: /* TEXTIN */
for (i = 0; i < len; i++, in32++) {
- if (fscanf(strm, "%d", in32) != 1) {
+ if (HDfscanf(strm, "%d", in32) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -595,7 +595,7 @@ readIntegerData(FILE *strm, struct Input *in)
switch (in->inputClass) {
case 0: /* TEXTIN */
for (i = 0; i < len; i++, in64++) {
- if (fscanf(strm, "%s", buffer) < 1) {
+ if (HDfscanf(strm, "%s", buffer) < 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -664,7 +664,7 @@ readUIntegerData(FILE *strm, struct Input *in)
case 6: /* TEXTUIN */
in08 = (H5DT_UINT8 *)in->data;
for (i = 0; i < len; i++, in08++) {
- if (fscanf(strm, "%hu", &temp16) != 1) {
+ if (HDfscanf(strm, "%hu", &temp16) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -693,7 +693,7 @@ readUIntegerData(FILE *strm, struct Input *in)
switch (in->inputClass) {
case 6: /* TEXTUIN */
for (i = 0; i < len; i++, in16++) {
- if (fscanf(strm, "%hu", in16) != 1) {
+ if (HDfscanf(strm, "%hu", in16) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -729,7 +729,7 @@ readUIntegerData(FILE *strm, struct Input *in)
switch (in->inputClass) {
case 6: /* TEXTUIN */
for (i = 0; i < len; i++, in32++) {
- if (fscanf(strm, "%u", in32) != 1) {
+ if (HDfscanf(strm, "%u", in32) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -766,7 +766,7 @@ readUIntegerData(FILE *strm, struct Input *in)
switch (in->inputClass) {
case 6: /* TEXTUIN */
for (i = 0; i < len; i++, in64++) {
- if (fscanf(strm, "%s", buffer) < 1) {
+ if (HDfscanf(strm, "%s", buffer) < 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -832,7 +832,7 @@ readFloatData(FILE *strm, struct Input *in)
switch (in->inputClass) {
case 1: /* TEXTFP */
for (i = 0; i < len; i++, fp32++) {
- if (fscanf(strm, "%f", fp32) != 1) {
+ if (HDfscanf(strm, "%f", fp32) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -845,7 +845,7 @@ readFloatData(FILE *strm, struct Input *in)
case 2: /*TEXTFPE */
for (i = 0; i < len; i++, fp32++) {
- if (fscanf(strm, "%f", fp32) != 1) {
+ if (HDfscanf(strm, "%f", fp32) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -884,7 +884,7 @@ readFloatData(FILE *strm, struct Input *in)
switch (in->inputClass) {
case 1: /* TEXTFP */
for (i = 0; i < len; i++, fp64++) {
- if (fscanf(strm, "%lf", fp64) != 1) {
+ if (HDfscanf(strm, "%lf", fp64) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -897,7 +897,7 @@ readFloatData(FILE *strm, struct Input *in)
case 2: /*TEXTFPE */
for (i = 0; i < len; i++, fp64++) {
- if (fscanf(strm, "%lf", fp64) != 1) {
+ if (HDfscanf(strm, "%lf", fp64) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -1469,16 +1469,16 @@ processConfigurationFile(char *infile, struct Input *in)
goto error;
}
- scanret = fscanf(strm, "%254s", key);
+ scanret = HDfscanf(strm, "%254s", key);
if ((scanret == 1) && !HDstrcmp("HDF5", key)) {
#ifdef H5DEBUGIMPORT
int pndx;
HDprintf("\nh5dump file\n");
#endif
in->h5dumpInput = 1;
- scanret = fscanf(strm, "%254s", temp); /* filename */
- scanret = fscanf(strm, "%254s", temp); /* start bracket */
- scanret = fscanf(strm, "%254s", key); /* DATASET */
+ scanret = HDfscanf(strm, "%254s", temp); /* filename */
+ scanret = HDfscanf(strm, "%254s", temp); /* start bracket */
+ scanret = HDfscanf(strm, "%254s", key); /* DATASET */
while (scanret == 1) {
if (!HDstrcmp("DATASET", key)) { /* PATH */
#ifdef H5DEBUGIMPORT
@@ -1488,7 +1488,7 @@ processConfigurationFile(char *infile, struct Input *in)
(void)HDfprintf(stderr, err3a, infile);
goto error;
}
- if (fscanf(strm, "%254s", temp) != 1) {
+ if (HDfscanf(strm, "%254s", temp) != 1) {
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
@@ -1500,7 +1500,7 @@ processConfigurationFile(char *infile, struct Input *in)
goto error;
}
in->configOptionVector[PATH] = 1;
- scanret = fscanf(strm, "%254s", temp); /* start bracket */
+ scanret = HDfscanf(strm, "%254s", temp); /* start bracket */
#ifdef H5DEBUGIMPORT
HDprintf("h5dump DATASET %s found\n", temp);
#endif
@@ -1514,7 +1514,7 @@ processConfigurationFile(char *infile, struct Input *in)
goto error;
}
- if (fscanf(strm, "%254s", temp) != 1) {
+ if (HDfscanf(strm, "%254s", temp) != 1) {
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
@@ -1550,20 +1550,20 @@ processConfigurationFile(char *infile, struct Input *in)
#ifdef H5DEBUGIMPORT
HDprintf("h5dump DATATYPE STRING found\n");
#endif
- if (fscanf(strm, "%254s", temp) != 1) { /* start bracket */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* start bracket */
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
#ifdef H5DEBUGIMPORT
HDprintf("h5dump DATATYPE STRING %s found\n", temp);
#endif
- if (fscanf(strm, "%254s", temp) != 1) { /* string properties */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* string properties */
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
while (get_next_prop) {
if (!HDstrcmp("STRSIZE", temp)) { /* STRSIZE */
- if (fscanf(strm, "%254s", temp) != 1) {
+ if (HDfscanf(strm, "%254s", temp) != 1) {
(void)HDfprintf(stderr, "%s", err19);
goto error;
}
@@ -1582,8 +1582,8 @@ processConfigurationFile(char *infile, struct Input *in)
#endif
}
}
- else if (!HDstrcmp("STRPAD", temp)) { /* STRPAD */
- if (fscanf(strm, "%254s", temp) != 1) { /* STRPAD type */
+ else if (!HDstrcmp("STRPAD", temp)) { /* STRPAD */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* STRPAD type */
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
@@ -1591,8 +1591,8 @@ processConfigurationFile(char *infile, struct Input *in)
HDprintf("h5dump DATATYPE STRING STRPAD %s found\n", temp);
#endif
}
- else if (!HDstrcmp("CSET", key)) { /* CSET */
- if (fscanf(strm, "%254s", temp) != 1) { /* CSET type */
+ else if (!HDstrcmp("CSET", key)) { /* CSET */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* CSET type */
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
@@ -1600,8 +1600,8 @@ processConfigurationFile(char *infile, struct Input *in)
HDprintf("h5dump DATATYPE STRING CSET %s found\n", temp);
#endif
}
- else if (!HDstrcmp("CTYPE", temp)) { /* CTYPE */
- if (fscanf(strm, "%254s", temp) != 1) { /* CTYPE type */
+ else if (!HDstrcmp("CTYPE", temp)) { /* CTYPE */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* CTYPE type */
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
@@ -1609,7 +1609,7 @@ processConfigurationFile(char *infile, struct Input *in)
HDprintf("h5dump DATATYPE STRING CTYPE %s found\n", temp);
#endif
} /* if(!HDstrcmp("CSET", key)) */
- if (fscanf(strm, "%254s", temp) != 1) {
+ if (HDfscanf(strm, "%254s", temp) != 1) {
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
@@ -1628,7 +1628,7 @@ processConfigurationFile(char *infile, struct Input *in)
#ifdef H5DEBUGIMPORT
HDprintf("h5dump DATASPACE key\n");
#endif
- if (fscanf(strm, "%254s", temp) != 1) {
+ if (HDfscanf(strm, "%254s", temp) != 1) {
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
@@ -1644,14 +1644,14 @@ processConfigurationFile(char *infile, struct Input *in)
#ifdef H5DEBUGIMPORT
HDprintf("h5dump DATASPACE SIMPLE found\n");
#endif
- if (fscanf(strm, "%254s", temp) != 1) { /* start bracket */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* start bracket */
(void)HDfprintf(stderr, err6b, infile);
goto error;
}
#ifdef H5DEBUGIMPORT
HDprintf("h5dump DATASPACE SIMPLE %s found\n", temp);
#endif
- if (fscanf(strm, "%254s", temp) != 1) { /* start paren */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* start paren */
(void)HDfprintf(stderr, err6b, infile);
goto error;
}
@@ -1662,7 +1662,7 @@ processConfigurationFile(char *infile, struct Input *in)
int get_next_dim = 1;
int i = 0;
- if (fscanf(strm, "%254s", temp) != 1) { /* Dimension with optional comma */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* Dimension with optional comma */
(void)HDfprintf(stderr, err16c, infile);
goto error;
}
@@ -1672,7 +1672,7 @@ processConfigurationFile(char *infile, struct Input *in)
while (get_next_dim) {
char *more = temp;
temp_dims[icount] = HDstrtoull(more, &more, 10);
- if (fscanf(strm, "%254s", temp) != 1) { /* Dimension or end paren */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* Dimension or end paren */
(void)HDfprintf(stderr, err6b, infile);
goto error;
}
@@ -1716,7 +1716,7 @@ processConfigurationFile(char *infile, struct Input *in)
(void)HDfprintf(stderr, err5b, infile);
goto error;
}
- if (fscanf(strm, "%254s", temp) != 1) {
+ if (HDfscanf(strm, "%254s", temp) != 1) {
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
@@ -1728,7 +1728,7 @@ processConfigurationFile(char *infile, struct Input *in)
(hsize_t *)HDmalloc((size_t)in->rank * sizeof(hsize_t))) == NULL) {
goto error;
}
- if (fscanf(strm, "%254s", temp) != 1) { /* start paren */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* start paren */
(void)HDfprintf(stderr, err6b, infile);
goto error;
}
@@ -1742,7 +1742,7 @@ processConfigurationFile(char *infile, struct Input *in)
#ifdef H5DEBUGIMPORT
HDprintf("h5dump DATASPACE SIMPLE process max dim values\n");
#endif
- if (fscanf(strm, "%254s", temp) != 1) { /* max dim with optional comma */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* max dim with optional comma */
(void)HDfprintf(stderr, err16c, infile);
goto error;
}
@@ -1762,7 +1762,7 @@ processConfigurationFile(char *infile, struct Input *in)
char *more = temp;
in->maxsizeOfDimension[i] = HDstrtoull(more, &more, 10);
}
- if (fscanf(strm, "%254s", temp) != 1) { /* max dim or end paren */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* max dim or end paren */
(void)HDfprintf(stderr, err16c, infile);
goto error;
}
@@ -1793,7 +1793,7 @@ processConfigurationFile(char *infile, struct Input *in)
(void)HDfprintf(stderr, err16c, infile);
goto error;
}
- scanret = fscanf(strm, "%254s", temp); /* end bracket */
+ scanret = HDfscanf(strm, "%254s", temp); /* end bracket */
#ifdef H5DEBUGIMPORT
HDprintf("h5dump DATASPACE SIMPLE %s found\n", temp);
#endif
@@ -1808,14 +1808,14 @@ processConfigurationFile(char *infile, struct Input *in)
#ifdef H5DEBUGIMPORT
HDprintf("h5dump STORAGE_LAYOUT key\n");
#endif
- if (fscanf(strm, "%254s", temp) != 1) { /* start bracket */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* start bracket */
(void)HDfprintf(stderr, err6b, infile);
goto error;
}
#ifdef H5DEBUGIMPORT
HDprintf("h5dump STORAGE_LAYOUT %s found\n", temp);
#endif
- if (fscanf(strm, "%254s", temp) != 1) { /* CHUNKED */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* CHUNKED */
(void)HDfprintf(stderr, err6b, infile);
goto error;
}
@@ -1827,7 +1827,7 @@ processConfigurationFile(char *infile, struct Input *in)
(void)HDfprintf(stderr, "Unable to allocate dynamic memory.\n");
goto error;
}
- if (fscanf(strm, "%254s", temp) != 1) { /* start paren */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* start paren */
(void)HDfprintf(stderr, err6b, infile);
goto error;
}
@@ -1838,7 +1838,7 @@ processConfigurationFile(char *infile, struct Input *in)
int get_next_dim = 1;
int icount = 0;
- if (fscanf(strm, "%254s", temp) != 1) { /* Dimension with optional comma */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* Dimension with optional comma */
(void)HDfprintf(stderr, err16c, infile);
goto error;
}
@@ -1848,7 +1848,7 @@ processConfigurationFile(char *infile, struct Input *in)
while (get_next_dim) {
char *more = temp;
in->sizeOfChunk[icount] = HDstrtoull(more, &more, 10);
- if (fscanf(strm, "%254s", temp) != 1) { /* Dimension or end paren */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* Dimension or end paren */
(void)HDfprintf(stderr, err6b, infile);
goto error;
}
@@ -1880,7 +1880,7 @@ processConfigurationFile(char *infile, struct Input *in)
(void)HDfprintf(stderr, err5b, infile);
goto error;
}
- if (fscanf(strm, "%254s", temp) != 1) { /* SIZE */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* SIZE */
(void)HDfprintf(stderr, err6b, infile);
goto error;
}
@@ -1888,7 +1888,7 @@ processConfigurationFile(char *infile, struct Input *in)
HDprintf("h5dump STORAGE_LAYOUT CHUNKED %s found\n", temp);
#endif
if (!HDstrcmp("SIZE", temp)) { /* SIZE */
- if (fscanf(strm, "%d", (&ival)) != 1) {
+ if (HDfscanf(strm, "%d", (&ival)) != 1) {
(void)HDfprintf(stderr, "%s", err19);
goto error;
}
@@ -1897,7 +1897,7 @@ processConfigurationFile(char *infile, struct Input *in)
#endif
}
while (HDstrcmp("}", temp) != 0) {
- if (fscanf(strm, "%254s", temp) != 1) { /* end bracket */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* end bracket */
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
@@ -1912,14 +1912,14 @@ processConfigurationFile(char *infile, struct Input *in)
#ifdef H5DEBUGIMPORT
HDprintf("h5dump FILTERS key\n");
#endif
- if (fscanf(strm, "%254s", temp) != 1) { /* start bracket */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* start bracket */
(void)HDfprintf(stderr, err6b, infile);
goto error;
}
#ifdef H5DEBUGIMPORT
HDprintf("h5dump FILTERS %s found\n", temp);
#endif
- if (fscanf(strm, "%254s", temp) != 1) {
+ if (HDfscanf(strm, "%254s", temp) != 1) {
(void)HDfprintf(stderr, err6b, infile);
goto error;
}
@@ -1930,28 +1930,28 @@ processConfigurationFile(char *infile, struct Input *in)
#ifdef H5DEBUGIMPORT
HDprintf("h5dump FILTERS COMPRESSION found\n");
#endif
- if (fscanf(strm, "%254s", temp) != 1) { /* DEFLATE */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* DEFLATE */
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
#ifdef H5DEBUGIMPORT
HDprintf("h5dump FILTERS COMPRESSION %s found\n", temp);
#endif
- if (fscanf(strm, "%254s", temp) != 1) { /* bgin bracket */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* bgin bracket */
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
#ifdef H5DEBUGIMPORT
HDprintf("h5dump FILTERS COMPRESSION %s found\n", temp);
#endif
- if (fscanf(strm, "%254s", temp) != 1) { /* LEVEL */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* LEVEL */
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
#ifdef H5DEBUGIMPORT
HDprintf("h5dump FILTERS COMPRESSION %s found\n", temp);
#endif
- if (fscanf(strm, "%d", (&ival)) != 1) {
+ if (HDfscanf(strm, "%d", (&ival)) != 1) {
(void)HDfprintf(stderr, "%s", err19);
goto error;
}
@@ -1959,7 +1959,7 @@ processConfigurationFile(char *infile, struct Input *in)
HDprintf("h5dump FILTERS COMPRESSION LEVEL %d found\n", ival);
#endif
in->compressionParam = ival;
- if (fscanf(strm, "%254s", temp) != 1) { /* end bracket */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* end bracket */
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
@@ -1981,7 +1981,7 @@ processConfigurationFile(char *infile, struct Input *in)
#endif
in->configOptionVector[COMPRESS] = 0;
}
- if (fscanf(strm, "%254s", temp) != 1) { /* end bracket */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* end bracket */
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
@@ -1995,14 +1995,14 @@ processConfigurationFile(char *infile, struct Input *in)
#ifdef H5DEBUGIMPORT
HDprintf("h5dump SUBSET key\n");
#endif
- if (fscanf(strm, "%254s", temp) != 1) { /* start bracket */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* start bracket */
(void)HDfprintf(stderr, err20, infile);
goto error;
}
#ifdef H5DEBUGIMPORT
HDprintf("h5dump SUBSET %s found\n", temp);
#endif
- if (fscanf(strm, "%254s", temp) != 1) { /* SUBSET keyword */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* SUBSET keyword */
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
@@ -2012,7 +2012,7 @@ processConfigurationFile(char *infile, struct Input *in)
while (get_next_prop) {
if (!HDstrcmp("COUNT", temp)) { /* COUNT */
int icount = 0;
- if (fscanf(strm, "%254s", temp) != 1) { /* start paren */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* start paren */
(void)HDfprintf(stderr, err6b, infile);
goto error;
}
@@ -2023,7 +2023,7 @@ processConfigurationFile(char *infile, struct Input *in)
int get_next_dim = 1;
int i = 0;
- if (fscanf(strm, "%254s", temp) != 1) { /* Dimension with optional comma */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* Dimension with optional comma */
(void)HDfprintf(stderr, err16c, infile);
goto error;
}
@@ -2033,7 +2033,7 @@ processConfigurationFile(char *infile, struct Input *in)
while (get_next_dim) {
char *more = temp;
temp_dims[icount] = HDstrtoull(more, &more, 10);
- if (fscanf(strm, "%254s", temp) != 1) { /* Dimension or end paren */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* Dimension or end paren */
(void)HDfprintf(stderr, err6b, infile);
goto error;
}
@@ -2068,7 +2068,7 @@ processConfigurationFile(char *infile, struct Input *in)
} /* if(!HDstrcmp("COUNT", temp)) COUNT */
if (!HDstrcmp("BLOCK", temp)) { /* BLOCK */
int icount = 0;
- if (fscanf(strm, "%254s", temp) != 1) { /* start paren */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* start paren */
(void)HDfprintf(stderr, err6b, infile);
goto error;
}
@@ -2079,7 +2079,7 @@ processConfigurationFile(char *infile, struct Input *in)
int get_next_dim = 1;
int i = 0;
- if (fscanf(strm, "%254s", temp) != 1) { /* Dimension with optional comma */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* Dimension with optional comma */
(void)HDfprintf(stderr, err16c, infile);
goto error;
}
@@ -2089,7 +2089,7 @@ processConfigurationFile(char *infile, struct Input *in)
while (get_next_dim) {
char *more = temp;
temp_dims[icount] = HDstrtoull(more, &more, 10);
- if (fscanf(strm, "%254s", temp) != 1) { /* Dimension or end paren */
+ if (HDfscanf(strm, "%254s", temp) != 1) { /* Dimension or end paren */
(void)HDfprintf(stderr, err6b, infile);
goto error;
}
@@ -2122,7 +2122,7 @@ processConfigurationFile(char *infile, struct Input *in)
in->configOptionVector[DIM] = 1;
} /* if(!HDstrcmp("(", key)) start paren */
} /* if(!HDstrcmp("BLOCK", temp)) BLOCK */
- if (fscanf(strm, "%254s", temp) != 1) {
+ if (HDfscanf(strm, "%254s", temp) != 1) {
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
@@ -2141,7 +2141,7 @@ processConfigurationFile(char *infile, struct Input *in)
scanret = 0;
break;
}
- scanret = fscanf(strm, "%254s", key);
+ scanret = HDfscanf(strm, "%254s", key);
}
#ifdef H5DEBUGIMPORT
HDprintf("h5dump path");
@@ -2182,7 +2182,7 @@ processConfigurationFile(char *infile, struct Input *in)
(void)HDfprintf(stderr, err3a, infile);
goto error;
}
- if (fscanf(strm, "%254s", temp) != 1) {
+ if (HDfscanf(strm, "%254s", temp) != 1) {
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
@@ -2199,7 +2199,7 @@ processConfigurationFile(char *infile, struct Input *in)
goto error;
}
- if (fscanf(strm, "%254s", temp) != 1) {
+ if (HDfscanf(strm, "%254s", temp) != 1) {
(void)HDfprintf(stderr, "%s", err18);
goto error;
}
@@ -2226,7 +2226,7 @@ processConfigurationFile(char *infile, struct Input *in)
(void)HDfprintf(stderr, err5a, infile);
goto error;
}
- if (fscanf(strm, "%254d", (&ival)) != 1) {
+ if (HDfscanf(strm, "%254d", (&ival)) != 1) {
(void)HDfprintf(stderr, "%s", err19);
goto error;
}
@@ -2423,7 +2423,7 @@ processConfigurationFile(char *infile, struct Input *in)
default:
break;
}
- scanret = fscanf(strm, "%254s", key);
+ scanret = HDfscanf(strm, "%254s", key);
}
/*
@@ -2602,7 +2602,7 @@ getOutputClass(struct Input *in, FILE *strm)
const char *err1 = "Unable to get 'string' value.\n";
const char *err2 = "Invalid value for output class.\n";
- if (fscanf(strm, "%254s", temp) != 1) {
+ if (HDfscanf(strm, "%254s", temp) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -2637,7 +2637,7 @@ getOutputSize(struct Input *in, FILE *strm)
const char *err1 = "Unable to get integer value.\n";
const char *err2 = "Invalid value for output size.\n";
- if (fscanf(strm, "%d", (&ival)) != 1) {
+ if (HDfscanf(strm, "%d", (&ival)) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -3502,7 +3502,7 @@ getInputByteOrder(struct Input *in, FILE *strm)
const char *err1 = "Unable to get 'string' value.\n";
const char *err2 = "Invalid value for input byte-order.\n";
- if (fscanf(strm, "%254s", temp) != 1) {
+ if (HDfscanf(strm, "%254s", temp) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -3524,7 +3524,7 @@ getRank(struct Input *in, FILE *strm)
const char *err1 = "Unable to get integer value.\n";
const char *err2 = "Invalid value for rank.\n";
- if (fscanf(strm, "%d", (&ival)) != 1) {
+ if (HDfscanf(strm, "%d", (&ival)) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -3553,7 +3553,7 @@ getDimensionSizes(struct Input *in, FILE *strm)
return (-1);
}
- while (fscanf(strm, "%llu", (&ullval)) == 1)
+ while (HDfscanf(strm, "%llu", (&ullval)) == 1)
in->sizeOfDimension[i++] = ullval;
if (in->rank != i) {
@@ -3579,7 +3579,7 @@ getChunkedDimensionSizes(struct Input *in, FILE *strm)
return (-1);
}
- while (fscanf(strm, "%llu", (&ullval)) == 1)
+ while (HDfscanf(strm, "%llu", (&ullval)) == 1)
in->sizeOfChunk[i++] = ullval;
if (in->rank != i) {
@@ -3612,7 +3612,7 @@ getMaximumDimensionSizes(struct Input *in, FILE *strm)
return (-1);
}
- while (fscanf(strm, "%lld", (&llval)) == 1) {
+ while (HDfscanf(strm, "%lld", (&llval)) == 1) {
if (llval == -1)
in->maxsizeOfDimension[i++] = H5S_UNLIMITED;
else
@@ -3642,7 +3642,7 @@ getOutputArchitecture(struct Input *in, FILE *strm)
const char *err1 = "Unable to get 'string' value.\n";
const char *err2 = "Invalid value for output architecture.\n";
- if (fscanf(strm, "%254s", temp) != 1) {
+ if (HDfscanf(strm, "%254s", temp) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -3675,7 +3675,7 @@ getOutputByteOrder(struct Input *in, FILE *strm)
const char *err1 = "Unable to get 'string' value.\n";
const char *err2 = "Invalid value for output byte-order.\n";
- if (fscanf(strm, "%254s", temp) != 1) {
+ if (HDfscanf(strm, "%254s", temp) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -3708,7 +3708,7 @@ getCompressionType(struct Input *in, FILE *strm)
const char *err1 = "Unable to get 'string' value.\n";
const char *err2 = "Invalid value for compression.\n";
- if (fscanf(strm, "%254s", temp) != 1) {
+ if (HDfscanf(strm, "%254s", temp) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -3750,7 +3750,7 @@ getCompressionParameter(struct Input *in, FILE *strm)
switch (in->compressionType) {
case 0: /* GZIP */
- if (fscanf(strm, "%d", (&ival)) != 1) {
+ if (HDfscanf(strm, "%d", (&ival)) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
@@ -3774,7 +3774,7 @@ getExternalFilename(struct Input *in, FILE *strm)
char temp[255];
const char *err1 = "Unable to get 'string' value.\n";
- if (fscanf(strm, "%254s", temp) != 1) {
+ if (HDfscanf(strm, "%254s", temp) != 1) {
(void)HDfprintf(stderr, "%s", err1);
return (-1);
}
diff --git a/tools/src/h5jam/h5jam.c b/tools/src/h5jam/h5jam.c
index 5bcbf45..7f3385c 100644
--- a/tools/src/h5jam/h5jam.c
+++ b/tools/src/h5jam/h5jam.c
@@ -34,14 +34,10 @@ char *ub_file = NULL;
* parameters. The long-named ones can be partially spelled. When
* adding more, make sure that they don't clash with each other.
*/
-static const char * s_opts = "hi:u:o:c:V"; /* add more later ? */
-static struct long_options l_opts[] = {
- {"help", no_arg, 'h'}, {"hel", no_arg, 'h'}, {"i", require_arg, 'i'}, /* input file */
- {"u", require_arg, 'u'}, /* user block file */
- {"o", require_arg, 'o'}, /* output file */
- {"clobber", no_arg, 'c'}, /* clobber existing UB */
- {"clobbe", no_arg, 'c'}, {"clobb", no_arg, 'c'}, {"clob", no_arg, 'c'},
- {"clo", no_arg, 'c'}, {"cl", no_arg, 'c'}, {NULL, 0, '\0'}};
+static const char * s_opts = "hi:u:o:c:V";
+static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'}, {"i", require_arg, 'i'},
+ {"u", require_arg, 'u'}, {"o", require_arg, 'o'},
+ {"clobber", no_arg, 'c'}, {NULL, 0, '\0'}};
/*-------------------------------------------------------------------------
* Function: usage
@@ -113,16 +109,16 @@ parse_command_line(int argc, const char *argv[])
int opt = FALSE;
/* parse command line options */
- while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+ while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
switch ((char)opt) {
case 'o':
- output_file = HDstrdup(opt_arg);
+ output_file = HDstrdup(H5_optarg);
break;
case 'i':
- input_file = HDstrdup(opt_arg);
+ input_file = HDstrdup(H5_optarg);
break;
case 'u':
- ub_file = HDstrdup(opt_arg);
+ ub_file = HDstrdup(H5_optarg);
break;
case 'c':
do_clobber = TRUE;
diff --git a/tools/src/h5jam/h5unjam.c b/tools/src/h5jam/h5unjam.c
index cde7ec7..fa23b06 100644
--- a/tools/src/h5jam/h5unjam.c
+++ b/tools/src/h5jam/h5unjam.c
@@ -35,14 +35,10 @@ char *ub_file = NULL;
* parameters. The long-named ones can be partially spelled. When
* adding more, make sure that they don't clash with each other.
*/
-static const char * s_opts = "hu:i:o:d:V";
-static struct long_options l_opts[] = {
- {"help", no_arg, 'h'}, {"hel", no_arg, 'h'}, {"i", require_arg, 'i'}, /* input file */
- {"u", require_arg, 'u'}, /* user block file */
- {"o", require_arg, 'o'}, /* output file */
- {"delete", no_arg, 'd'}, /* delete ub */
- {"delet", no_arg, 'd'}, {"dele", no_arg, 'd'}, {"del", no_arg, 'd'},
- {"de", no_arg, 'd'}, {NULL, 0, '\0'}};
+static const char * s_opts = "hu:i:o:d:V";
+static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'}, {"i", require_arg, 'i'},
+ {"u", require_arg, 'u'}, {"o", require_arg, 'o'},
+ {"delete", no_arg, 'd'}, {NULL, 0, '\0'}};
/*-------------------------------------------------------------------------
* Function: usage
@@ -101,23 +97,23 @@ parse_command_line(int argc, const char *argv[])
int opt = FALSE;
/* parse command line options */
- while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+ while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
switch ((char)opt) {
case 'o':
- output_file = HDstrdup(opt_arg);
+ output_file = HDstrdup(H5_optarg);
if (output_file)
h5tools_set_data_output_file(output_file, 1);
break;
case 'i':
- input_file = HDstrdup(opt_arg);
+ input_file = HDstrdup(H5_optarg);
if (input_file)
h5tools_set_input_file(input_file, 1);
break;
;
case 'u':
- ub_file = HDstrdup(opt_arg);
+ ub_file = HDstrdup(H5_optarg);
if (ub_file)
h5tools_set_output_file(ub_file, 1);
else
diff --git a/tools/src/h5perf/CMakeLists.txt b/tools/src/h5perf/CMakeLists.txt
new file mode 100644
index 0000000..36b0b2f
--- /dev/null
+++ b/tools/src/h5perf/CMakeLists.txt
@@ -0,0 +1,103 @@
+cmake_minimum_required (VERSION 3.12)
+project (HDF5_TOOLS_SRC_H5PERF C)
+
+# --------------------------------------------------------------------
+# Add the executables
+# --------------------------------------------------------------------
+#-- Adding test for h5perf_serial
+set (h5perf_serial_SOURCES
+ ${HDF5_TOOLS_SRC_H5PERF_SOURCE_DIR}/sio_perf.c
+ ${HDF5_TOOLS_SRC_H5PERF_SOURCE_DIR}/sio_engine.c
+)
+add_executable (h5perf_serial ${h5perf_serial_SOURCES})
+target_include_directories (h5perf_serial PRIVATE "${HDF5_TEST_SRC_DIR};${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+if (NOT ONLY_SHARED_LIBS)
+ TARGET_C_PROPERTIES (h5perf_serial STATIC)
+ target_link_libraries (h5perf_serial PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
+else ()
+ TARGET_C_PROPERTIES (h5perf_serial SHARED)
+ target_link_libraries (h5perf_serial PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
+endif ()
+set_target_properties (h5perf_serial PROPERTIES FOLDER perform)
+set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5perf_serial")
+
+set (H5_DEP_EXECUTABLES h5perf_serial)
+
+#-----------------------------------------------------------------------------
+# Add Target to clang-format
+#-----------------------------------------------------------------------------
+if (HDF5_ENABLE_FORMATTERS)
+ clang_format (HDF5_TOOLS_SRC_H5PERF_h5perf_serial_FORMAT h5perf_serial)
+endif ()
+
+if (H5_HAVE_PARALLEL)
+ if (UNIX)
+ #-- Adding test for perf - only on unix systems
+ set (perf_SOURCES
+ ${HDF5_TOOLS_SRC_H5PERF_SOURCE_DIR}/perf.c
+ )
+ add_executable (perf ${perf_SOURCES})
+ target_include_directories (perf PRIVATE "${HDF5_TEST_SRC_DIR};${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+ if (NOT ONLY_SHARED_LIBS)
+ TARGET_C_PROPERTIES (perf STATIC)
+ target_link_libraries (perf PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>")
+ else ()
+ TARGET_C_PROPERTIES (perf SHARED)
+ target_link_libraries (perf PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>")
+ endif ()
+ set_target_properties (perf PROPERTIES FOLDER perform)
+ set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};perf")
+
+ set (H5_DEP_EXECUTABLES perf)
+
+ #-----------------------------------------------------------------------------
+ # Add Target to clang-format
+ #-----------------------------------------------------------------------------
+ if (HDF5_ENABLE_FORMATTERS)
+ clang_format (HDF5_TOOLS_SRC_H5PERF_perf_FORMAT perf)
+ endif ()
+ endif ()
+
+ #-- Adding test for h5perf
+ set (h5perf_SOURCES
+ ${HDF5_TOOLS_SRC_H5PERF_SOURCE_DIR}/pio_perf.c
+ ${HDF5_TOOLS_SRC_H5PERF_SOURCE_DIR}/pio_engine.c
+ )
+ add_executable (h5perf ${h5perf_SOURCES})
+ target_include_directories (h5perf PRIVATE "${HDF5_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+ if (NOT ONLY_SHARED_LIBS)
+ TARGET_C_PROPERTIES (h5perf STATIC)
+ target_link_libraries (h5perf PRIVATE ${LINK_LIBS} ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>")
+ else ()
+ TARGET_C_PROPERTIES (h5perf SHARED)
+ target_link_libraries (h5perf PRIVATE ${LINK_LIBS} ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_LIBRARIES}>")
+ endif ()
+ set_target_properties (h5perf PROPERTIES FOLDER perform)
+ set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5perf")
+
+ set (H5_DEP_EXECUTABLES h5perf)
+
+ #-----------------------------------------------------------------------------
+ # Add Target to clang-format
+ #-----------------------------------------------------------------------------
+ if (HDF5_ENABLE_FORMATTERS)
+ clang_format (HDF5_TOOLS_SRC_H5PERF_h5perf_FORMAT h5perf)
+ endif ()
+endif ()
+
+#-----------------------------------------------------------------------------
+# Rules for Installation of tools using make Install target
+#-----------------------------------------------------------------------------
+if (HDF5_EXPORTED_TARGETS)
+ foreach (exec ${H5_DEP_EXECUTABLES})
+ INSTALL_PROGRAM_PDB (${exec} ${HDF5_INSTALL_BIN_DIR} toolsapplications)
+ endforeach ()
+
+ install (
+ TARGETS
+ ${H5_DEP_EXECUTABLES}
+ EXPORT
+ ${HDF5_EXPORTED_TARGETS}
+ RUNTIME DESTINATION ${HDF5_INSTALL_BIN_DIR} COMPONENT toolsapplications
+ )
+endif ()
diff --git a/tools/src/h5perf/Makefile.am b/tools/src/h5perf/Makefile.am
new file mode 100644
index 0000000..e8a9fdd
--- /dev/null
+++ b/tools/src/h5perf/Makefile.am
@@ -0,0 +1,63 @@
+#
+# Copyright by The HDF Group.
+# Copyright by the Board of Trustees of the University of Illinois.
+# All rights reserved.
+#
+# This file is part of HDF5. The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://www.hdfgroup.org/licenses.
+# If you do not have access to either file, you may request a copy from
+# help@hdfgroup.org.
+##
+## Makefile.am
+## Run automake to generate a Makefile.in from this file.
+##
+#
+# HDF5 Library Performance Makefile(.in)
+#
+
+include $(top_srcdir)/config/commence.am
+
+AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/test -I$(top_srcdir)/tools/lib
+
+# bin_PROGRAMS will be installed.
+if BUILD_PARALLEL_CONDITIONAL
+ bin_PROGRAMS=h5perf_serial perf h5perf
+else
+ bin_PROGRAMS=h5perf_serial
+endif
+
+# Add h5perf and h5perf_serial specific linker flags here
+h5perf_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+h5perf_serial_LDFLAGS = $(LT_STATIC_EXEC) $(AM_LDFLAGS)
+
+# Some programs are not built or run by default, but can be built by hand or by
+# specifying --enable-build-all at configure time.
+# Also, some of these programs should only be built in parallel.
+# Currently there is no such program.
+if BUILD_PARALLEL_CONDITIONAL
+ PARA_BUILD_ALL=
+endif
+if BUILD_ALL_CONDITIONAL
+ BUILD_ALL_PROGS=$(PARA_BUILD_ALL)
+endif
+
+# Define programs that will be run in 'make check'
+# List them in the order they should be run.
+# Parallel test programs.
+if BUILD_PARALLEL_CONDITIONAL
+ TEST_PROG_PARA=h5perf perf
+endif
+
+h5perf_SOURCES=pio_perf.c pio_engine.c
+h5perf_serial_SOURCES=sio_perf.c sio_engine.c
+
+# All of the programs depend on the main hdf5 library, and some of them
+# depend on test or tools library.
+LDADD=$(LIBHDF5)
+h5perf_LDADD=$(LIBH5TOOLS) $(LIBHDF5)
+h5perf_serial_LDADD=$(LIBH5TOOLS) $(LIBHDF5)
+perf_LDADD=$(LIBHDF5)
+
+include $(top_srcdir)/config/conclude.am
diff --git a/tools/src/h5perf/perf.c b/tools/src/h5perf/perf.c
new file mode 100644
index 0000000..2fbcee5
--- /dev/null
+++ b/tools/src/h5perf/perf.c
@@ -0,0 +1,802 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * Copyright by the Board of Trustees of the University of Illinois. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the COPYING file, which can be found at the root of the source code *
+ * distribution tree, or in https://www.hdfgroup.org/licenses. *
+ * If you do not have access to either file, you may request a copy from *
+ * help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * Author: Albert Cheng of NCSA, May 1, 2001.
+ * This is derived from code given to me by Robert Ross.
+ *
+ * NOTE: This code assumes that all command line arguments make it out to all
+ * the processes that make up the parallel job, which isn't always the case.
+ * So if it doesn't work on some platform, that might be why.
+ */
+
+#include "hdf5.h"
+#include "H5private.h"
+
+#ifdef H5_HAVE_PARALLEL
+
+#ifdef H5_STDC_HEADERS
+#include <errno.h>
+#include <fcntl.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <time.h>
+
+#ifdef H5_HAVE_SYS_STAT_H
+#include <sys/stat.h>
+#endif
+
+#if defined(H5_TIME_WITH_SYS_TIME)
+#include <sys/time.h>
+#include <time.h>
+#elif defined(H5_HAVE_SYS_TIME_H)
+#include <sys/time.h>
+#else
+#include <time.h>
+#endif
+
+#ifdef H5_HAVE_SYS_TYPES_H
+#include <sys/types.h>
+#endif
+
+#ifdef H5_HAVE_UNISTD_H
+#include <unistd.h>
+#endif
+
+#include <mpi.h>
+#ifndef MPI_FILE_NULL /*MPIO may be defined in mpi.h already */
+#include <mpio.h>
+#endif
+
+/* Macro definitions */
+/* Verify:
+ * if val is false (0), print mesg and if fatal is true (non-zero), die.
+ */
+#define H5FATAL 1
+#define VRFY(val, mesg, fatal) \
+ do { \
+ if (!val) { \
+ printf("Proc %d: ", mynod); \
+ printf("*** Assertion failed (%s) at line %4d in %s\n", mesg, (int)__LINE__, __FILE__); \
+ if (fatal) { \
+ fflush(stdout); \
+ goto die_jar_jar_die; \
+ } \
+ } \
+ } while (0)
+#define RANK 1
+#define MAX_PATH 1024
+
+hsize_t dims[RANK]; /* dataset dim sizes */
+hsize_t block[RANK], stride[RANK], count[RANK];
+hsize_t start[RANK];
+hid_t fid; /* HDF5 file ID */
+hid_t acc_tpl; /* File access templates */
+hid_t sid; /* Dataspace ID */
+hid_t file_dataspace; /* File dataspace ID */
+hid_t mem_dataspace; /* memory dataspace ID */
+hid_t dataset; /* Dataset ID */
+hsize_t opt_alignment = 1;
+hsize_t opt_threshold = 1;
+int opt_split_vfd = 0;
+char * meta_ext, *raw_ext; /* holds the meta and raw file extension if */
+ /* opt_split_vfd is set */
+
+/* DEFAULT VALUES FOR OPTIONS */
+int64_t opt_block = 1048576 * 16;
+int opt_iter = 1;
+int opt_stripe = -1;
+int opt_correct = 0;
+int amode = O_RDWR | O_CREAT;
+char opt_file[256] = "perftest.out";
+char opt_pvfstab[256] = "notset";
+int opt_pvfstab_set = 0;
+
+const char *FILENAME[] = {opt_file, NULL};
+
+/* function prototypes */
+static int parse_args(int argc, char **argv);
+
+#ifndef H5_HAVE_UNISTD_H
+/* globals needed for getopt */
+extern char *optarg;
+#endif
+
+#ifndef HDF5_PARAPREFIX
+#define HDF5_PARAPREFIX ""
+#endif
+char * paraprefix = NULL; /* for command line option para-prefix */
+MPI_Info h5_io_info_g = MPI_INFO_NULL; /* MPI INFO object for IO */
+
+static char *h5_fixname_real(const char *base_name, hid_t fapl, const char *_suffix, char *fullname,
+ size_t size, hbool_t nest_printf, hbool_t subst_for_superblock);
+
+int
+main(int argc, char **argv)
+{
+ char * buf, *tmp, *buf2 = NULL, *tmp2 = NULL, *check;
+ int i, j, mynod = 0, nprocs = 1, my_correct = 1, correct, myerrno;
+ double stim, etim;
+ double write_tim = 0;
+ double read_tim = 0;
+ double read_bw, write_bw;
+ double max_read_tim, max_write_tim;
+ double min_read_tim, min_write_tim;
+ double ave_read_tim, ave_write_tim;
+ int64_t iter_jump = 0;
+ char filename[MAX_PATH];
+ herr_t ret; /* Generic return value */
+
+ /* startup MPI and determine the rank of this process */
+ MPI_Init(&argc, &argv);
+ MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
+ MPI_Comm_rank(MPI_COMM_WORLD, &mynod);
+
+ /* parse the command line arguments */
+ parse_args(argc, argv);
+
+ if (mynod == 0)
+ printf("# Using hdf5-io calls.\n");
+
+#ifdef H5_HAVE_UNISTD_H
+ /* Kind of a weird hack- if the location of the pvfstab file was
+ * specified on the command line, then spit out this location into
+ * the appropriate environment variable.
+ */
+ if (opt_pvfstab_set) {
+ if ((setenv("PVFSTAB_FILE", opt_pvfstab, 1)) < 0) {
+ perror("setenv");
+ goto die_jar_jar_die;
+ }
+ }
+#endif
+
+ /* this is how much of the file data is covered on each iteration of
+ * the test. used to help determine the seek offset on each
+ * iteration */
+ iter_jump = nprocs * opt_block;
+
+ /* setup a buffer of data to write */
+ if (!(tmp = (char *)malloc((size_t)opt_block + 256))) {
+ perror("malloc");
+ goto die_jar_jar_die;
+ }
+ buf = tmp + 128 - (((long)tmp) % 128); /* align buffer */
+
+ if (opt_correct) {
+ /* do the same buffer setup for verifiable data */
+ if (!(tmp2 = (char *)malloc((size_t)opt_block + 256))) {
+ perror("malloc2");
+ goto die_jar_jar_die;
+ }
+ buf2 = tmp + 128 - (((long)tmp) % 128);
+ }
+
+ /* setup file access template with parallel IO access. */
+ if (opt_split_vfd) {
+ hid_t mpio_pl;
+
+ mpio_pl = H5Pcreate(H5P_FILE_ACCESS);
+ VRFY((acc_tpl >= 0), "", H5FATAL);
+ ret = H5Pset_fapl_mpio(mpio_pl, MPI_COMM_WORLD, MPI_INFO_NULL);
+ VRFY((ret >= 0), "", H5FATAL);
+
+ /* set optional allocation alignment */
+ if (opt_alignment * opt_threshold != 1) {
+ ret = H5Pset_alignment(acc_tpl, opt_threshold, opt_alignment);
+ VRFY((ret >= 0), "H5Pset_alignment succeeded", !H5FATAL);
+ }
+
+ /* setup file access template */
+ acc_tpl = H5Pcreate(H5P_FILE_ACCESS);
+ VRFY((acc_tpl >= 0), "", H5FATAL);
+ ret = H5Pset_fapl_split(acc_tpl, meta_ext, mpio_pl, raw_ext, mpio_pl);
+ VRFY((ret >= 0), "H5Pset_fapl_split succeeded", H5FATAL);
+ ret = H5Pclose(mpio_pl);
+ VRFY((ret >= 0), "H5Pclose mpio_pl succeeded", H5FATAL);
+ }
+ else {
+ /* setup file access template */
+ acc_tpl = H5Pcreate(H5P_FILE_ACCESS);
+ VRFY((acc_tpl >= 0), "", H5FATAL);
+ ret = H5Pset_fapl_mpio(acc_tpl, MPI_COMM_WORLD, MPI_INFO_NULL);
+ VRFY((ret >= 0), "", H5FATAL);
+
+ /* set optional allocation alignment */
+ if (opt_alignment * opt_threshold != 1) {
+ ret = H5Pset_alignment(acc_tpl, opt_threshold, opt_alignment);
+ VRFY((ret >= 0), "H5Pset_alignment succeeded", !H5FATAL);
+ }
+ }
+
+ h5_fixname_real(FILENAME[0], acc_tpl, NULL, filename, sizeof filename, FALSE, FALSE);
+
+ /* create the parallel file */
+ fid = H5Fcreate(filename, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl);
+ VRFY((fid >= 0), "H5Fcreate succeeded", H5FATAL);
+
+ /* define a contiquous dataset of opt_iter*nprocs*opt_block chars */
+ dims[0] = (hsize_t)opt_iter * (hsize_t)nprocs * (hsize_t)opt_block;
+ sid = H5Screate_simple(RANK, dims, NULL);
+ VRFY((sid >= 0), "H5Screate_simple succeeded", H5FATAL);
+ dataset = H5Dcreate2(fid, "Dataset1", H5T_NATIVE_CHAR, sid, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT);
+ VRFY((dataset >= 0), "H5Dcreate2 succeeded", H5FATAL);
+
+ /* create the memory dataspace and the file dataspace */
+ dims[0] = (hsize_t)opt_block;
+ mem_dataspace = H5Screate_simple(RANK, dims, NULL);
+ VRFY((mem_dataspace >= 0), "", H5FATAL);
+ file_dataspace = H5Dget_space(dataset);
+ VRFY((file_dataspace >= 0), "H5Dget_space succeeded", H5FATAL);
+
+ /* now each process writes a block of opt_block chars in round robbin
+ * fashion until the whole dataset is covered.
+ */
+ for (j = 0; j < opt_iter; j++) {
+ /* setup a file dataspace selection */
+ start[0] = (hsize_t)((j * iter_jump) + (mynod * opt_block));
+ stride[0] = block[0] = (hsize_t)opt_block;
+ count[0] = 1;
+ ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded", H5FATAL);
+
+ if (opt_correct) /* fill in buffer for iteration */ {
+ for (i = mynod + j, check = buf; i < opt_block; i++, check++)
+ *check = (char)i;
+ }
+
+ /* discover the starting time of the operation */
+ MPI_Barrier(MPI_COMM_WORLD);
+ stim = MPI_Wtime();
+
+ /* write data */
+ ret = H5Dwrite(dataset, H5T_NATIVE_CHAR, mem_dataspace, file_dataspace, H5P_DEFAULT, buf);
+ VRFY((ret >= 0), "H5Dwrite dataset1 succeeded", !H5FATAL);
+
+ /* discover the ending time of the operation */
+ etim = MPI_Wtime();
+
+ write_tim += (etim - stim);
+
+ /* we are done with this "write" iteration */
+ }
+
+ /* close dataset and file */
+ ret = H5Dclose(dataset);
+ VRFY((ret >= 0), "H5Dclose succeeded", H5FATAL);
+ ret = H5Fclose(fid);
+ VRFY((ret >= 0), "H5Fclose succeeded", H5FATAL);
+
+ /* wait for everyone to synchronize at this point */
+ MPI_Barrier(MPI_COMM_WORLD);
+
+ /* reopen the file for reading */
+ fid = H5Fopen(filename, H5F_ACC_RDONLY, acc_tpl);
+ VRFY((fid >= 0), "", H5FATAL);
+
+ /* open the dataset */
+ dataset = H5Dopen2(fid, "Dataset1", H5P_DEFAULT);
+ VRFY((dataset >= 0), "H5Dopen succeeded", H5FATAL);
+
+ /* we can re-use the same mem_dataspace and file_dataspace
+ * the H5Dwrite used since the dimension size is the same.
+ */
+
+ /* we are going to repeat the read the same pattern the write used */
+ for (j = 0; j < opt_iter; j++) {
+ /* setup a file dataspace selection */
+ start[0] = (hsize_t)((j * iter_jump) + (mynod * opt_block));
+ stride[0] = block[0] = (hsize_t)opt_block;
+ count[0] = 1;
+ ret = H5Sselect_hyperslab(file_dataspace, H5S_SELECT_SET, start, stride, count, block);
+ VRFY((ret >= 0), "H5Sset_hyperslab succeeded", H5FATAL);
+ /* seek to the appropriate spot give the current iteration and
+ * rank within the MPI processes */
+
+ /* discover the start time */
+ MPI_Barrier(MPI_COMM_WORLD);
+ stim = MPI_Wtime();
+
+ /* read in the file data */
+ if (!opt_correct) {
+ ret = H5Dread(dataset, H5T_NATIVE_CHAR, mem_dataspace, file_dataspace, H5P_DEFAULT, buf);
+ }
+ else {
+ ret = H5Dread(dataset, H5T_NATIVE_CHAR, mem_dataspace, file_dataspace, H5P_DEFAULT, buf2);
+ }
+ myerrno = errno;
+
+ /* discover the end time */
+ etim = MPI_Wtime();
+ read_tim += (etim - stim);
+ VRFY((ret >= 0), "H5Dwrite dataset1 succeeded", !H5FATAL);
+
+ if (ret < 0)
+ HDfprintf(stderr, "node %d, read error, loc = %" PRId64 ": %s\n", mynod, mynod * opt_block,
+ strerror(myerrno));
+
+ /* if the user wanted to check correctness, compare the write
+ * buffer to the read buffer */
+ if (opt_correct && memcmp(buf, buf2, (size_t)opt_block)) {
+ HDfprintf(stderr, "node %d, correctness test failed\n", mynod);
+ my_correct = 0;
+ MPI_Allreduce(&my_correct, &correct, 1, MPI_INT, MPI_MIN, MPI_COMM_WORLD);
+ }
+
+ /* we are done with this read iteration */
+ }
+
+ /* close dataset and file */
+ ret = H5Dclose(dataset);
+ VRFY((ret >= 0), "H5Dclose succeeded", H5FATAL);
+ ret = H5Fclose(fid);
+ VRFY((ret >= 0), "H5Fclose succeeded", H5FATAL);
+ ret = H5Pclose(acc_tpl);
+ VRFY((ret >= 0), "H5Pclose succeeded", H5FATAL);
+
+ /* compute the read and write times */
+ MPI_Allreduce(&read_tim, &max_read_tim, 1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD);
+ MPI_Allreduce(&read_tim, &min_read_tim, 1, MPI_DOUBLE, MPI_MIN, MPI_COMM_WORLD);
+ MPI_Allreduce(&read_tim, &ave_read_tim, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
+
+ /* calculate the average from the sum */
+ ave_read_tim = ave_read_tim / nprocs;
+
+ MPI_Allreduce(&write_tim, &max_write_tim, 1, MPI_DOUBLE, MPI_MAX, MPI_COMM_WORLD);
+ MPI_Allreduce(&write_tim, &min_write_tim, 1, MPI_DOUBLE, MPI_MIN, MPI_COMM_WORLD);
+ MPI_Allreduce(&write_tim, &ave_write_tim, 1, MPI_DOUBLE, MPI_SUM, MPI_COMM_WORLD);
+
+ /* calculate the average from the sum */
+ ave_write_tim = ave_write_tim / nprocs;
+
+ /* print out the results on one node */
+ if (mynod == 0) {
+ read_bw = (double)((int64_t)(opt_block * nprocs * opt_iter)) / (max_read_tim * 1000000.0);
+ write_bw = (double)((int64_t)(opt_block * nprocs * opt_iter)) / (max_write_tim * 1000000.0);
+
+ printf("nr_procs = %d, nr_iter = %d, blk_sz = %ld\n", nprocs, opt_iter, (long)opt_block);
+
+ printf("# total_size = %ld\n", (long)(opt_block * nprocs * opt_iter));
+
+ printf("# Write: min_time = %f, max_time = %f, mean_time = %f\n", min_write_tim, max_write_tim,
+ ave_write_tim);
+ printf("# Read: min_time = %f, max_time = %f, mean_time = %f\n", min_read_tim, max_read_tim,
+ ave_read_tim);
+
+ printf("Write bandwidth = %f Mbytes/sec\n", write_bw);
+ printf("Read bandwidth = %f Mbytes/sec\n", read_bw);
+
+ if (opt_correct) {
+ printf("Correctness test %s.\n", correct ? "passed" : "failed");
+ }
+ }
+
+die_jar_jar_die:
+
+#ifdef H5_HAVE_UNISTD
+ /* Clear the environment variable if it was set earlier */
+ if (opt_pvfstab_set) {
+ unsetenv("PVFSTAB_FILE");
+ }
+#endif
+
+ free(tmp);
+ if (opt_correct)
+ free(tmp2);
+
+ MPI_Finalize();
+
+ return (0);
+}
+
+static int
+parse_args(int argc, char **argv)
+{
+ int c;
+
+ while ((c = getopt(argc, argv, "s:b:i:f:p:a:2:c")) != EOF) {
+ switch (c) {
+ case 's': /* stripe */
+ opt_stripe = atoi(optarg);
+ break;
+ case 'b': /* block size */
+ opt_block = atoi(optarg);
+ break;
+ case 'i': /* iterations */
+ opt_iter = atoi(optarg);
+ break;
+ case 'f': /* filename */
+ strncpy(opt_file, optarg, 255);
+ FILENAME[0] = opt_file;
+ break;
+ case 'p': /* pvfstab file */
+ strncpy(opt_pvfstab, optarg, 255);
+ opt_pvfstab_set = 1;
+ break;
+ case 'a': /* aligned allocation.
+ * syntax: -a<alignment>/<threshold>
+ * e.g., -a4096/512 allocate at 4096 bytes
+ * boundary if request size >= 512.
+ */
+ {
+ char *p;
+
+ opt_alignment = (hsize_t)HDatoi(optarg);
+ if (NULL != (p = (char *)HDstrchr(optarg, '/')))
+ opt_threshold = (hsize_t)HDatoi(p + 1);
+ }
+ HDfprintf(stdout, "alignment/threshold=%" PRIuHSIZE "/%" PRIuHSIZE "\n", opt_alignment,
+ opt_threshold);
+ break;
+ case '2': /* use 2-files, i.e., split file driver */
+ opt_split_vfd = 1;
+ /* get meta and raw file extension. */
+ /* syntax is <raw_ext>,<meta_ext> */
+ meta_ext = raw_ext = optarg;
+ while (*raw_ext != '\0') {
+ if (*raw_ext == ',') {
+ *raw_ext = '\0';
+ raw_ext++;
+ break;
+ }
+ raw_ext++;
+ }
+ printf("split-file-vfd used: %s,%s\n", meta_ext, raw_ext);
+ break;
+ case 'c': /* correctness */
+ opt_correct = 1;
+ break;
+ case '?': /* unknown */
+ default:
+ break;
+ }
+ }
+
+ return (0);
+}
+/*-------------------------------------------------------------------------
+ * Function: getenv_all
+ *
+ * Purpose: Used to get the environment that the root MPI task has.
+ * name specifies which environment variable to look for
+ * val is the string to which the value of that environment
+ * variable will be copied.
+ *
+ * NOTE: The pointer returned by this function is only
+ * valid until the next call to getenv_all and the data
+ * stored there must be copied somewhere else before any
+ * further calls to getenv_all take place.
+ *
+ * Return: pointer to a string containing the value of the environment variable
+ * NULL if the varialbe doesn't exist in task 'root's environment.
+ *
+ * Programmer: Leon Arber
+ * 4/4/05
+ *
+ * Modifications:
+ * Use original getenv if MPI is not initialized. This happens
+ * one uses the PHDF5 library to build a serial nature code.
+ * Albert 2006/04/07
+ *
+ *-------------------------------------------------------------------------
+ */
+char *
+getenv_all(MPI_Comm comm, int root, const char *name)
+{
+ int mpi_size, mpi_rank, mpi_initialized, mpi_finalized;
+ int len;
+ static char *env = NULL;
+
+ HDassert(name);
+
+ MPI_Initialized(&mpi_initialized);
+ MPI_Finalized(&mpi_finalized);
+
+ if (mpi_initialized && !mpi_finalized) {
+ MPI_Comm_rank(comm, &mpi_rank);
+ MPI_Comm_size(comm, &mpi_size);
+ HDassert(root < mpi_size);
+
+ /* The root task does the getenv call
+ * and sends the result to the other tasks */
+ if (mpi_rank == root) {
+ env = HDgetenv(name);
+ if (env) {
+ len = (int)HDstrlen(env);
+ MPI_Bcast(&len, 1, MPI_INT, root, comm);
+ MPI_Bcast(env, len, MPI_CHAR, root, comm);
+ }
+ else {
+ /* len -1 indicates that the variable was not in the environment */
+ len = -1;
+ MPI_Bcast(&len, 1, MPI_INT, root, comm);
+ }
+ }
+ else {
+ MPI_Bcast(&len, 1, MPI_INT, root, comm);
+ if (len >= 0) {
+ if (env == NULL)
+ env = (char *)HDmalloc((size_t)len + 1);
+ else if (HDstrlen(env) < (size_t)len)
+ env = (char *)HDrealloc(env, (size_t)len + 1);
+
+ MPI_Bcast(env, len, MPI_CHAR, root, comm);
+ env[len] = '\0';
+ }
+ else {
+ if (env)
+ HDfree(env);
+ env = NULL;
+ }
+ }
+#ifndef NDEBUG
+ MPI_Barrier(comm);
+#endif
+ }
+ else {
+ /* use original getenv */
+ if (env)
+ HDfree(env);
+ env = HDgetenv(name);
+ } /* end if */
+
+ return env;
+}
+
+/*-------------------------------------------------------------------------
+ * Function: h5_fixname_real
+ *
+ * Purpose: Create a file name from a file base name like `test' and
+ * return it through the FULLNAME (at most SIZE characters
+ * counting the null terminator). The full name is created by
+ * prepending the contents of HDF5_PREFIX (separated from the
+ * base name by a slash) and appending a file extension based on
+ * the driver supplied, resulting in something like
+ * `ufs:/u/matzke/test.h5'.
+ *
+ * Return: Success: The FULLNAME pointer.
+ *
+ * Failure: NULL if BASENAME or FULLNAME is the null
+ * pointer or if FULLNAME isn't large enough for
+ * the result.
+ *
+ * Programmer: Robb Matzke
+ * Thursday, November 19, 1998
+ *
+ *-------------------------------------------------------------------------
+ */
+static char *
+h5_fixname_real(const char *base_name, hid_t fapl, const char *_suffix, char *fullname, size_t size,
+ hbool_t nest_printf, hbool_t subst_for_superblock)
+{
+ const char *prefix = NULL;
+ const char *env = NULL; /* HDF5_DRIVER environment variable */
+ char * ptr, last = '\0';
+ const char *suffix = _suffix;
+ size_t i, j;
+ hid_t driver = -1;
+ int isppdriver = 0; /* if the driver is MPI parallel */
+
+ if (!base_name || !fullname || size < 1)
+ return NULL;
+
+ HDmemset(fullname, 0, size);
+
+ /* figure out the suffix */
+ if (H5P_DEFAULT != fapl) {
+ if ((driver = H5Pget_driver(fapl)) < 0)
+ return NULL;
+
+ if (suffix) {
+ if (H5FD_FAMILY == driver) {
+ if (subst_for_superblock)
+ suffix = "00000.h5";
+ else
+ suffix = nest_printf ? "%%05d.h5" : "%05d.h5";
+ }
+ else if (H5FD_MULTI == driver) {
+
+ /* Get the environment variable, if it exists, in case
+ * we are using the split driver since both of those
+ * use the multi VFD under the hood.
+ */
+ env = HDgetenv("HDF5_DRIVER");
+#ifdef HDF5_DRIVER
+ /* Use the environment variable, then the compile-time constant */
+ if (!env)
+ env = HDF5_DRIVER;
+#endif
+ if (env && !HDstrcmp(env, "split")) {
+ /* split VFD */
+ if (subst_for_superblock)
+ suffix = "-m.h5";
+ else
+ suffix = NULL;
+ }
+ else {
+ /* multi VFD */
+ if (subst_for_superblock)
+ suffix = "-s.h5";
+ else
+ suffix = NULL;
+ }
+ }
+ }
+ }
+
+ /* Must first check fapl is not H5P_DEFAULT (-1) because H5FD_XXX
+ * could be of value -1 if it is not defined.
+ */
+ isppdriver = H5P_DEFAULT != fapl && (H5FD_MPIO == driver);
+
+ /* Check what prefix to use for test files. Process HDF5_PARAPREFIX and
+ * HDF5_PREFIX.
+ * Use different ones depending on parallel or serial driver used.
+ * (The #ifdef is needed to prevent compile failure in case MPI is not
+ * configured.)
+ */
+ if (isppdriver) {
+ /*
+ * For parallel:
+ * First use command line option, then the environment
+ * variable, then try the constant
+ */
+ static int explained = 0;
+
+ prefix = (paraprefix ? paraprefix : getenv_all(MPI_COMM_WORLD, 0, "HDF5_PARAPREFIX"));
+
+ if (!prefix && !explained) {
+ /* print hint by process 0 once. */
+ int mpi_rank;
+
+ MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);
+
+ if (mpi_rank == 0)
+ HDprintf("*** Hint ***\n"
+ "You can use environment variable HDF5_PARAPREFIX to "
+ "run parallel test files in a\n"
+ "different directory or to add file type prefix. e.g.,\n"
+ " HDF5_PARAPREFIX=pfs:/PFS/user/me\n"
+ " export HDF5_PARAPREFIX\n"
+ "*** End of Hint ***\n");
+
+ explained = TRUE;
+#ifdef HDF5_PARAPREFIX
+ prefix = HDF5_PARAPREFIX;
+#endif /* HDF5_PARAPREFIX */
+ }
+ }
+ else {
+ /*
+ * For serial:
+ * First use the environment variable, then try the constant
+ */
+ prefix = HDgetenv("HDF5_PREFIX");
+
+#ifdef HDF5_PREFIX
+ if (!prefix)
+ prefix = HDF5_PREFIX;
+#endif /* HDF5_PREFIX */
+ }
+
+ /* Prepend the prefix value to the base name */
+ if (prefix && *prefix) {
+ if (isppdriver) {
+ /* This is a parallel system */
+ char *subdir;
+
+ if (!HDstrcmp(prefix, HDF5_PARAPREFIX)) {
+ /*
+ * If the prefix specifies the HDF5_PARAPREFIX directory, then
+ * default to using the "/tmp/$USER" or "/tmp/$LOGIN"
+ * directory instead.
+ */
+ char *user, *login;
+
+ user = HDgetenv("USER");
+ login = HDgetenv("LOGIN");
+ subdir = (user ? user : login);
+
+ if (subdir) {
+ for (i = 0; i < size && prefix[i]; i++)
+ fullname[i] = prefix[i];
+
+ fullname[i++] = '/';
+
+ for (j = 0; i < size && subdir[j]; ++i, ++j)
+ fullname[i] = subdir[j];
+ }
+ }
+
+ if (!fullname[0]) {
+ /* We didn't append the prefix yet */
+ HDstrncpy(fullname, prefix, size);
+ fullname[size - 1] = '\0';
+ }
+
+ if (HDstrlen(fullname) + HDstrlen(base_name) + 1 < size) {
+ /*
+ * Append the base_name with a slash first. Multiple
+ * slashes are handled below.
+ */
+ h5_stat_t buf;
+
+ if (HDstat(fullname, &buf) < 0)
+ /* The directory doesn't exist just yet */
+ if (HDmkdir(fullname, (mode_t)0755) < 0 && errno != EEXIST)
+ /*
+ * We couldn't make the "/tmp/${USER,LOGIN}"
+ * subdirectory. Default to PREFIX's original
+ * prefix value.
+ */
+ HDstrcpy(fullname, prefix);
+
+ HDstrcat(fullname, "/");
+ HDstrcat(fullname, base_name);
+ }
+ else {
+ /* Buffer is too small */
+ return NULL;
+ }
+ }
+ else {
+ if (HDsnprintf(fullname, size, "%s/%s", prefix, base_name) == (int)size)
+ /* Buffer is too small */
+ return NULL;
+ }
+ }
+ else if (HDstrlen(base_name) >= size) {
+ /* Buffer is too small */
+ return NULL;
+ }
+ else {
+ HDstrcpy(fullname, base_name);
+ }
+
+ /* Append a suffix */
+ if (suffix) {
+ if (HDstrlen(fullname) + HDstrlen(suffix) >= size)
+ return NULL;
+
+ HDstrcat(fullname, suffix);
+ }
+
+ /* Remove any double slashes in the filename */
+ for (ptr = fullname, i = j = 0; ptr && i < size; i++, ptr++) {
+ if (*ptr != '/' || last != '/')
+ fullname[j++] = *ptr;
+
+ last = *ptr;
+ }
+
+ return fullname;
+}
+
+/*
+ * Local variables:
+ * c-indent-level: 3
+ * c-basic-offset: 3
+ * tab-width: 3
+ * End:
+ */
+
+#else /* H5_HAVE_PARALLEL */
+/* dummy program since H5_HAVE_PARALLEL is not configured in */
+int
+main(int H5_ATTR_UNUSED argc, char H5_ATTR_UNUSED **argv)
+{
+ printf("No parallel performance because parallel is not configured in\n");
+ return (0);
+}
+#endif /* H5_HAVE_PARALLEL */
diff --git a/tools/src/h5perf/pio_engine.c b/tools/src/h5perf/pio_engine.c
new file mode 100644
index 0000000..65194b0
--- /dev/null
+++ b/tools/src/h5perf/pio_engine.c
@@ -0,0 +1,2747 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the COPYING file, which can be found at the root of the source code *
+ * distribution tree, or in https://www.hdfgroup.org/licenses. *
+ * If you do not have access to either file, you may request a copy from *
+ * help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * Author: Albert Cheng of NCSA, Oct 24, 2001.
+ */
+
+#include "hdf5.h"
+
+#ifdef H5_STDC_HEADERS
+#include <errno.h>
+#include <fcntl.h>
+#include <stdio.h>
+#include <stdlib.h>
+#endif
+
+#ifdef H5_HAVE_UNISTD_H
+#include <sys/types.h>
+#include <unistd.h>
+#endif
+
+#ifdef H5_HAVE_SYS_STAT_H
+#include <sys/stat.h>
+#endif
+
+#ifdef H5_HAVE_PARALLEL
+
+#include <mpi.h>
+
+#ifndef MPI_FILE_NULL /*MPIO may be defined in mpi.h already */
+#include <mpio.h>
+#endif /* !MPI_FILE_NULL */
+
+#include "pio_perf.h"
+
+/* Macro definitions */
+
+#if H5_VERS_MAJOR == 1 && H5_VERS_MINOR == 6
+#define H5DCREATE(fd, name, type, space, dcpl) H5Dcreate(fd, name, type, space, dcpl)
+#define H5DOPEN(fd, name) H5Dopen(fd, name)
+#else
+#define H5DCREATE(fd, name, type, space, dcpl) \
+ H5Dcreate2(fd, name, type, space, H5P_DEFAULT, dcpl, H5P_DEFAULT)
+#define H5DOPEN(fd, name) H5Dopen2(fd, name, H5P_DEFAULT)
+#endif
+
+/* sizes of various items. these sizes won't change during program execution */
+/* The following three must have the same type */
+#define ELMT_H5_TYPE H5T_NATIVE_UCHAR
+
+#define GOTOERROR(errcode) \
+ { \
+ ret_code = errcode; \
+ goto done; \
+ }
+#define ERRMSG(mesg) \
+ { \
+ HDfprintf(stderr, "Proc %d: ", pio_mpi_rank_g); \
+ HDfprintf(stderr, "*** Assertion failed (%s) at line %4d in %s\n", mesg, (int)__LINE__, __FILE__); \
+ }
+
+/* verify: if val is false (0), print mesg. */
+#define VRFY(val, mesg) \
+ do { \
+ if (!val) { \
+ ERRMSG(mesg); \
+ GOTOERROR(FAIL); \
+ } \
+ } while (0)
+
+/* POSIX I/O macros */
+#ifdef H5_HAVE_WIN32_API
+/* Can't link against the library, so this test will use the older, non-Unicode
+ * _open() call on Windows.
+ */
+#define HDopen(S, F, ...) _open(S, F | _O_BINARY, __VA_ARGS__)
+#endif /* H5_HAVE_WIN32_API */
+#define POSIXCREATE(fn) HDopen(fn, O_CREAT | O_TRUNC | O_RDWR, 0600)
+#define POSIXOPEN(fn, F) HDopen(fn, F, 0600)
+#define POSIXCLOSE(F) HDclose(F)
+#define POSIXSEEK(F, L) HDlseek(F, L, SEEK_SET)
+#define POSIXWRITE(F, B, S) HDwrite(F, B, S)
+#define POSIXREAD(F, B, S) HDread(F, B, S)
+
+enum { PIO_CREATE = 1, PIO_WRITE = 2, PIO_READ = 4 };
+
+/* Global variables */
+static int clean_file_g = -1; /*whether to cleanup temporary test */
+/*files. -1 is not defined; */
+/*0 is no cleanup; 1 is do cleanup */
+
+/*
+ * In a parallel machine, the filesystem suitable for compiling is
+ * unlikely a parallel file system that is suitable for parallel I/O.
+ * There is no standard pathname for the parallel file system. /tmp
+ * is about the best guess.
+ */
+#ifndef HDF5_PARAPREFIX
+#define HDF5_PARAPREFIX ""
+#endif /* !HDF5_PARAPREFIX */
+
+#ifndef MIN
+#define MIN(a, b) ((a) < (b) ? (a) : (b))
+#endif /* !MIN */
+
+/* the different types of file descriptors we can expect */
+typedef union _file_descr {
+ int posixfd; /* POSIX file handle*/
+ MPI_File mpifd; /* MPI file */
+ hid_t h5fd; /* HDF5 file */
+} file_descr;
+
+/* local functions */
+static char * pio_create_filename(iotype iot, const char *base_name, char *fullname, size_t size);
+static herr_t do_write(results *res, file_descr *fd, parameters *parms, long ndsets, off_t nelmts,
+ size_t buf_size, void *buffer);
+static herr_t do_read(results *res, file_descr *fd, parameters *parms, long ndsets, off_t nelmts,
+ size_t buf_size, void *buffer /*out*/);
+static herr_t do_fopen(parameters *param, char *fname, file_descr *fd /*out*/, int flags);
+static herr_t do_fclose(iotype iot, file_descr *fd);
+static void do_cleanupfile(iotype iot, char *fname);
+static off_t sqrto(off_t);
+
+/*
+ * Function: do_pio
+ * Purpose: PIO Engine where Parallel IO are executed.
+ * Return: results
+ * Programmer: Albert Cheng, Bill Wendling 2001/12/12
+ * Modifications:
+ * Added 2D testing (Christian Chilan, 10. August 2005)
+ */
+results
+do_pio(parameters param)
+{
+ /* return codes */
+ herr_t ret_code = 0; /*return code */
+ results res;
+
+ file_descr fd;
+ iotype iot;
+
+ char fname[FILENAME_MAX];
+ long nf;
+ long ndsets;
+ off_t nbytes; /*number of bytes per dataset */
+ off_t snbytes; /*general dataset size */
+ /*for 1D, it is the actual dataset size */
+ /*for 2D, it is the size of a side of the dataset square */
+ char * buffer = NULL; /*data buffer pointer */
+ size_t buf_size; /*general buffer size in bytes */
+ /*for 1D, it is the actual buffer size */
+ /*for 2D, it is the length of the buffer rectangle */
+ size_t blk_size; /*data block size in bytes */
+ size_t bsize; /*actual buffer size */
+
+ /* HDF5 variables */
+ herr_t hrc; /*HDF5 return code */
+
+ /* Sanity check parameters */
+
+ /* IO type */
+ iot = param.io_type;
+
+ switch (iot) {
+ case MPIO:
+ fd.mpifd = MPI_FILE_NULL;
+ res.timers = io_time_new(MPI_CLOCK);
+ break;
+ case POSIXIO:
+ fd.posixfd = -1;
+ res.timers = io_time_new(MPI_CLOCK);
+ break;
+ case PHDF5:
+ fd.h5fd = -1;
+ res.timers = io_time_new(MPI_CLOCK);
+ break;
+ default:
+ /* unknown request */
+ HDfprintf(stderr, "Unknown IO type request (%d)\n", iot);
+ GOTOERROR(FAIL);
+ }
+
+ ndsets = param.num_dsets; /* number of datasets per file */
+ nbytes = param.num_bytes; /* number of bytes per dataset */
+ buf_size = param.buf_size;
+ blk_size = param.blk_size;
+
+ if (!param.dim2d) {
+ snbytes = nbytes; /* General dataset size */
+ bsize = buf_size; /* Actual buffer size */
+ }
+ else {
+ snbytes = sqrto(nbytes); /* General dataset size */
+ bsize = buf_size * blk_size; /* Actual buffer size */
+ }
+
+ if (param.num_files < 0) {
+ HDfprintf(stderr, "number of files must be >= 0 (%ld)\n", param.num_files);
+ GOTOERROR(FAIL);
+ }
+
+ if (ndsets < 0) {
+ HDfprintf(stderr, "number of datasets per file must be >= 0 (%ld)\n", ndsets);
+ GOTOERROR(FAIL);
+ }
+
+ if (param.num_procs <= 0) {
+ HDfprintf(stderr, "maximum number of process to use must be > 0 (%d)\n", param.num_procs);
+ GOTOERROR(FAIL);
+ }
+
+ /* Validate transfer buffer size & block size*/
+ if (blk_size <= 0) {
+ HDfprintf(stderr, "Transfer block size (%zu) must be > 0\n", blk_size);
+ GOTOERROR(FAIL);
+ }
+ if (buf_size <= 0) {
+ HDfprintf(stderr, "Transfer buffer size (%zu) must be > 0\n", buf_size);
+ GOTOERROR(FAIL);
+ }
+ if ((buf_size % blk_size) != 0) {
+ HDfprintf(stderr,
+ "Transfer buffer size (%zu) must be a multiple of the "
+ "interleaved I/O block size (%zu)\n",
+ buf_size, blk_size);
+ GOTOERROR(FAIL);
+ }
+ if ((snbytes % pio_mpi_nprocs_g) != 0) {
+ HDfprintf(stderr,
+ "Dataset size (%" H5_PRINTF_LL_WIDTH "d) must be a multiple of the "
+ "number of processes (%d)\n",
+ (long long)snbytes, pio_mpi_nprocs_g);
+ GOTOERROR(FAIL);
+ }
+
+ if (!param.dim2d) {
+ if (((size_t)(snbytes / pio_mpi_nprocs_g) % buf_size) != 0) {
+ HDfprintf(stderr,
+ "Dataset size/process (%" H5_PRINTF_LL_WIDTH "d) must be a multiple of the "
+ "trasfer buffer size (%zu)\n",
+ (long long)(snbytes / pio_mpi_nprocs_g), buf_size);
+ GOTOERROR(FAIL);
+ }
+ }
+ else {
+ if (((size_t)snbytes % buf_size) != 0) {
+ HDfprintf(stderr,
+ "Dataset side size (%" H5_PRINTF_LL_WIDTH "d) must be a multiple of the "
+ "trasfer buffer size (%zu)\n",
+ (long long)snbytes, buf_size);
+ GOTOERROR(FAIL);
+ }
+ }
+
+ /* Allocate transfer buffer */
+ if ((buffer = malloc(bsize)) == NULL) {
+ HDfprintf(stderr, "malloc for transfer buffer size (%zu) failed\n", bsize);
+ GOTOERROR(FAIL);
+ }
+
+ if (pio_debug_level >= 4) {
+ int myrank;
+
+ MPI_Comm_rank(pio_comm_g, &myrank);
+
+ /* output all of the times for all iterations */
+ if (myrank == 0)
+ HDfprintf(output, "Timer details:\n");
+ }
+
+ for (nf = 1; nf <= param.num_files; nf++) {
+ /*
+ * Write performance measurement
+ */
+ /* Open file for write */
+ char base_name[256];
+
+ HDsprintf(base_name, "#pio_tmp_%lu", nf);
+ pio_create_filename(iot, base_name, fname, sizeof(fname));
+ if (pio_debug_level > 0)
+ HDfprintf(output, "rank %d: data filename=%s\n", pio_mpi_rank_g, fname);
+
+ /* Need barrier to make sure everyone starts at the same time */
+ MPI_Barrier(pio_comm_g);
+
+ io_time_set(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, TSTART);
+ hrc = do_fopen(&param, fname, &fd, PIO_CREATE | PIO_WRITE);
+
+ VRFY((hrc == SUCCESS), "do_fopen failed");
+
+ io_time_set(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, TSTART);
+ hrc = do_write(&res, &fd, &param, ndsets, nbytes, buf_size, buffer);
+ io_time_set(res.timers, HDF5_FINE_WRITE_FIXED_DIMS, TSTOP);
+
+ VRFY((hrc == SUCCESS), "do_write failed");
+
+ /* Close file for write */
+ hrc = do_fclose(iot, &fd);
+
+ io_time_set(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS, TSTOP);
+ VRFY((hrc == SUCCESS), "do_fclose failed");
+
+ if (!param.h5_write_only) {
+ /*
+ * Read performance measurement
+ */
+ /* Need barrier to make sure everyone is done writing and has
+ * closed the file. Also to make sure everyone starts reading
+ * at the same time.
+ */
+ MPI_Barrier(pio_comm_g);
+
+ /* Open file for read */
+ io_time_set(res.timers, HDF5_GROSS_READ_FIXED_DIMS, TSTART);
+ hrc = do_fopen(&param, fname, &fd, PIO_READ);
+
+ VRFY((hrc == SUCCESS), "do_fopen failed");
+
+ io_time_set(res.timers, HDF5_FINE_READ_FIXED_DIMS, TSTART);
+ hrc = do_read(&res, &fd, &param, ndsets, nbytes, buf_size, buffer);
+ io_time_set(res.timers, HDF5_FINE_READ_FIXED_DIMS, TSTOP);
+ VRFY((hrc == SUCCESS), "do_read failed");
+
+ /* Close file for read */
+ hrc = do_fclose(iot, &fd);
+
+ io_time_set(res.timers, HDF5_GROSS_READ_FIXED_DIMS, TSTOP);
+ VRFY((hrc == SUCCESS), "do_fclose failed");
+ }
+
+ /* Need barrier to make sure everyone is done with the file */
+ /* before it may be removed by do_cleanupfile */
+ MPI_Barrier(pio_comm_g);
+ do_cleanupfile(iot, fname);
+ }
+
+done:
+ /* clean up */
+ /* release HDF5 objects */
+
+ /* close any opened files */
+ /* no remove(fname) because that should have happened normally. */
+ switch (iot) {
+ case POSIXIO:
+ if (fd.posixfd != -1)
+ hrc = do_fclose(iot, &fd);
+ break;
+ case MPIO:
+ if (fd.mpifd != MPI_FILE_NULL)
+ hrc = do_fclose(iot, &fd);
+ break;
+ case PHDF5:
+ if (fd.h5fd != -1)
+ hrc = do_fclose(iot, &fd);
+ break;
+ default:
+ break;
+ }
+
+ /* release generic resources */
+ if (buffer)
+ HDfree(buffer);
+ res.ret_code = ret_code;
+ return res;
+}
+
+/*
+ * Function: pio_create_filename
+ * Purpose: Create a new filename to write to. Determine the correct
+ * suffix to append to the filename by the type of I/O we're
+ * doing. Also, place in the /tmp/{$USER,$LOGIN} directory if
+ * USER or LOGIN are specified in the environment.
+ * Return: Pointer to filename or NULL
+ * Programmer: Bill Wendling, 21. November 2001
+ * Modifications:
+ */
+static char *
+pio_create_filename(iotype iot, const char *base_name, char *fullname, size_t size)
+{
+ const char *prefix, *suffix = "";
+ char * ptr, last = '\0';
+ size_t i, j;
+
+ if (!base_name || !fullname || size < 1)
+ return NULL;
+
+ HDmemset(fullname, 0, size);
+
+ switch (iot) {
+ case POSIXIO:
+ suffix = ".posix";
+ break;
+ case MPIO:
+ suffix = ".mpio";
+ break;
+ case PHDF5:
+ suffix = ".h5";
+ break;
+ default:
+ break;
+ }
+
+ /* First use the environment variable and then try the constant */
+ prefix = HDgetenv("HDF5_PARAPREFIX");
+
+#ifdef HDF5_PARAPREFIX
+ if (!prefix)
+ prefix = HDF5_PARAPREFIX;
+#endif /* HDF5_PARAPREFIX */
+
+ /* Prepend the prefix value to the base name */
+ if (prefix && *prefix) {
+ /* If the prefix specifies the HDF5_PARAPREFIX directory, then
+ * default to using the "/tmp/$USER" or "/tmp/$LOGIN"
+ * directory instead. */
+ register char *user, *login, *subdir;
+
+ user = HDgetenv("USER");
+ login = HDgetenv("LOGIN");
+ subdir = (user ? user : login);
+
+ if (subdir) {
+ for (i = 0; i < size - 1 && prefix[i]; i++)
+ fullname[i] = prefix[i];
+
+ fullname[i++] = '/';
+
+ for (j = 0; i < size && subdir[j]; i++, j++)
+ fullname[i] = subdir[j];
+ }
+ else {
+ /* We didn't append the prefix yet */
+ HDstrncpy(fullname, prefix, size);
+ fullname[size - 1] = '\0';
+ }
+
+ if ((HDstrlen(fullname) + HDstrlen(base_name) + 1) < size) {
+ /* Append the base_name with a slash first. Multiple slashes are
+ * handled below. */
+ h5_stat_t buf;
+
+ if (HDstat(fullname, &buf) < 0)
+ /* The directory doesn't exist just yet */
+ if (HDmkdir(fullname, (mode_t)0755) < 0 && errno != EEXIST) {
+ /* We couldn't make the "/tmp/${USER,LOGIN}" subdirectory.
+ * Default to PREFIX's original prefix value. */
+ HDstrcpy(fullname, prefix);
+ }
+
+ HDstrcat(fullname, "/");
+ HDstrcat(fullname, base_name);
+ }
+ else {
+ /* Buffer is too small */
+ return NULL;
+ }
+ }
+ else if (HDstrlen(base_name) >= size) {
+ /* Buffer is too small */
+ return NULL;
+ }
+ else {
+ HDstrcpy(fullname, base_name);
+ }
+
+ /* Append a suffix */
+ if (suffix) {
+ if (HDstrlen(fullname) + HDstrlen(suffix) >= size)
+ return NULL;
+
+ HDstrcat(fullname, suffix);
+ }
+
+ /* Remove any double slashes in the filename */
+ for (ptr = fullname, i = j = 0; ptr && i < size; i++, ptr++) {
+ if (*ptr != '/' || last != '/')
+ fullname[j++] = *ptr;
+
+ last = *ptr;
+ }
+
+ return fullname;
+}
+
+/*
+ * Function: do_write
+ * Purpose: Write the required amount of data to the file.
+ * Return: SUCCESS or FAIL
+ * Programmer: Albert Cheng, Bill Wendling, 2001/12/13
+ * Modifications:
+ * Added 2D testing (Christian Chilan, 10. August 2005)
+ */
+static herr_t
+do_write(results *res, file_descr *fd, parameters *parms, long ndsets, off_t nbytes, size_t buf_size,
+ void *buffer)
+{
+ int ret_code = SUCCESS;
+ int rc; /*routine return code */
+ long ndset;
+ size_t blk_size; /* The block size to subdivide the xfer buffer into */
+ off_t nbytes_xfer; /* Total number of bytes transferred so far */
+ size_t nbytes_xfer_advance; /* Number of bytes transferred in a single I/O operation */
+ size_t nbytes_toxfer; /* Number of bytes to transfer a particular time */
+ char dname[64];
+ off_t dset_offset = 0; /*dataset offset in a file */
+ off_t bytes_begin[2]; /*first elmt this process transfer */
+ off_t bytes_count; /*number of elmts this process transfer */
+ off_t snbytes = 0; /*size of a side of the dataset square */
+ unsigned char *buf_p; /* Current buffer pointer */
+
+ /* POSIX variables */
+ off_t file_offset; /* File offset of the next transfer */
+ off_t file_offset_advance; /* File offset advance after each I/O operation */
+ off_t posix_file_offset; /* Base file offset of the next transfer */
+
+ /* MPI variables */
+ MPI_Offset mpi_file_offset; /* Base file offset of the next transfer*/
+ MPI_Offset mpi_offset; /* Offset in MPI file */
+ MPI_Offset mpi_offset_advance; /* Offset advance after each I/O operation */
+ MPI_Datatype mpi_file_type; /* MPI derived type for 1D file */
+ MPI_Datatype mpi_blk_type; /* MPI derived type for 1D buffer */
+ MPI_Datatype mpi_cont_type; /* MPI derived type for 2D contiguous file */
+ MPI_Datatype mpi_partial_buffer_cont; /* MPI derived type for partial 2D contiguous buffer */
+ MPI_Datatype mpi_inter_type; /* MPI derived type for 2D interleaved file */
+ MPI_Datatype mpi_partial_buffer_inter; /* MPI derived type for partial 2D interleaved buffer */
+ MPI_Datatype mpi_full_buffer; /* MPI derived type for 2D full buffer */
+ MPI_Datatype mpi_full_chunk; /* MPI derived type for 2D full chunk */
+ MPI_Datatype mpi_chunk_inter_type; /* MPI derived type for 2D chunk interleaved file */
+ MPI_Datatype mpi_collective_type; /* Generic MPI derived type for 2D collective access */
+ MPI_Status mpi_status;
+ int mrc; /* MPI return code */
+
+ /* HDF5 variables */
+ herr_t hrc; /*HDF5 return code */
+ hsize_t h5dims[2]; /*dataset dim sizes */
+ hid_t h5dset_space_id = H5I_INVALID_HID; /*dataset space ID */
+ hid_t h5mem_space_id = H5I_INVALID_HID; /*memory dataspace ID */
+ hid_t h5ds_id = H5I_INVALID_HID; /*dataset handle */
+ hsize_t h5block[2]; /*dataspace selection */
+ hsize_t h5stride[2];
+ hsize_t h5count[2];
+ hsize_t h5start[2];
+ hssize_t h5offset[2]; /* Selection offset within dataspace */
+ hid_t h5dcpl = H5I_INVALID_HID; /* Dataset creation property list */
+ hid_t h5dxpl = H5I_INVALID_HID; /* Dataset transfer property list */
+
+ /* Get the parameters from the parameter block */
+ blk_size = parms->blk_size;
+
+ /* There are two kinds of transfer patterns, contiguous and interleaved.
+ * Let 0,1,2,...,n be data accessed by process 0,1,2,...,n
+ * where n is rank of the last process.
+ * In contiguous pattern, data are accessed as
+ * 000...111...222...nnn...
+ * In interleaved pattern, data are accessed as
+ * 012...n012...n...
+ * These are all in the scope of one dataset.
+ */
+
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ /* Contiguous Pattern: */
+ if (!parms->interleaved) {
+ bytes_begin[0] = (off_t)(((double)nbytes * pio_mpi_rank_g) / pio_mpi_nprocs_g);
+ } /* end if */
+ /* Interleaved Pattern: */
+ else {
+ bytes_begin[0] = (off_t)(blk_size * (size_t)pio_mpi_rank_g);
+ } /* end else */
+
+ /* Prepare buffer for verifying data */
+ if (parms->verify)
+ memset(buffer, pio_mpi_rank_g + 1, buf_size);
+ } /* end if */
+ /* 2D dataspace */
+ else {
+ /* nbytes is always the number of bytes per dataset (1D or 2D). If the
+ dataspace is 2D, snbytes is the size of a side of the dataset square.
+ */
+ snbytes = sqrto(nbytes);
+
+ /* Contiguous Pattern: */
+ if (!parms->interleaved) {
+ bytes_begin[0] = (off_t)((double)snbytes * pio_mpi_rank_g / pio_mpi_nprocs_g);
+ bytes_begin[1] = 0;
+ } /* end if */
+ /* Interleaved Pattern: */
+ else {
+ bytes_begin[0] = 0;
+
+ if (!parms->h5_use_chunks || parms->io_type == PHDF5)
+ bytes_begin[1] = (off_t)(blk_size * (size_t)pio_mpi_rank_g);
+ else
+ bytes_begin[1] = (off_t)(blk_size * blk_size * (size_t)pio_mpi_rank_g);
+ } /* end else */
+
+ /* Prepare buffer for verifying data */
+ if (parms->verify)
+ HDmemset(buffer, pio_mpi_rank_g + 1, buf_size * blk_size);
+ } /* end else */
+
+ /* Calculate the total number of bytes (bytes_count) to be
+ * transferred by this process. It may be different for different
+ * transfer pattern due to rounding to integral values.
+ */
+ /*
+ * Calculate the beginning bytes of this process and the next.
+ * bytes_count is the difference between these two beginnings.
+ * This way, it eliminates any rounding errors.
+ * (This is tricky, don't mess with the formula, rounding errors
+ * can easily get introduced) */
+ bytes_count = (off_t)(((double)nbytes * (pio_mpi_rank_g + 1)) / pio_mpi_nprocs_g) -
+ (off_t)(((double)nbytes * pio_mpi_rank_g) / pio_mpi_nprocs_g);
+
+ /* debug */
+ if (pio_debug_level >= 4) {
+ HDprint_rank(output);
+ if (!parms->dim2d) {
+ HDfprintf(output,
+ "Debug(do_write): "
+ "buf_size=%zu, bytes_begin=%" H5_PRINTF_LL_WIDTH "d, bytes_count=%" H5_PRINTF_LL_WIDTH
+ "d\n",
+ buf_size, (long long)bytes_begin[0], (long long)bytes_count);
+ }
+ else {
+ HDfprintf(output,
+ "Debug(do_write): "
+ "linear buf_size=%zu, bytes_begin=(%" H5_PRINTF_LL_WIDTH "d,%" H5_PRINTF_LL_WIDTH
+ "d), bytes_count=%" H5_PRINTF_LL_WIDTH "d\n",
+ buf_size * blk_size, (long long)bytes_begin[0], (long long)bytes_begin[1],
+ (long long)bytes_count);
+ }
+ }
+
+ /* I/O Access specific setup */
+ switch (parms->io_type) {
+ case POSIXIO:
+ /* No extra setup */
+ break;
+
+ case MPIO: /* MPI-I/O setup */
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ /* Build block's derived type */
+ mrc = MPI_Type_contiguous((int)blk_size, MPI_BYTE, &mpi_blk_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Build file's derived type */
+ mrc = MPI_Type_vector((int)(buf_size / blk_size), (int)1, (int)pio_mpi_nprocs_g, mpi_blk_type,
+ &mpi_file_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Commit file type */
+ mrc = MPI_Type_commit(&mpi_file_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+
+ /* Commit buffer type */
+ mrc = MPI_Type_commit(&mpi_blk_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+ } /* end if */
+ /* 2D dataspace */
+ else {
+ /* Build partial buffer derived type for contiguous access */
+
+ mrc = MPI_Type_contiguous((int)buf_size, MPI_BYTE, &mpi_partial_buffer_cont);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Commit partial buffer derived type */
+ mrc = MPI_Type_commit(&mpi_partial_buffer_cont);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+
+ /* Build contiguous file's derived type */
+ mrc = MPI_Type_vector((int)blk_size, (int)1, (int)((size_t)snbytes / buf_size),
+ mpi_partial_buffer_cont, &mpi_cont_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Commit contiguous file type */
+ mrc = MPI_Type_commit(&mpi_cont_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+
+ /* Build partial buffer derived type for interleaved access */
+ mrc = MPI_Type_contiguous((int)blk_size, MPI_BYTE, &mpi_partial_buffer_inter);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Commit partial buffer derived type */
+ mrc = MPI_Type_commit(&mpi_partial_buffer_inter);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+
+ /* Build interleaved file's derived type */
+ mrc = MPI_Type_vector((int)buf_size, (int)1, (int)((size_t)snbytes / blk_size),
+ mpi_partial_buffer_inter, &mpi_inter_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Commit interleaved file type */
+ mrc = MPI_Type_commit(&mpi_inter_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+
+ /* Build full buffer derived type */
+ mrc = MPI_Type_contiguous((int)(blk_size * buf_size), MPI_BYTE, &mpi_full_buffer);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Commit full buffer derived type */
+ mrc = MPI_Type_commit(&mpi_full_buffer);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+
+ /* Build full chunk derived type */
+ mrc = MPI_Type_contiguous((int)(blk_size * blk_size), MPI_BYTE, &mpi_full_chunk);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Commit full chunk derived type */
+ mrc = MPI_Type_commit(&mpi_full_chunk);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+
+ /* Build chunk interleaved file's derived type */
+ mrc = MPI_Type_vector((int)(buf_size / blk_size), (int)1, (int)((size_t)snbytes / blk_size),
+ mpi_full_chunk, &mpi_chunk_inter_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Commit chunk interleaved file type */
+ mrc = MPI_Type_commit(&mpi_chunk_inter_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+
+ } /* end else */
+ break;
+
+ case PHDF5: /* HDF5 setup */
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ if (nbytes > 0) {
+ /* define a contiguous dataset of nbytes native bytes */
+ h5dims[0] = (hsize_t)nbytes;
+ h5dset_space_id = H5Screate_simple(1, h5dims, NULL);
+ VRFY((h5dset_space_id >= 0), "H5Screate_simple");
+
+ /* Set up the file dset space id to select the pattern to access */
+ if (!parms->interleaved) {
+ /* Contiguous pattern */
+ h5start[0] = (hsize_t)bytes_begin[0];
+ h5stride[0] = h5block[0] = blk_size;
+ h5count[0] = buf_size / blk_size;
+ } /* end if */
+ else {
+ /* Interleaved access pattern */
+ /* Skip offset over blocks of other processes */
+ h5start[0] = (hsize_t)bytes_begin[0];
+ h5stride[0] = blk_size * (size_t)pio_mpi_nprocs_g;
+ h5block[0] = blk_size;
+ h5count[0] = buf_size / blk_size;
+ } /* end else */
+ hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, h5start, h5stride, h5count,
+ h5block);
+ VRFY((hrc >= 0), "H5Sselect_hyperslab");
+ } /* end if */
+ else {
+ h5dset_space_id = H5Screate(H5S_SCALAR);
+ VRFY((h5dset_space_id >= 0), "H5Screate");
+ } /* end else */
+
+ /* Create the memory dataspace that corresponds to the xfer buffer */
+ if (buf_size > 0) {
+ h5dims[0] = buf_size;
+ h5mem_space_id = H5Screate_simple(1, h5dims, NULL);
+ VRFY((h5mem_space_id >= 0), "H5Screate_simple");
+ } /* end if */
+ else {
+ h5mem_space_id = H5Screate(H5S_SCALAR);
+ VRFY((h5mem_space_id >= 0), "H5Screate");
+ } /* end else */
+ } /* end if */
+ /* 2D dataspace */
+ else {
+ if (nbytes > 0) {
+ /* define a contiguous dataset of nbytes native bytes */
+ h5dims[0] = (hsize_t)snbytes;
+ h5dims[1] = (hsize_t)snbytes;
+ h5dset_space_id = H5Screate_simple(2, h5dims, NULL);
+ VRFY((h5dset_space_id >= 0), "H5Screate_simple");
+
+ /* Set up the file dset space id to select the pattern to access */
+ if (!parms->interleaved) {
+ /* Contiguous pattern */
+ h5start[0] = (hsize_t)bytes_begin[0];
+ h5start[1] = (hsize_t)bytes_begin[1];
+ h5stride[0] = 1;
+ h5stride[1] = h5block[0] = h5block[1] = blk_size;
+ h5count[0] = 1;
+ h5count[1] = buf_size / blk_size;
+ } /* end if */
+ else {
+ /* Interleaved access pattern */
+ /* Skip offset over blocks of other processes */
+ h5start[0] = (hsize_t)bytes_begin[0];
+ h5start[1] = (hsize_t)bytes_begin[1];
+ h5stride[0] = blk_size;
+ h5stride[1] = blk_size * (size_t)pio_mpi_nprocs_g;
+ h5block[0] = h5block[1] = blk_size;
+ h5count[0] = buf_size / blk_size;
+ h5count[1] = 1;
+ } /* end else */
+ hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, h5start, h5stride, h5count,
+ h5block);
+ VRFY((hrc >= 0), "H5Sselect_hyperslab");
+ } /* end if */
+ else {
+ h5dset_space_id = H5Screate(H5S_SCALAR);
+ VRFY((h5dset_space_id >= 0), "H5Screate");
+ } /* end else */
+
+ /* Create the memory dataspace that corresponds to the xfer buffer */
+ if (buf_size > 0) {
+ if (!parms->interleaved) {
+ h5dims[0] = blk_size;
+ h5dims[1] = buf_size;
+ }
+ else {
+ h5dims[0] = buf_size;
+ h5dims[1] = blk_size;
+ }
+ h5mem_space_id = H5Screate_simple(2, h5dims, NULL);
+ VRFY((h5mem_space_id >= 0), "H5Screate_simple");
+ } /* end if */
+ else {
+ h5mem_space_id = H5Screate(H5S_SCALAR);
+ VRFY((h5mem_space_id >= 0), "H5Screate");
+ } /* end else */
+ } /* end else */
+
+ /* Create the dataset transfer property list */
+ h5dxpl = H5Pcreate(H5P_DATASET_XFER);
+ if (h5dxpl < 0) {
+ HDfprintf(stderr, "HDF5 Property List Create failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ /* Change to collective I/O, if asked */
+ if (parms->collective) {
+ hrc = H5Pset_dxpl_mpio(h5dxpl, H5FD_MPIO_COLLECTIVE);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Property List Set failed\n");
+ GOTOERROR(FAIL);
+ } /* end if */
+ } /* end if */
+ break;
+
+ default:
+ break;
+ } /* end switch */
+
+ for (ndset = 1; ndset <= ndsets; ++ndset) {
+
+ /* Calculate dataset offset within a file */
+
+ /* create dataset */
+ switch (parms->io_type) {
+ case POSIXIO:
+ case MPIO:
+ /* both posix and mpi io just need dataset offset in file*/
+ dset_offset = (ndset - 1) * nbytes;
+ break;
+
+ case PHDF5:
+ h5dcpl = H5Pcreate(H5P_DATASET_CREATE);
+ if (h5dcpl < 0) {
+ HDfprintf(stderr, "HDF5 Property List Create failed\n");
+ GOTOERROR(FAIL);
+ }
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ /* Make the dataset chunked if asked */
+ if (parms->h5_use_chunks) {
+ /* Set the chunk size to be the same as the buffer size */
+ h5dims[0] = blk_size;
+ hrc = H5Pset_chunk(h5dcpl, 1, h5dims);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Property List Set failed\n");
+ GOTOERROR(FAIL);
+ } /* end if */
+ } /* end if */
+ } /* end if */
+ else {
+ /* 2D dataspace */
+ if (parms->h5_use_chunks) {
+ /* Set the chunk size to be the same as the block size */
+ h5dims[0] = blk_size;
+ h5dims[1] = blk_size;
+ hrc = H5Pset_chunk(h5dcpl, 2, h5dims);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Property List Set failed\n");
+ GOTOERROR(FAIL);
+ } /* end if */
+ } /* end if */
+ } /* end else */
+
+ HDsprintf(dname, "Dataset_%ld", ndset);
+ h5ds_id = H5DCREATE(fd->h5fd, dname, ELMT_H5_TYPE, h5dset_space_id, h5dcpl);
+
+ if (h5ds_id < 0) {
+ HDfprintf(stderr, "HDF5 Dataset Create failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ hrc = H5Pclose(h5dcpl);
+ /* verifying the close of the dcpl */
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Property List Close failed\n");
+ GOTOERROR(FAIL);
+ }
+ break;
+
+ default:
+ break;
+ }
+
+ /* The task is to transfer bytes_count bytes, starting at
+ * bytes_begin position, using transfer buffer of buf_size bytes.
+ * If interleaved, select buf_size at a time, in round robin
+ * fashion, according to number of process. Otherwise, select
+ * all bytes_count in contiguous.
+ */
+ nbytes_xfer = 0;
+
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ /* Set base file offset for all I/O patterns and POSIX access */
+ posix_file_offset = dset_offset + bytes_begin[0];
+
+ /* Set base file offset for all I/O patterns and MPI access */
+ mpi_file_offset = (MPI_Offset)(dset_offset + bytes_begin[0]);
+ } /* end if */
+ else {
+ /* Set base file offset for all I/O patterns and POSIX access */
+ posix_file_offset = dset_offset + bytes_begin[0] * snbytes + bytes_begin[1];
+
+ /* Set base file offset for all I/O patterns and MPI access */
+ mpi_file_offset = (MPI_Offset)(dset_offset + bytes_begin[0] * snbytes + bytes_begin[1]);
+ } /* end else */
+
+ /* Start "raw data" write timer */
+ io_time_set(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, TSTART);
+
+ while (nbytes_xfer < bytes_count) {
+ /* Write */
+ /* Calculate offset of write within a dataset/file */
+ switch (parms->io_type) {
+ case POSIXIO:
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ /* Contiguous pattern */
+ if (!parms->interleaved) {
+ /* Compute file offset */
+ file_offset = posix_file_offset + (off_t)nbytes_xfer;
+
+ /* only care if seek returns error */
+ rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0;
+ VRFY((rc == 0), "POSIXSEEK");
+
+ /* check if all bytes are written */
+ rc = ((ssize_t)buf_size == POSIXWRITE(fd->posixfd, buffer, buf_size));
+ VRFY((rc != 0), "POSIXWRITE");
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (ssize_t)buf_size;
+ } /* end if */
+ /* Interleaved access pattern */
+ else {
+ /* Set the base of user's buffer */
+ buf_p = (unsigned char *)buffer;
+
+ /* Set the number of bytes to transfer this time */
+ nbytes_toxfer = buf_size;
+
+ /* Loop over the buffers to write */
+ while (nbytes_toxfer > 0) {
+ /* Skip offset over blocks of other processes */
+ file_offset = posix_file_offset + (off_t)(nbytes_xfer * pio_mpi_nprocs_g);
+
+ /* only care if seek returns error */
+ rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0;
+ VRFY((rc == 0), "POSIXSEEK");
+
+ /* check if all bytes are written */
+ rc = ((ssize_t)blk_size == POSIXWRITE(fd->posixfd, buf_p, blk_size));
+ VRFY((rc != 0), "POSIXWRITE");
+
+ /* Advance location in buffer */
+ buf_p += blk_size;
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (ssize_t)blk_size;
+
+ /* Decrement number of bytes left this time */
+ nbytes_toxfer -= blk_size;
+ } /* end while */
+ } /* end else */
+ } /* end if */
+ /* 2D dataspace */
+ else {
+ /* Contiguous storage */
+ if (!parms->h5_use_chunks) {
+ /* Contiguous access pattern */
+ if (!parms->interleaved) {
+ /* Compute file offset */
+ file_offset = posix_file_offset +
+ (off_t)((((size_t)nbytes_xfer / blk_size) / (size_t)snbytes) *
+ (blk_size * (size_t)snbytes) +
+ (((size_t)nbytes_xfer / blk_size) % (size_t)snbytes));
+
+ /* Number of bytes to be transferred per I/O operation */
+ nbytes_xfer_advance = buf_size;
+
+ /* Global offset advance after each I/O operation */
+ file_offset_advance = (off_t)snbytes;
+ } /* end if */
+ /* Interleaved access pattern */
+ else {
+ /* Compute file offset */
+ file_offset =
+ posix_file_offset +
+ (off_t)(((((size_t)nbytes_xfer / buf_size) * (size_t)pio_mpi_nprocs_g) /
+ (size_t)snbytes) *
+ (buf_size * (size_t)snbytes) +
+ (((size_t)nbytes_xfer / buf_size) * (size_t)pio_mpi_nprocs_g) %
+ (size_t)snbytes);
+
+ /* Number of bytes to be transferred per I/O operation */
+ nbytes_xfer_advance = blk_size;
+
+ /* Global offset advance after each I/O operation */
+ file_offset_advance = (off_t)snbytes;
+ } /* end else */
+ } /* end if */
+ /* Chunked storage */
+ else {
+ /*Contiguous access pattern */
+ if (!parms->interleaved) {
+ /* Compute file offset */
+ file_offset = posix_file_offset + (off_t)nbytes_xfer;
+
+ /* Number of bytes to be transferred per I/O operation */
+ nbytes_xfer_advance = blk_size * buf_size;
+
+ /* Global offset advance after each I/O operation */
+ file_offset_advance = 0;
+ } /* end if */
+ /*Interleaved access pattern */
+ else {
+ /* Compute file offset */
+ /* Before simplification */
+ /* file_offset=posix_file_offset+(off_t)((nbytes_xfer/(buf_size/blk_size)
+ *pio_mpi_nprocs_g)/(snbytes/blk_size*(blk_size*blk_size))*(buf_size/blk_size
+ *snbytes/blk_size*(blk_size*blk_size))+((nbytes_xfer/(buf_size/blk_size))
+ *pio_mpi_nprocs_g)%(snbytes/blk_size*(blk_size*blk_size))); */
+
+ file_offset = posix_file_offset +
+ (off_t)((((size_t)nbytes_xfer / (buf_size / blk_size) *
+ (size_t)pio_mpi_nprocs_g) /
+ ((size_t)snbytes * blk_size)) *
+ (buf_size * (size_t)snbytes) +
+ (((size_t)nbytes_xfer / (buf_size / blk_size)) *
+ (size_t)pio_mpi_nprocs_g) %
+ ((size_t)snbytes * blk_size));
+
+ /* Number of bytes to be transferred per I/O operation */
+ nbytes_xfer_advance = blk_size * blk_size;
+
+ /* Global offset advance after each I/O operation */
+ /* file_offset_advance = (off_t)(snbytes/blk_size*(blk_size*blk_size)); */
+ file_offset_advance = (off_t)snbytes * (off_t)blk_size;
+ } /* end else */
+ } /* end else */
+
+ /* Common code for file access */
+
+ /* Set the base of user's buffer */
+ buf_p = (unsigned char *)buffer;
+
+ /* Set the number of bytes to transfer this time */
+ nbytes_toxfer = buf_size * blk_size;
+
+ /* Loop over portions of the buffer to write */
+ while (nbytes_toxfer > 0) {
+ /* only care if seek returns error */
+ rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0;
+ VRFY((rc == 0), "POSIXSEEK");
+
+ /* check if all bytes are written */
+ rc = ((ssize_t)nbytes_xfer_advance ==
+ POSIXWRITE(fd->posixfd, buf_p, nbytes_xfer_advance));
+ VRFY((rc != 0), "POSIXWRITE");
+
+ /* Advance location in buffer */
+ buf_p += nbytes_xfer_advance;
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (ssize_t)nbytes_xfer_advance;
+
+ /* Decrement number of bytes left this time */
+ nbytes_toxfer -= nbytes_xfer_advance;
+
+ /* Partially advance file offset */
+ file_offset += file_offset_advance;
+ } /* end while */
+
+ } /* end else */
+
+ break;
+
+ case MPIO:
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ /* Independent file access */
+ if (!parms->collective) {
+ /* Contiguous pattern */
+ if (!parms->interleaved) {
+ /* Compute offset in file */
+ mpi_offset = mpi_file_offset + nbytes_xfer;
+
+ /* Perform independent write */
+ mrc =
+ MPI_File_write_at(fd->mpifd, mpi_offset, buffer,
+ (int)(buf_size / blk_size), mpi_blk_type, &mpi_status);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_WRITE");
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (ssize_t)buf_size;
+ } /* end if */
+ /* Interleaved access pattern */
+ else {
+ /* Set the base of user's buffer */
+ buf_p = (unsigned char *)buffer;
+
+ /* Set the number of bytes to transfer this time */
+ nbytes_toxfer = buf_size;
+
+ /* Loop over the buffers to write */
+ while (nbytes_toxfer > 0) {
+ /* Skip offset over blocks of other processes */
+ mpi_offset = mpi_file_offset + (nbytes_xfer * pio_mpi_nprocs_g);
+
+ /* Perform independent write */
+ mrc = MPI_File_write_at(fd->mpifd, mpi_offset, buf_p, (int)1,
+ mpi_blk_type, &mpi_status);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_WRITE");
+
+ /* Advance location in buffer */
+ buf_p += blk_size;
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (ssize_t)blk_size;
+
+ /* Decrement number of bytes left this time */
+ nbytes_toxfer -= blk_size;
+ } /* end while */
+ } /* end else */
+ } /* end if */
+ /* Collective file access */
+ else {
+ /* Contiguous access pattern */
+ if (!parms->interleaved) {
+ /* Compute offset in file */
+ mpi_offset = mpi_file_offset + nbytes_xfer;
+
+ /* Perform independent write */
+ mrc = MPI_File_write_at_all(fd->mpifd, mpi_offset, buffer,
+ (int)(buf_size / blk_size), mpi_blk_type,
+ &mpi_status);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_WRITE");
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (ssize_t)buf_size;
+ } /* end if */
+ /* Interleaved access pattern */
+ else {
+ /* Compute offset in file */
+ mpi_offset = mpi_file_offset + (nbytes_xfer * pio_mpi_nprocs_g);
+
+ /* Set the file view */
+ mrc = MPI_File_set_view(fd->mpifd, mpi_offset, mpi_blk_type, mpi_file_type,
+ (char *)"native", h5_io_info_g);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_VIEW");
+
+ /* Perform write */
+ mrc = MPI_File_write_at_all(fd->mpifd, 0, buffer, (int)(buf_size / blk_size),
+ mpi_blk_type, &mpi_status);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_WRITE");
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (ssize_t)buf_size;
+ } /* end else */
+ } /* end else */
+ } /* end if */
+ /* 2D dataspace */
+ else {
+ /* Contiguous storage */
+ if (!parms->h5_use_chunks) {
+ /* Contiguous access pattern */
+ if (!parms->interleaved) {
+ /* Compute offset in file */
+ mpi_offset =
+ mpi_file_offset +
+ (MPI_Offset)((((size_t)nbytes_xfer / blk_size) / (size_t)snbytes) *
+ (blk_size * (size_t)snbytes)) +
+ (MPI_Offset)(((size_t)nbytes_xfer / blk_size) % (size_t)snbytes);
+
+ /* Number of bytes to be transferred per I/O operation */
+ nbytes_xfer_advance = buf_size;
+
+ /* Global offset advance after each I/O operation */
+ mpi_offset_advance = snbytes;
+
+ /* MPI type to be used for collective access */
+ mpi_collective_type = mpi_cont_type;
+ } /* end if */
+ /* Interleaved access pattern */
+ else {
+ /* Compute offset in file */
+ mpi_offset =
+ mpi_file_offset +
+ (MPI_Offset)(
+ ((((size_t)nbytes_xfer / buf_size) * (size_t)pio_mpi_nprocs_g) /
+ (size_t)snbytes) *
+ (buf_size * (size_t)snbytes)) +
+ (MPI_Offset)(
+ (((size_t)nbytes_xfer / buf_size) * (size_t)pio_mpi_nprocs_g) %
+ (size_t)snbytes);
+
+ /* Number of bytes to be transferred per I/O operation */
+ nbytes_xfer_advance = blk_size;
+
+ /* Global offset advance after each I/O operation */
+ mpi_offset_advance = snbytes;
+
+ /* MPI type to be used for collective access */
+ mpi_collective_type = mpi_inter_type;
+ } /* end else */
+ } /* end if */
+ /* Chunked storage */
+ else {
+ /*Contiguous access pattern */
+ if (!parms->interleaved) {
+ /* Compute offset in file */
+ mpi_offset = mpi_file_offset + nbytes_xfer;
+
+ /* Number of bytes to be transferred per I/O operation */
+ nbytes_xfer_advance = blk_size * buf_size;
+
+ /* Global offset advance after each I/O operation */
+ mpi_offset_advance = 0;
+
+ /* MPI type to be used for collective access */
+ mpi_collective_type = mpi_full_buffer;
+ } /* end if */
+ /*Interleaved access pattern */
+ else {
+ /* Compute offset in file */
+ /* Before simplification */
+ /* mpi_offset=mpi_file_offset+(nbytes_xfer/(buf_size/blk_size)
+ *pio_mpi_nprocs_g)/(snbytes/blk_size*(blk_size*blk_size))*
+ (buf_size/blk_size*snbytes/blk_size*(blk_size*blk_size))+
+ ((nbytes_xfer/(buf_size/blk_size))*pio_mpi_nprocs_g)%(snbytes
+ /blk_size*(blk_size*blk_size)); */
+ mpi_offset = mpi_file_offset +
+ (MPI_Offset)((((size_t)nbytes_xfer / (buf_size / blk_size) *
+ (size_t)pio_mpi_nprocs_g) /
+ ((size_t)snbytes * blk_size)) *
+ (buf_size * (size_t)snbytes)) +
+ (MPI_Offset)((((size_t)nbytes_xfer / (buf_size / blk_size)) *
+ (size_t)pio_mpi_nprocs_g) %
+ ((size_t)snbytes * blk_size));
+
+ /* Number of bytes to be transferred per I/O operation */
+ nbytes_xfer_advance = blk_size * blk_size;
+
+ /* Global offset advance after each I/O operation */
+ /* mpi_offset_advance = (MPI_Offset)(snbytes/blk_size*(blk_size*blk_size)); */
+ mpi_offset_advance = (MPI_Offset)((size_t)snbytes * blk_size);
+
+ /* MPI type to be used for collective access */
+ mpi_collective_type = mpi_chunk_inter_type;
+ } /* end else */
+ } /* end else */
+
+ /* Common code for independent file access */
+ if (!parms->collective) {
+ /* Set the base of user's buffer */
+ buf_p = (unsigned char *)buffer;
+
+ /* Set the number of bytes to transfer this time */
+ nbytes_toxfer = buf_size * blk_size;
+
+ /* Loop over portions of the buffer to write */
+ while (nbytes_toxfer > 0) {
+ /* Perform independent write */
+ mrc = MPI_File_write_at(fd->mpifd, mpi_offset, buf_p,
+ (int)nbytes_xfer_advance, MPI_BYTE, &mpi_status);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_WRITE");
+
+ /* Advance location in buffer */
+ buf_p += nbytes_xfer_advance;
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (ssize_t)nbytes_xfer_advance;
+
+ /* Decrement number of bytes left this time */
+ nbytes_toxfer -= nbytes_xfer_advance;
+
+ /* Partially advance global offset in dataset */
+ mpi_offset += mpi_offset_advance;
+ } /* end while */
+ } /* end if */
+
+ /* Common code for collective file access */
+ else {
+ /* Set the file view */
+ mrc = MPI_File_set_view(fd->mpifd, mpi_offset, MPI_BYTE, mpi_collective_type,
+ (char *)"native", h5_io_info_g);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_VIEW");
+
+ /* Perform write */
+ MPI_File_write_at_all(fd->mpifd, 0, buffer, (int)(buf_size * blk_size), MPI_BYTE,
+ &mpi_status);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_WRITE");
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (off_t)buf_size * (off_t)blk_size;
+ } /* end else */
+
+ } /* end else */
+
+ break;
+
+ case PHDF5:
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ /* Set up the file dset space id to move the selection to process */
+ if (!parms->interleaved) {
+ /* Contiguous pattern */
+ h5offset[0] = nbytes_xfer;
+ } /* end if */
+ else {
+ /* Interleaved access pattern */
+ /* Skip offset over blocks of other processes */
+ h5offset[0] = (nbytes_xfer * pio_mpi_nprocs_g);
+ } /* end else */
+ hrc = H5Soffset_simple(h5dset_space_id, h5offset);
+ VRFY((hrc >= 0), "H5Soffset_simple");
+
+ /* Write the buffer out */
+ hrc =
+ H5Dwrite(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, h5dset_space_id, h5dxpl, buffer);
+ VRFY((hrc >= 0), "H5Dwrite");
+
+ /* Increment number of bytes transferred */
+ nbytes_xfer += (ssize_t)buf_size;
+ } /* end if */
+ /* 2D dataspace */
+ else {
+ /* Set up the file dset space id to move the selection to process */
+ if (!parms->interleaved) {
+ /* Contiguous pattern */
+ h5offset[0] =
+ (hssize_t)(((size_t)nbytes_xfer / ((size_t)snbytes * blk_size)) * blk_size);
+ h5offset[1] =
+ (hssize_t)(((size_t)nbytes_xfer % ((size_t)snbytes * blk_size)) / blk_size);
+
+ } /* end if */
+ else {
+ /* Interleaved access pattern */
+ /* Skip offset over blocks of other processes */
+ h5offset[0] = (hssize_t)((((size_t)nbytes_xfer * (size_t)pio_mpi_nprocs_g) /
+ ((size_t)snbytes * buf_size)) *
+ buf_size);
+ h5offset[1] = (hssize_t)((((size_t)nbytes_xfer * (size_t)pio_mpi_nprocs_g) %
+ ((size_t)snbytes * buf_size)) /
+ buf_size);
+
+ } /* end else */
+ hrc = H5Soffset_simple(h5dset_space_id, h5offset);
+ VRFY((hrc >= 0), "H5Soffset_simple");
+
+ /* Write the buffer out */
+ hrc =
+ H5Dwrite(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, h5dset_space_id, h5dxpl, buffer);
+ VRFY((hrc >= 0), "H5Dwrite");
+
+ /* Increment number of bytes transferred */
+ nbytes_xfer += (off_t)buf_size * (off_t)blk_size;
+
+ } /* end else */
+
+ break;
+
+ default:
+ break;
+ } /* switch (parms->io_type) */
+ } /* end while */
+
+ /* Stop "raw data" write timer */
+ io_time_set(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, TSTOP);
+
+ /* Calculate write time */
+
+ /* Close dataset. Only HDF5 needs to do an explicit close. */
+ if (parms->io_type == PHDF5) {
+ hrc = H5Dclose(h5ds_id);
+
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Dataset Close failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ h5ds_id = H5I_INVALID_HID;
+ } /* end if */
+ } /* end for */
+
+done:
+ /* release MPI-I/O objects */
+ if (parms->io_type == MPIO) {
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ /* Free file type */
+ mrc = MPI_Type_free(&mpi_file_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+
+ /* Free buffer type */
+ mrc = MPI_Type_free(&mpi_blk_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+ } /* end if */
+ /* 2D dataspace */
+ else {
+ /* Free partial buffer type for contiguous access */
+ mrc = MPI_Type_free(&mpi_partial_buffer_cont);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+
+ /* Free contiguous file type */
+ mrc = MPI_Type_free(&mpi_cont_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+
+ /* Free partial buffer type for interleaved access */
+ mrc = MPI_Type_free(&mpi_partial_buffer_inter);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+
+ /* Free interleaved file type */
+ mrc = MPI_Type_free(&mpi_inter_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+
+ /* Free full buffer type */
+ mrc = MPI_Type_free(&mpi_full_buffer);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+
+ /* Free full chunk type */
+ mrc = MPI_Type_free(&mpi_full_chunk);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+
+ /* Free chunk interleaved file type */
+ mrc = MPI_Type_free(&mpi_chunk_inter_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+ } /* end else */
+ } /* end if */
+
+ /* release HDF5 objects */
+ if (h5dset_space_id != -1) {
+ hrc = H5Sclose(h5dset_space_id);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Dataset Space Close failed\n");
+ ret_code = FAIL;
+ }
+ else {
+ h5dset_space_id = H5I_INVALID_HID;
+ }
+ }
+
+ if (h5mem_space_id != -1) {
+ hrc = H5Sclose(h5mem_space_id);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Memory Space Close failed\n");
+ ret_code = FAIL;
+ }
+ else {
+ h5mem_space_id = H5I_INVALID_HID;
+ }
+ }
+
+ if (h5dxpl != -1) {
+ hrc = H5Pclose(h5dxpl);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Dataset Transfer Property List Close failed\n");
+ ret_code = FAIL;
+ }
+ else {
+ h5dxpl = H5I_INVALID_HID;
+ }
+ }
+
+ return ret_code;
+}
+
+static off_t
+sqrto(off_t x)
+{
+ double root_x = sqrt((double)x);
+ return (off_t)root_x;
+}
+
+/*
+ * Function: do_read
+ * Purpose: read the required amount of data from the file.
+ * Return: SUCCESS or FAIL
+ * Programmer: Albert Cheng 2001/12/13
+ * Modifications:
+ * Added 2D testing (Christian Chilan, 10. August 2005)
+ */
+static herr_t
+do_read(results *res, file_descr *fd, parameters *parms, long ndsets, off_t nbytes, size_t buf_size,
+ void *buffer /*out*/)
+{
+ int ret_code = SUCCESS;
+ int rc; /*routine return code */
+ long ndset;
+ size_t blk_size; /* The block size to subdivide the xfer buffer into */
+ size_t bsize; /* Size of the actual buffer */
+ off_t nbytes_xfer; /* Total number of bytes transferred so far */
+ size_t nbytes_xfer_advance; /* Number of bytes transferred in a single I/O operation */
+ size_t nbytes_toxfer; /* Number of bytes to transfer a particular time */
+ char dname[64];
+ off_t dset_offset = 0; /*dataset offset in a file */
+ off_t bytes_begin[2]; /*first elmt this process transfer */
+ off_t bytes_count; /*number of elmts this process transfer */
+ off_t snbytes = 0; /*size of a side of the dataset square */
+ unsigned char *buf_p; /* Current buffer pointer */
+
+ /* POSIX variables */
+ off_t file_offset; /* File offset of the next transfer */
+ off_t file_offset_advance; /* File offset advance after each I/O operation */
+ off_t posix_file_offset; /* Base file offset of the next transfer */
+
+ /* MPI variables */
+ MPI_Offset mpi_file_offset; /* Base file offset of the next transfer*/
+ MPI_Offset mpi_offset; /* Offset in MPI file */
+ MPI_Offset mpi_offset_advance; /* Offset advance after each I/O operation */
+ MPI_Datatype mpi_file_type; /* MPI derived type for 1D file */
+ MPI_Datatype mpi_blk_type; /* MPI derived type for 1D buffer */
+ MPI_Datatype mpi_cont_type; /* MPI derived type for 2D contiguous file */
+ MPI_Datatype mpi_partial_buffer_cont; /* MPI derived type for partial 2D contiguous buffer */
+ MPI_Datatype mpi_inter_type; /* MPI derived type for 2D interleaved file */
+ MPI_Datatype mpi_partial_buffer_inter; /* MPI derived type for partial 2D interleaved buffer */
+ MPI_Datatype mpi_full_buffer; /* MPI derived type for 2D full buffer */
+ MPI_Datatype mpi_full_chunk; /* MPI derived type for 2D full chunk */
+ MPI_Datatype mpi_chunk_inter_type; /* MPI derived type for 2D chunk interleaved file */
+ MPI_Datatype mpi_collective_type; /* Generic MPI derived type for 2D collective access */
+ MPI_Status mpi_status;
+ int mrc; /* MPI return code */
+
+ /* HDF5 variables */
+ herr_t hrc; /*HDF5 return code */
+ hsize_t h5dims[2]; /*dataset dim sizes */
+ hid_t h5dset_space_id = H5I_INVALID_HID; /*dataset space ID */
+ hid_t h5mem_space_id = H5I_INVALID_HID; /*memory dataspace ID */
+ hid_t h5ds_id = H5I_INVALID_HID; /*dataset handle */
+ hsize_t h5block[2]; /*dataspace selection */
+ hsize_t h5stride[2];
+ hsize_t h5count[2];
+ hsize_t h5start[2];
+ hssize_t h5offset[2]; /* Selection offset within dataspace */
+ hid_t h5dxpl = H5I_INVALID_HID; /* Dataset transfer property list */
+
+ /* Get the parameters from the parameter block */
+ blk_size = parms->blk_size;
+
+ /* There are two kinds of transfer patterns, contiguous and interleaved.
+ * Let 0,1,2,...,n be data accessed by process 0,1,2,...,n
+ * where n is rank of the last process.
+ * In contiguous pattern, data are accessed as
+ * 000...111...222...nnn...
+ * In interleaved pattern, data are accessed as
+ * 012...n012...n...
+ * These are all in the scope of one dataset.
+ */
+
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ bsize = buf_size;
+ /* Contiguous Pattern: */
+ if (!parms->interleaved) {
+ bytes_begin[0] = (off_t)(((double)nbytes * pio_mpi_rank_g) / pio_mpi_nprocs_g);
+ } /* end if */
+ /* Interleaved Pattern: */
+ else {
+ bytes_begin[0] = (off_t)blk_size * (off_t)pio_mpi_rank_g;
+ } /* end else */
+ } /* end if */
+ /* 2D dataspace */
+ else {
+ /* nbytes is always the number of bytes per dataset (1D or 2D). If the
+ dataspace is 2D, snbytes is the size of a side of the 'dataset square'.
+ */
+ snbytes = sqrto(nbytes);
+
+ bsize = buf_size * blk_size;
+
+ /* Contiguous Pattern: */
+ if (!parms->interleaved) {
+ bytes_begin[0] = (off_t)((double)snbytes * pio_mpi_rank_g / pio_mpi_nprocs_g);
+ bytes_begin[1] = 0;
+ } /* end if */
+ /* Interleaved Pattern: */
+ else {
+ bytes_begin[0] = 0;
+
+ if (!parms->h5_use_chunks || parms->io_type == PHDF5)
+ bytes_begin[1] = (off_t)blk_size * (off_t)pio_mpi_rank_g;
+ else
+ bytes_begin[1] = (off_t)blk_size * (off_t)blk_size * (off_t)pio_mpi_rank_g;
+ } /* end else */
+ } /* end else */
+
+ /* Calculate the total number of bytes (bytes_count) to be
+ * transferred by this process. It may be different for different
+ * transfer pattern due to rounding to integral values.
+ */
+ /*
+ * Calculate the beginning bytes of this process and the next.
+ * bytes_count is the difference between these two beginnings.
+ * This way, it eliminates any rounding errors.
+ * (This is tricky, don't mess with the formula, rounding errors
+ * can easily get introduced) */
+ bytes_count = (off_t)(((double)nbytes * (pio_mpi_rank_g + 1)) / pio_mpi_nprocs_g) -
+ (off_t)(((double)nbytes * pio_mpi_rank_g) / pio_mpi_nprocs_g);
+
+ /* debug */
+ if (pio_debug_level >= 4) {
+ HDprint_rank(output);
+ if (!parms->dim2d) {
+ HDfprintf(output,
+ "Debug(do_write): "
+ "buf_size=%zu, bytes_begin=%" H5_PRINTF_LL_WIDTH "d, bytes_count=%" H5_PRINTF_LL_WIDTH
+ "d\n",
+ buf_size, (long long)bytes_begin[0], (long long)bytes_count);
+ }
+ else {
+ HDfprintf(output,
+ "Debug(do_write): "
+ "linear buf_size=%zu, bytes_begin=(%" H5_PRINTF_LL_WIDTH "d,%" H5_PRINTF_LL_WIDTH
+ "d), bytes_count=%" H5_PRINTF_LL_WIDTH "d\n",
+ buf_size * blk_size, (long long)bytes_begin[0], (long long)bytes_begin[1],
+ (long long)bytes_count);
+ }
+ }
+
+ /* I/O Access specific setup */
+ switch (parms->io_type) {
+ case POSIXIO:
+ /* No extra setup */
+ break;
+
+ case MPIO: /* MPI-I/O setup */
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ /* Build block's derived type */
+ mrc = MPI_Type_contiguous((int)blk_size, MPI_BYTE, &mpi_blk_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Build file's derived type */
+ mrc = MPI_Type_vector((int)(buf_size / blk_size), (int)1, (int)pio_mpi_nprocs_g, mpi_blk_type,
+ &mpi_file_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Commit file type */
+ mrc = MPI_Type_commit(&mpi_file_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+
+ /* Commit buffer type */
+ mrc = MPI_Type_commit(&mpi_blk_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+ } /* end if */
+ /* 2D dataspace */
+ else {
+ /* Build partial buffer derived type for contiguous access */
+ mrc = MPI_Type_contiguous((int)buf_size, MPI_BYTE, &mpi_partial_buffer_cont);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Commit partial buffer derived type */
+ mrc = MPI_Type_commit(&mpi_partial_buffer_cont);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+
+ /* Build contiguous file's derived type */
+ mrc = MPI_Type_vector((int)blk_size, (int)1, (int)((size_t)snbytes / buf_size),
+ mpi_partial_buffer_cont, &mpi_cont_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Commit contiguous file type */
+ mrc = MPI_Type_commit(&mpi_cont_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+
+ /* Build partial buffer derived type for interleaved access */
+ mrc = MPI_Type_contiguous((int)blk_size, MPI_BYTE, &mpi_partial_buffer_inter);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Commit partial buffer derived type */
+ mrc = MPI_Type_commit(&mpi_partial_buffer_inter);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+
+ /* Build interleaved file's derived type */
+ mrc = MPI_Type_vector((int)buf_size, (int)1, (int)((size_t)snbytes / blk_size),
+ mpi_partial_buffer_inter, &mpi_inter_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Commit interleaved file type */
+ mrc = MPI_Type_commit(&mpi_inter_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+
+ /* Build full buffer derived type */
+ mrc = MPI_Type_contiguous((int)(blk_size * buf_size), MPI_BYTE, &mpi_full_buffer);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Commit full buffer derived type */
+ mrc = MPI_Type_commit(&mpi_full_buffer);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+
+ /* Build full chunk derived type */
+ mrc = MPI_Type_contiguous((int)(blk_size * blk_size), MPI_BYTE, &mpi_full_chunk);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Commit full chunk derived type */
+ mrc = MPI_Type_commit(&mpi_full_chunk);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+
+ /* Build chunk interleaved file's derived type */
+ mrc = MPI_Type_vector((int)(buf_size / blk_size), (int)1, (int)((size_t)snbytes / blk_size),
+ mpi_full_chunk, &mpi_chunk_inter_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_CREATE");
+
+ /* Commit chunk interleaved file type */
+ mrc = MPI_Type_commit(&mpi_chunk_inter_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_COMMIT");
+ } /* end else */
+ break;
+
+ case PHDF5: /* HDF5 setup */
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ if (nbytes > 0) {
+ /* define a contiguous dataset of nbytes native bytes */
+ h5dims[0] = (hsize_t)nbytes;
+ h5dset_space_id = H5Screate_simple(1, h5dims, NULL);
+ VRFY((h5dset_space_id >= 0), "H5Screate_simple");
+
+ /* Set up the file dset space id to select the pattern to access */
+ if (!parms->interleaved) {
+ /* Contiguous pattern */
+ h5start[0] = (hsize_t)bytes_begin[0];
+ h5stride[0] = h5block[0] = blk_size;
+ h5count[0] = buf_size / blk_size;
+ } /* end if */
+ else {
+ /* Interleaved access pattern */
+ /* Skip offset over blocks of other processes */
+ h5start[0] = (hsize_t)bytes_begin[0];
+ h5stride[0] = blk_size * (size_t)pio_mpi_nprocs_g;
+ h5block[0] = blk_size;
+ h5count[0] = buf_size / blk_size;
+ } /* end else */
+ hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, h5start, h5stride, h5count,
+ h5block);
+ VRFY((hrc >= 0), "H5Sselect_hyperslab");
+ } /* end if */
+ else {
+ h5dset_space_id = H5Screate(H5S_SCALAR);
+ VRFY((h5dset_space_id >= 0), "H5Screate");
+ } /* end else */
+
+ /* Create the memory dataspace that corresponds to the xfer buffer */
+ if (buf_size > 0) {
+ h5dims[0] = buf_size;
+ h5mem_space_id = H5Screate_simple(1, h5dims, NULL);
+ VRFY((h5mem_space_id >= 0), "H5Screate_simple");
+ } /* end if */
+ else {
+ h5mem_space_id = H5Screate(H5S_SCALAR);
+ VRFY((h5mem_space_id >= 0), "H5Screate");
+ } /* end else */
+ } /* end if */
+ /* 2D dataspace */
+ else {
+ if (nbytes > 0) {
+ /* define a contiguous dataset of nbytes native bytes */
+ h5dims[0] = (hsize_t)snbytes;
+ h5dims[1] = (hsize_t)snbytes;
+ h5dset_space_id = H5Screate_simple(2, h5dims, NULL);
+ VRFY((h5dset_space_id >= 0), "H5Screate_simple");
+
+ /* Set up the file dset space id to select the pattern to access */
+ if (!parms->interleaved) {
+ /* Contiguous pattern */
+ h5start[0] = (hsize_t)bytes_begin[0];
+ h5start[1] = (hsize_t)bytes_begin[1];
+ h5stride[0] = 1;
+ h5stride[1] = h5block[0] = h5block[1] = blk_size;
+ h5count[0] = 1;
+ h5count[1] = buf_size / blk_size;
+ } /* end if */
+ else {
+ /* Interleaved access pattern */
+ /* Skip offset over blocks of other processes */
+ h5start[0] = (hsize_t)bytes_begin[0];
+ h5start[1] = (hsize_t)bytes_begin[1];
+ h5stride[0] = blk_size;
+ h5stride[1] = blk_size * (size_t)pio_mpi_nprocs_g;
+ h5block[0] = h5block[1] = blk_size;
+ h5count[0] = buf_size / blk_size;
+ h5count[1] = 1;
+ } /* end else */
+ hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, h5start, h5stride, h5count,
+ h5block);
+ VRFY((hrc >= 0), "H5Sselect_hyperslab");
+ } /* end if */
+ else {
+ h5dset_space_id = H5Screate(H5S_SCALAR);
+ VRFY((h5dset_space_id >= 0), "H5Screate");
+ } /* end else */
+
+ /* Create the memory dataspace that corresponds to the xfer buffer */
+ if (buf_size > 0) {
+ if (!parms->interleaved) {
+ h5dims[0] = blk_size;
+ h5dims[1] = buf_size;
+ }
+ else {
+ h5dims[0] = buf_size;
+ h5dims[1] = blk_size;
+ }
+ h5mem_space_id = H5Screate_simple(2, h5dims, NULL);
+ VRFY((h5mem_space_id >= 0), "H5Screate_simple");
+ } /* end if */
+ else {
+ h5mem_space_id = H5Screate(H5S_SCALAR);
+ VRFY((h5mem_space_id >= 0), "H5Screate");
+ } /* end else */
+ } /* end else */
+
+ /* Create the dataset transfer property list */
+ h5dxpl = H5Pcreate(H5P_DATASET_XFER);
+ if (h5dxpl < 0) {
+ HDfprintf(stderr, "HDF5 Property List Create failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ /* Change to collective I/O, if asked */
+ if (parms->collective) {
+ hrc = H5Pset_dxpl_mpio(h5dxpl, H5FD_MPIO_COLLECTIVE);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Property List Set failed\n");
+ GOTOERROR(FAIL);
+ } /* end if */
+ } /* end if */
+ break;
+
+ default:
+ break;
+ } /* end switch */
+
+ for (ndset = 1; ndset <= ndsets; ++ndset) {
+
+ /* Calculate dataset offset within a file */
+
+ /* create dataset */
+ switch (parms->io_type) {
+ case POSIXIO:
+ case MPIO:
+ /* both posix and mpi io just need dataset offset in file*/
+ dset_offset = (ndset - 1) * nbytes;
+ break;
+
+ case PHDF5:
+ HDsprintf(dname, "Dataset_%ld", ndset);
+ h5ds_id = H5DOPEN(fd->h5fd, dname);
+ if (h5ds_id < 0) {
+ HDfprintf(stderr, "HDF5 Dataset open failed\n");
+ GOTOERROR(FAIL);
+ }
+ break;
+
+ default:
+ break;
+ }
+
+ /* The task is to transfer bytes_count bytes, starting at
+ * bytes_begin position, using transfer buffer of buf_size bytes.
+ * If interleaved, select buf_size at a time, in round robin
+ * fashion, according to number of process. Otherwise, select
+ * all bytes_count in contiguous.
+ */
+ nbytes_xfer = 0;
+
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ /* Set base file offset for all I/O patterns and POSIX access */
+ posix_file_offset = dset_offset + bytes_begin[0];
+
+ /* Set base file offset for all I/O patterns and MPI access */
+ mpi_file_offset = (MPI_Offset)(dset_offset + bytes_begin[0]);
+ } /* end if */
+ else {
+ /* Set base file offset for all I/O patterns and POSIX access */
+ posix_file_offset = dset_offset + bytes_begin[0] * snbytes + bytes_begin[1];
+
+ /* Set base file offset for all I/O patterns and MPI access */
+ mpi_file_offset = (MPI_Offset)(dset_offset + bytes_begin[0] * snbytes + bytes_begin[1]);
+ } /* end else */
+
+ /* Start "raw data" read timer */
+ io_time_set(res->timers, HDF5_RAW_READ_FIXED_DIMS, TSTART);
+
+ while (nbytes_xfer < bytes_count) {
+ /* Read */
+ /* Calculate offset of read within a dataset/file */
+ switch (parms->io_type) {
+ case POSIXIO:
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ /* Contiguous pattern */
+ if (!parms->interleaved) {
+ /* Compute file offset */
+ file_offset = posix_file_offset + (off_t)nbytes_xfer;
+
+ /* only care if seek returns error */
+ rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0;
+ VRFY((rc == 0), "POSIXSEEK");
+
+ /* check if all bytes are read */
+ rc = ((ssize_t)buf_size == POSIXREAD(fd->posixfd, buffer, buf_size));
+ VRFY((rc != 0), "POSIXREAD");
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (off_t)buf_size;
+ } /* end if */
+ /* Interleaved access pattern */
+ else {
+ /* Set the base of user's buffer */
+ buf_p = (unsigned char *)buffer;
+
+ /* Set the number of bytes to transfer this time */
+ nbytes_toxfer = buf_size;
+
+ /* Loop over the buffers to read */
+ while (nbytes_toxfer > 0) {
+ /* Skip offset over blocks of other processes */
+ file_offset = posix_file_offset + (off_t)(nbytes_xfer * pio_mpi_nprocs_g);
+
+ /* only care if seek returns error */
+ rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0;
+ VRFY((rc == 0), "POSIXSEEK");
+
+ /* check if all bytes are read */
+ rc = ((ssize_t)blk_size == POSIXREAD(fd->posixfd, buf_p, blk_size));
+ VRFY((rc != 0), "POSIXREAD");
+
+ /* Advance location in buffer */
+ buf_p += blk_size;
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (off_t)blk_size;
+
+ /* Decrement number of bytes left this time */
+ nbytes_toxfer -= blk_size;
+ } /* end while */
+ } /* end else */
+ } /* end if */
+ /* 2D dataspace */
+ else {
+ /* Contiguous storage */
+ if (!parms->h5_use_chunks) {
+ /* Contiguous access pattern */
+ if (!parms->interleaved) {
+ /* Compute file offset */
+ file_offset = posix_file_offset +
+ (off_t)((((size_t)nbytes_xfer / blk_size) / (size_t)snbytes) *
+ (blk_size * (size_t)snbytes) +
+ (((size_t)nbytes_xfer / blk_size) % (size_t)snbytes));
+
+ /* Number of bytes to be transferred per I/O operation */
+ nbytes_xfer_advance = buf_size;
+
+ /* Global offset advance after each I/O operation */
+ file_offset_advance = (off_t)snbytes;
+ } /* end if */
+ /* Interleaved access pattern */
+ else {
+ /* Compute file offset */
+ file_offset =
+ posix_file_offset +
+ (off_t)(((((size_t)nbytes_xfer / buf_size) * (size_t)pio_mpi_nprocs_g) /
+ (size_t)snbytes) *
+ (buf_size * (size_t)snbytes) +
+ (((size_t)nbytes_xfer / buf_size) * (size_t)pio_mpi_nprocs_g) %
+ (size_t)snbytes);
+
+ /* Number of bytes to be transferred per I/O operation */
+ nbytes_xfer_advance = blk_size;
+
+ /* Global offset advance after each I/O operation */
+ file_offset_advance = (off_t)snbytes;
+ } /* end else */
+ } /* end if */
+ /* Chunked storage */
+ else {
+ /*Contiguous access pattern */
+ if (!parms->interleaved) {
+ /* Compute file offset */
+ file_offset = posix_file_offset + (off_t)nbytes_xfer;
+
+ /* Number of bytes to be transferred per I/O operation */
+ nbytes_xfer_advance = blk_size * buf_size;
+
+ /* Global offset advance after each I/O operation */
+ file_offset_advance = 0;
+ } /* end if */
+ /*Interleaved access pattern */
+ else {
+ /* Compute file offset */
+ /* Before simplification */
+ /* file_offset=posix_file_offset+(off_t)((nbytes_xfer/(buf_size/blk_size)
+ *pio_mpi_nprocs_g)/(snbytes/blk_size*(blk_size*blk_size))*(buf_size/blk_size
+ *snbytes/blk_size*(blk_size*blk_size))+((nbytes_xfer/(buf_size/blk_size))
+ *pio_mpi_nprocs_g)%(snbytes/blk_size*(blk_size*blk_size))); */
+
+ file_offset = posix_file_offset +
+ (off_t)((((size_t)nbytes_xfer / (buf_size / blk_size) *
+ (size_t)pio_mpi_nprocs_g) /
+ ((size_t)snbytes * blk_size)) *
+ (buf_size * (size_t)snbytes) +
+ (((size_t)nbytes_xfer / (buf_size / blk_size)) *
+ (size_t)pio_mpi_nprocs_g) %
+ ((size_t)snbytes * blk_size));
+
+ /* Number of bytes to be transferred per I/O operation */
+ nbytes_xfer_advance = blk_size * blk_size;
+
+ /* Global offset advance after each I/O operation */
+ /* file_offset_advance = (off_t)(snbytes/blk_size*(blk_size*blk_size)); */
+ file_offset_advance = (off_t)((size_t)snbytes * blk_size);
+ } /* end else */
+ } /* end else */
+
+ /* Common code for file access */
+
+ /* Set the base of user's buffer */
+ buf_p = (unsigned char *)buffer;
+
+ /* Set the number of bytes to transfer this time */
+ nbytes_toxfer = buf_size * blk_size;
+
+ /* Loop over portions of the buffer to read */
+ while (nbytes_toxfer > 0) {
+ /* only care if seek returns error */
+ rc = POSIXSEEK(fd->posixfd, file_offset) < 0 ? -1 : 0;
+ VRFY((rc == 0), "POSIXSEEK");
+
+ /* check if all bytes are read */
+ rc = ((ssize_t)nbytes_xfer_advance ==
+ POSIXREAD(fd->posixfd, buf_p, nbytes_xfer_advance));
+ VRFY((rc != 0), "POSIXREAD");
+
+ /* Advance location in buffer */
+ buf_p += nbytes_xfer_advance;
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (off_t)nbytes_xfer_advance;
+
+ /* Decrement number of bytes left this time */
+ nbytes_toxfer -= nbytes_xfer_advance;
+
+ /* Partially advance file offset */
+ file_offset += file_offset_advance;
+ } /* end while */
+
+ } /* end else */
+ break;
+
+ case MPIO:
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ /* Independent file access */
+ if (!parms->collective) {
+ /* Contiguous pattern */
+ if (!parms->interleaved) {
+ /* Compute offset in file */
+ mpi_offset = mpi_file_offset + nbytes_xfer;
+
+ /* Perform independent read */
+ mrc = MPI_File_read_at(fd->mpifd, mpi_offset, buffer,
+ (int)(buf_size / blk_size), mpi_blk_type, &mpi_status);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_READ");
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (off_t)buf_size;
+ } /* end if */
+ /* Interleaved access pattern */
+ else {
+ /* Set the base of user's buffer */
+ buf_p = (unsigned char *)buffer;
+
+ /* Set the number of bytes to transfer this time */
+ nbytes_toxfer = buf_size;
+
+ /* Loop over the buffers to read */
+ while (nbytes_toxfer > 0) {
+ /* Skip offset over blocks of other processes */
+ mpi_offset = mpi_file_offset + (nbytes_xfer * pio_mpi_nprocs_g);
+
+ /* Perform independent read */
+ mrc = MPI_File_read_at(fd->mpifd, mpi_offset, buf_p, (int)1, mpi_blk_type,
+ &mpi_status);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_READ");
+
+ /* Advance location in buffer */
+ buf_p += blk_size;
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (off_t)blk_size;
+
+ /* Decrement number of bytes left this time */
+ nbytes_toxfer -= blk_size;
+ } /* end while */
+ } /* end else */
+ } /* end if */
+ /* Collective file access */
+ else {
+ /* Contiguous access pattern */
+ if (!parms->interleaved) {
+ /* Compute offset in file */
+ mpi_offset = mpi_file_offset + nbytes_xfer;
+
+ /* Perform collective read */
+ mrc = MPI_File_read_at_all(fd->mpifd, mpi_offset, buffer,
+ (int)(buf_size / blk_size), mpi_blk_type,
+ &mpi_status);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_READ");
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (off_t)buf_size;
+ } /* end if */
+ /* Interleaved access pattern */
+ else {
+ /* Compute offset in file */
+ mpi_offset = mpi_file_offset + (nbytes_xfer * pio_mpi_nprocs_g);
+
+ /* Set the file view */
+ mrc = MPI_File_set_view(fd->mpifd, mpi_offset, mpi_blk_type, mpi_file_type,
+ (char *)"native", h5_io_info_g);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_VIEW");
+
+ /* Perform collective read */
+ mrc = MPI_File_read_at_all(fd->mpifd, 0, buffer, (int)(buf_size / blk_size),
+ mpi_blk_type, &mpi_status);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_READ");
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (off_t)buf_size;
+ } /* end else */
+ } /* end else */
+ } /* end if */
+ /* 2D dataspace */
+ else {
+ /* Contiguous storage */
+ if (!parms->h5_use_chunks) {
+ /* Contiguous access pattern */
+ if (!parms->interleaved) {
+ /* Compute offset in file */
+ mpi_offset =
+ mpi_file_offset +
+ (MPI_Offset)((((size_t)nbytes_xfer / blk_size) / (size_t)snbytes) *
+ (blk_size * (size_t)snbytes)) +
+ (MPI_Offset)(((size_t)nbytes_xfer / blk_size) % (size_t)snbytes);
+
+ /* Number of bytes to be transferred per I/O operation */
+ nbytes_xfer_advance = buf_size;
+
+ /* Global offset advance after each I/O operation */
+ mpi_offset_advance = snbytes;
+
+ /* MPI type to be used for collective access */
+ mpi_collective_type = mpi_cont_type;
+ } /* end if */
+ /* Interleaved access pattern */
+ else {
+ /* Compute offset in file */
+ mpi_offset =
+ mpi_file_offset +
+ (MPI_Offset)(
+ ((((size_t)nbytes_xfer / buf_size) * (size_t)pio_mpi_nprocs_g) /
+ (size_t)snbytes) *
+ (buf_size * (size_t)snbytes)) +
+ (MPI_Offset)(
+ (((size_t)nbytes_xfer / buf_size) * (size_t)pio_mpi_nprocs_g) %
+ (size_t)snbytes);
+
+ /* Number of bytes to be transferred per I/O operation */
+ nbytes_xfer_advance = blk_size;
+
+ /* Global offset advance after each I/O operation */
+ mpi_offset_advance = snbytes;
+
+ /* MPI type to be used for collective access */
+ mpi_collective_type = mpi_inter_type;
+ } /* end else */
+ } /* end if */
+ /* Chunked storage */
+ else {
+ /*Contiguous access pattern */
+ if (!parms->interleaved) {
+ /* Compute offset in file */
+ mpi_offset = mpi_file_offset + nbytes_xfer;
+
+ /* Number of bytes to be transferred per I/O operation */
+ nbytes_xfer_advance = blk_size * buf_size;
+
+ /* Global offset advance after each I/O operation */
+ mpi_offset_advance = 0;
+
+ /* MPI type to be used for collective access */
+ mpi_collective_type = mpi_full_buffer;
+ } /* end if */
+ /*Interleaved access pattern */
+ else {
+ /* Compute offset in file */
+ /* Before simplification */
+ /* mpi_offset=mpi_file_offset+(nbytes_xfer/(buf_size/blk_size)
+ *pio_mpi_nprocs_g)/(snbytes/blk_size*(blk_size*blk_size))*
+ (buf_size/blk_size*snbytes/blk_size*(blk_size*blk_size))+
+ ((nbytes_xfer/(buf_size/blk_size))*pio_mpi_nprocs_g)%(snbytes
+ /blk_size*(blk_size*blk_size)); */
+ mpi_offset = mpi_file_offset +
+ (MPI_Offset)((((size_t)nbytes_xfer / (buf_size / blk_size) *
+ (size_t)pio_mpi_nprocs_g) /
+ ((size_t)snbytes * blk_size)) *
+ (buf_size * (size_t)snbytes)) +
+ (MPI_Offset)((((size_t)nbytes_xfer / (buf_size / blk_size)) *
+ (size_t)pio_mpi_nprocs_g) %
+ ((size_t)snbytes * blk_size));
+
+ /* Number of bytes to be transferred per I/O operation */
+ nbytes_xfer_advance = blk_size * blk_size;
+
+ /* Global offset advance after each I/O operation */
+ /* mpi_offset_advance = (MPI_Offset)(snbytes/blk_size*(blk_size*blk_size)); */
+ mpi_offset_advance = (MPI_Offset)((size_t)snbytes * blk_size);
+
+ /* MPI type to be used for collective access */
+ mpi_collective_type = mpi_chunk_inter_type;
+ } /* end else */
+ } /* end else */
+
+ /* Common code for independent file access */
+ if (!parms->collective) {
+ /* Set the base of user's buffer */
+ buf_p = (unsigned char *)buffer;
+
+ /* Set the number of bytes to transfer this time */
+ nbytes_toxfer = buf_size * blk_size;
+
+ /* Loop over portions of the buffer to read */
+ while (nbytes_toxfer > 0) {
+ /* Perform independent read */
+ mrc = MPI_File_read_at(fd->mpifd, mpi_offset, buf_p, (int)nbytes_xfer_advance,
+ MPI_BYTE, &mpi_status);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_READ");
+
+ /* Advance location in buffer */
+ buf_p += nbytes_xfer_advance;
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (off_t)nbytes_xfer_advance;
+
+ /* Decrement number of bytes left this time */
+ nbytes_toxfer -= nbytes_xfer_advance;
+
+ /* Partially advance global offset in dataset */
+ mpi_offset += mpi_offset_advance;
+ } /* end while */
+ } /* end if */
+
+ /* Common code for collective file access */
+ else {
+ /* Set the file view */
+ mrc = MPI_File_set_view(fd->mpifd, mpi_offset, MPI_BYTE, mpi_collective_type,
+ (char *)"native", h5_io_info_g);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_VIEW");
+
+ /* Perform read */
+ MPI_File_read_at_all(fd->mpifd, 0, buffer, (int)(buf_size * blk_size), MPI_BYTE,
+ &mpi_status);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_READ");
+
+ /* Advance global offset in dataset */
+ nbytes_xfer += (off_t)buf_size * (off_t)blk_size;
+ } /* end else */
+
+ } /* end else */
+ break;
+
+ case PHDF5:
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ /* Set up the file dset space id to move the selection to process */
+ if (!parms->interleaved) {
+ /* Contiguous pattern */
+ h5offset[0] = nbytes_xfer;
+ } /* end if */
+ else {
+ /* Interleaved access pattern */
+ /* Skip offset over blocks of other processes */
+ h5offset[0] = (nbytes_xfer * pio_mpi_nprocs_g);
+ } /* end else */
+ hrc = H5Soffset_simple(h5dset_space_id, h5offset);
+ VRFY((hrc >= 0), "H5Soffset_simple");
+
+ /* Read the buffer in */
+ hrc = H5Dread(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, h5dset_space_id, h5dxpl, buffer);
+ VRFY((hrc >= 0), "H5Dread");
+
+ /* Increment number of bytes transferred */
+ nbytes_xfer += (off_t)buf_size;
+ } /* end if */
+ /* 2D dataspace */
+ else {
+ /* Set up the file dset space id to move the selection to process */
+ if (!parms->interleaved) {
+ /* Contiguous pattern */
+ h5offset[0] =
+ (hssize_t)(((size_t)nbytes_xfer / ((size_t)snbytes * blk_size)) * blk_size);
+ h5offset[1] =
+ (hssize_t)(((size_t)nbytes_xfer % ((size_t)snbytes * blk_size)) / blk_size);
+ } /* end if */
+ else {
+ /* Interleaved access pattern */
+ /* Skip offset over blocks of other processes */
+ h5offset[0] = (hssize_t)((((size_t)nbytes_xfer * (size_t)pio_mpi_nprocs_g) /
+ ((size_t)snbytes * buf_size)) *
+ buf_size);
+ h5offset[1] = (hssize_t)((((size_t)nbytes_xfer * (size_t)pio_mpi_nprocs_g) %
+ ((size_t)snbytes * buf_size)) /
+ buf_size);
+
+ } /* end else */
+ hrc = H5Soffset_simple(h5dset_space_id, h5offset);
+ VRFY((hrc >= 0), "H5Soffset_simple");
+
+ /* Write the buffer out */
+ hrc = H5Dread(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, h5dset_space_id, h5dxpl, buffer);
+ VRFY((hrc >= 0), "H5Dread");
+
+ /* Increment number of bytes transferred */
+ nbytes_xfer += (off_t)buf_size * (off_t)blk_size;
+
+ } /* end else */
+ break;
+
+ default:
+ break;
+ } /* switch (parms->io_type) */
+
+ /* Verify raw data, if asked */
+ if (parms->verify) {
+ /* Verify data read */
+ unsigned char *ucharptr = (unsigned char *)buffer;
+ size_t i;
+ int nerror = 0;
+
+ for (i = 0; i < bsize; ++i) {
+ if (*ucharptr++ != pio_mpi_rank_g + 1) {
+ if (++nerror < 20) {
+ /* report at most 20 errors */
+ HDprint_rank(output);
+ HDfprintf(output,
+ "read data error, expected (%d), "
+ "got (%d)\n",
+ pio_mpi_rank_g + 1, (int)*(ucharptr - 1));
+ } /* end if */
+ } /* end if */
+ } /* end for */
+ if (nerror >= 20) {
+ HDprint_rank(output);
+ HDfprintf(output, "...");
+ HDfprintf(output, "total read data errors=%d\n", nerror);
+ } /* end if */
+ } /* if (parms->verify) */
+
+ } /* end while */
+
+ /* Stop "raw data" read timer */
+ io_time_set(res->timers, HDF5_RAW_READ_FIXED_DIMS, TSTOP);
+
+ /* Calculate read time */
+
+ /* Close dataset. Only HDF5 needs to do an explicit close. */
+ if (parms->io_type == PHDF5) {
+ hrc = H5Dclose(h5ds_id);
+
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Dataset Close failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ h5ds_id = H5I_INVALID_HID;
+ } /* end if */
+ } /* end for */
+
+done:
+ /* release MPI-I/O objects */
+ if (parms->io_type == MPIO) {
+ /* 1D dataspace */
+ if (!parms->dim2d) {
+ /* Free file type */
+ mrc = MPI_Type_free(&mpi_file_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+
+ /* Free buffer type */
+ mrc = MPI_Type_free(&mpi_blk_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+ } /* end if */
+ /* 2D dataspace */
+ else {
+ /* Free partial buffer type for contiguous access */
+ mrc = MPI_Type_free(&mpi_partial_buffer_cont);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+
+ /* Free contiguous file type */
+ mrc = MPI_Type_free(&mpi_cont_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+
+ /* Free partial buffer type for interleaved access */
+ mrc = MPI_Type_free(&mpi_partial_buffer_inter);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+
+ /* Free interleaved file type */
+ mrc = MPI_Type_free(&mpi_inter_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+
+ /* Free full buffer type */
+ mrc = MPI_Type_free(&mpi_full_buffer);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+
+ /* Free full chunk type */
+ mrc = MPI_Type_free(&mpi_full_chunk);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+
+ /* Free chunk interleaved file type */
+ mrc = MPI_Type_free(&mpi_chunk_inter_type);
+ VRFY((mrc == MPI_SUCCESS), "MPIO_TYPE_FREE");
+ } /* end else */
+ } /* end if */
+
+ /* release HDF5 objects */
+ if (h5dset_space_id != -1) {
+ hrc = H5Sclose(h5dset_space_id);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Dataset Space Close failed\n");
+ ret_code = FAIL;
+ }
+ else {
+ h5dset_space_id = H5I_INVALID_HID;
+ }
+ }
+
+ if (h5mem_space_id != -1) {
+ hrc = H5Sclose(h5mem_space_id);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Memory Space Close failed\n");
+ ret_code = FAIL;
+ }
+ else {
+ h5mem_space_id = H5I_INVALID_HID;
+ }
+ }
+
+ if (h5dxpl != -1) {
+ hrc = H5Pclose(h5dxpl);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Dataset Transfer Property List Close failed\n");
+ ret_code = FAIL;
+ }
+ else {
+ h5dxpl = H5I_INVALID_HID;
+ }
+ }
+
+ return ret_code;
+}
+
+/*
+ * Function: do_fopen
+ * Purpose: Open the specified file.
+ * Return: SUCCESS or FAIL
+ * Programmer: Albert Cheng, Bill Wendling, 2001/12/13
+ * Modifications:
+ */
+static herr_t
+do_fopen(parameters *param, char *fname, file_descr *fd /*out*/, int flags)
+{
+ int ret_code = SUCCESS, mrc;
+ hid_t acc_tpl = H5I_INVALID_HID; /* file access templates */
+
+ switch (param->io_type) {
+ case POSIXIO:
+ if (flags & (PIO_CREATE | PIO_WRITE))
+ fd->posixfd = POSIXCREATE(fname);
+ else
+ fd->posixfd = POSIXOPEN(fname, O_RDONLY);
+
+ if (fd->posixfd < 0) {
+ HDfprintf(stderr, "POSIX File Open failed(%s)\n", fname);
+ GOTOERROR(FAIL);
+ }
+
+ /* The perils of POSIX I/O in a parallel environment. The problem is:
+ *
+ * - Process n opens a file with truncation and then starts
+ * writing to the file.
+ * - Process m also opens the file with truncation, but after
+ * process n has already started to write to the file. Thus,
+ * all of the stuff process n wrote is now lost.
+ */
+ MPI_Barrier(pio_comm_g);
+
+ break;
+
+ case MPIO:
+ if (flags & (PIO_CREATE | PIO_WRITE)) {
+ MPI_File_delete(fname, h5_io_info_g);
+ mrc = MPI_File_open(pio_comm_g, fname, MPI_MODE_CREATE | MPI_MODE_RDWR, h5_io_info_g,
+ &fd->mpifd);
+
+ if (mrc != MPI_SUCCESS) {
+ HDfprintf(stderr, "MPI File Open failed(%s)\n", fname);
+ GOTOERROR(FAIL);
+ }
+
+ /*since MPI_File_open with MPI_MODE_CREATE does not truncate */
+ /*filesize , set size to 0 explicitedly. */
+ mrc = MPI_File_set_size(fd->mpifd, (MPI_Offset)0);
+ if (mrc != MPI_SUCCESS) {
+ HDfprintf(stderr, "MPI_File_set_size failed\n");
+ GOTOERROR(FAIL);
+ }
+ }
+ else {
+ mrc = MPI_File_open(pio_comm_g, fname, MPI_MODE_RDONLY, h5_io_info_g, &fd->mpifd);
+ if (mrc != MPI_SUCCESS) {
+ HDfprintf(stderr, "MPI File Open failed(%s)\n", fname);
+ GOTOERROR(FAIL);
+ }
+ }
+
+ break;
+
+ case PHDF5:
+ if ((acc_tpl = H5Pcreate(H5P_FILE_ACCESS)) < 0) {
+ HDfprintf(stderr, "HDF5 Property List Create failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ /* Set the file driver to the MPI-IO driver */
+ if (H5Pset_fapl_mpio(acc_tpl, pio_comm_g, h5_io_info_g) < 0) {
+ HDfprintf(stderr, "HDF5 Property List Set failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ /* Set the alignment of objects in HDF5 file */
+ if (H5Pset_alignment(acc_tpl, param->h5_thresh, param->h5_align) < 0) {
+ HDfprintf(stderr, "HDF5 Property List Set failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ /* create the parallel file */
+ if (flags & (PIO_CREATE | PIO_WRITE))
+ fd->h5fd = H5Fcreate(fname, H5F_ACC_TRUNC, H5P_DEFAULT, acc_tpl);
+ else
+ fd->h5fd = H5Fopen(fname, H5F_ACC_RDONLY, acc_tpl);
+ if (fd->h5fd < 0) {
+ HDfprintf(stderr, "HDF5 File Create failed(%s)\n", fname);
+ GOTOERROR(FAIL);
+ }
+
+ /* verifying the close of the acc_tpl */
+ if (H5Pclose(acc_tpl) < 0) {
+ HDfprintf(stderr, "HDF5 Property List Close failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ break;
+
+ default:
+ break;
+ }
+
+done:
+ return ret_code;
+}
+
+/*
+ * Function: do_fclose
+ * Purpose: Close the specified file descriptor.
+ * Return: SUCCESS or FAIL
+ * Programmer: Albert Cheng, Bill Wendling, 2001/12/13
+ * Modifications:
+ */
+static herr_t
+do_fclose(iotype iot, file_descr *fd /*out*/)
+{
+ herr_t ret_code = SUCCESS, hrc;
+ int mrc = 0, rc = 0;
+
+ switch (iot) {
+ case POSIXIO:
+ rc = POSIXCLOSE(fd->posixfd);
+
+ if (rc != 0) {
+ HDfprintf(stderr, "POSIX File Close failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ fd->posixfd = -1;
+ break;
+
+ case MPIO:
+ mrc = MPI_File_close(&fd->mpifd);
+
+ if (mrc != MPI_SUCCESS) {
+ HDfprintf(stderr, "MPI File close failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ fd->mpifd = MPI_FILE_NULL;
+ break;
+
+ case PHDF5:
+ hrc = H5Fclose(fd->h5fd);
+
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 File Close failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ fd->h5fd = -1;
+ break;
+
+ default:
+ break;
+ }
+
+done:
+ return ret_code;
+}
+
+/*
+ * Function: do_fclose
+ * Purpose: Cleanup temporary file unless HDF5_NOCLEANUP is set.
+ * Only Proc 0 of the PIO communicator will do the cleanup.
+ * Other processes just return.
+ * Return: void
+ * Programmer: Albert Cheng 2001/12/12
+ * Modifications:
+ */
+static void
+do_cleanupfile(iotype iot, char *fname)
+{
+ if (pio_mpi_rank_g != 0)
+ return;
+
+ if (clean_file_g == -1)
+ clean_file_g = (getenv("HDF5_NOCLEANUP") == NULL) ? 1 : 0;
+
+ if (clean_file_g) {
+ switch (iot) {
+ case POSIXIO:
+ HDremove(fname);
+ break;
+ case MPIO:
+ case PHDF5:
+ MPI_File_delete(fname, h5_io_info_g);
+ break;
+ default:
+ break;
+ }
+ }
+}
+
+#ifdef TIME_MPI
+/* instrument the MPI_File_wrirte_xxx and read_xxx calls to measure
+ * pure time spent in MPI_File code.
+ */
+int
+MPI_File_read_at(MPI_File fh, MPI_Offset offset, void *buf, int count, MPI_Datatype datatype,
+ MPI_Status *status)
+{
+ int err;
+ io_time_set(timer_g, HDF5_MPI_READ, TSTART);
+ err = PMPI_File_read_at(fh, offset, buf, count, datatype, status);
+ io_time_set(timer_g, HDF5_MPI_READ, TSTOP);
+ return err;
+}
+
+int
+MPI_File_read_at_all(MPI_File fh, MPI_Offset offset, void *buf, int count, MPI_Datatype datatype,
+ MPI_Status *status)
+{
+ int err;
+ io_time_set(timer_g, HDF5_MPI_READ, TSTART);
+ err = PMPI_File_read_at_all(fh, offset, buf, count, datatype, status);
+ io_time_set(timer_g, HDF5_MPI_READ, TSTOP);
+ return err;
+}
+
+int
+MPI_File_write_at(MPI_File fh, MPI_Offset offset, void *buf, int count, MPI_Datatype datatype,
+ MPI_Status *status)
+{
+ int err;
+ io_time_set(timer_g, HDF5_MPI_WRITE, TSTART);
+ err = PMPI_File_write_at(fh, offset, buf, count, datatype, status);
+ io_time_set(timer_g, HDF5_MPI_WRITE, TSTOP);
+ return err;
+}
+
+int
+MPI_File_write_at_all(MPI_File fh, MPI_Offset offset, void *buf, int count, MPI_Datatype datatype,
+ MPI_Status *status)
+{
+ int err;
+ io_time_set(timer_g, HDF5_MPI_WRITE, TSTART);
+ err = PMPI_File_write_at_all(fh, offset, buf, count, datatype, status);
+ io_time_set(timer_g, HDF5_MPI_WRITE, TSTOP);
+ return err;
+}
+
+#endif /* TIME_MPI */
+#endif /* H5_HAVE_PARALLEL */
diff --git a/tools/src/h5perf/pio_perf.c b/tools/src/h5perf/pio_perf.c
new file mode 100644
index 0000000..41245d9
--- /dev/null
+++ b/tools/src/h5perf/pio_perf.c
@@ -0,0 +1,1718 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the COPYING file, which can be found at the root of the source code *
+ * distribution tree, or in https://www.hdfgroup.org/licenses. *
+ * If you do not have access to either file, you may request a copy from *
+ * help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * Parallel HDF5 Performance Testing Code
+ * --------------------------------------
+ *
+ * Portable code to test performance on the different platforms we support.
+ * This is what the report should look like:
+ *
+ * nprocs = Max#Procs
+ * IO API = POSIXIO
+ * # Files = 1, # of dsets = 1000, Elements per dset = 37000
+ * Write Results = x MB/s
+ * Read Results = x MB/s
+ * # Files = 1, # of dsets = 3000, Elements per dset = 37000
+ * Write Results = x MB/s
+ * Read Results = x MB/s
+ *
+ * . . .
+ *
+ * IO API = MPIO
+ * # Files = 1, # of dsets = 1000, Elements per dset = 37000
+ * Write Results = x MB/s
+ * Read Results = x MB/s
+ * # Files = 1, # of dsets = 3000, Elements per dset = 37000
+ * Write Results = x MB/s
+ * Read Results = x MB/s
+ *
+ * . . .
+ *
+ * IO API = PHDF5
+ * # Files = 1, # of dsets = 1000, Elements per dset = 37000
+ * Write Results = x MB/s
+ * Read Results = x MB/s
+ * # Files = 1, # of dsets = 3000, Elements per dset = 37000
+ * Write Results = x MB/s
+ * Read Results = x MB/s
+ *
+ * . . .
+ *
+ * nprocs = Max#Procs / 2
+ *
+ * . . .
+ *
+ */
+
+/* system header files */
+#include <stdarg.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "hdf5.h"
+
+#ifdef H5_HAVE_PARALLEL
+
+/* library header files */
+#include <mpi.h>
+
+/* our header files */
+#include "pio_perf.h"
+
+/* useful macros */
+#define TAB_SPACE 4
+
+#define ONE_KB 1024
+#define ONE_MB (ONE_KB * ONE_KB)
+#define ONE_GB (ONE_MB * ONE_KB)
+
+#define PIO_POSIX 0x1
+#define PIO_MPI 0x2
+#define PIO_HDF5 0x4
+
+#ifdef STANDALONE
+#define DBL_EPSILON 2.2204460492503131e-16
+#define H5_DBL_ABS_EQUAL(X, Y) (fabs((X) - (Y)) < DBL_EPSILON)
+#endif
+
+/* report 0.0 in case t is zero too */
+#define MB_PER_SEC(bytes, t) (H5_DBL_ABS_EQUAL((t), 0.0) ? 0.0 : ((((double)bytes) / ONE_MB) / (t)))
+
+#ifndef TRUE
+#define TRUE 1
+#endif /* TRUE */
+#ifndef FALSE
+#define FALSE (!TRUE)
+#endif /* FALSE */
+
+/* global variables */
+FILE * output; /* output file */
+int comm_world_rank_g; /* my rank in MPI_COMM_RANK */
+int comm_world_nprocs_g; /* num. of processes of MPI_COMM_WORLD */
+MPI_Comm pio_comm_g; /* Communicator to run the PIO */
+int pio_mpi_rank_g; /* MPI rank of pio_comm_g */
+int pio_mpi_nprocs_g; /* Number of processes of pio_comm_g */
+int pio_debug_level = 0; /* The debug level:
+ * 0 - Off
+ * 1 - Minimal
+ * 2 - Some more
+ * 3 - Maximal
+ * 4 - Maximal & then some
+ */
+
+/* local variables */
+static const char *progname = "h5perf";
+
+#ifndef HDF5_PARAPREFIX
+#define HDF5_PARAPREFIX ""
+#endif
+char * paraprefix = NULL; /* for command line option para-prefix */
+MPI_Info h5_io_info_g = MPI_INFO_NULL; /* MPI INFO object for IO */
+
+/*
+ * Command-line options: The user can specify short or long-named
+ * parameters. The long-named ones can be partially spelled. When
+ * adding more, make sure that they don't clash with each other.
+ */
+#if 1
+static const char *s_opts = "a:A:B:cCd:D:e:F:ghi:Imno:p:P:stT:wx:X:";
+#else
+static const char *s_opts = "a:A:bB:cCd:D:e:F:ghi:Imno:p:P:stT:wx:X:";
+#endif /* 1 */
+static struct h5_long_options l_opts[] = {{"align", require_arg, 'a'},
+ {"api", require_arg, 'A'},
+#if 0
+ /* a sighting of the elusive binary option */
+ { "binary", no_arg, 'b' },
+#endif /* 0 */
+ {"block-size", require_arg, 'B'},
+ {"chunk", no_arg, 'c'},
+ {"collective", no_arg, 'C'},
+ {"debug", require_arg, 'D'},
+ {"geometry", no_arg, 'g'},
+ {"help", no_arg, 'h'},
+ {"interleaved", require_arg, 'I'},
+ {"max-num-processes", require_arg, 'P'},
+ {"min-num-processes", require_arg, 'p'},
+ {"max-xfer-size", require_arg, 'X'},
+ {"min-xfer-size", require_arg, 'x'},
+ {"num-bytes", require_arg, 'e'},
+ {"num-dsets", require_arg, 'd'},
+ {"num-files", require_arg, 'F'},
+ {"num-iterations", require_arg, 'i'},
+ {"output", require_arg, 'o'},
+ {"threshold", require_arg, 'T'},
+ {"write-only", require_arg, 'w'},
+ {NULL, 0, '\0'}};
+
+struct options {
+ long io_types; /* bitmask of which I/O types to test */
+ const char *output_file; /* file to print report to */
+ long num_dsets; /* number of datasets */
+ long num_files; /* number of files */
+ off_t num_bpp; /* number of bytes per proc per dset */
+ int num_iters; /* number of iterations */
+ int max_num_procs; /* maximum number of processes to use */
+ int min_num_procs; /* minimum number of processes to use */
+ size_t max_xfer_size; /* maximum transfer buffer size */
+ size_t min_xfer_size; /* minimum transfer buffer size */
+ size_t blk_size; /* Block size */
+ unsigned interleaved; /* Interleaved vs. contiguous blocks */
+ unsigned collective; /* Collective vs. independent I/O */
+ unsigned dim2d; /* 1D vs. 2D geometry */
+ int print_times; /* print times as well as throughputs */
+ int print_raw; /* print raw data throughput info */
+ off_t h5_alignment; /* alignment in HDF5 file */
+ off_t h5_threshold; /* threshold for alignment in HDF5 file */
+ int h5_use_chunks; /* Make HDF5 dataset chunked */
+ int h5_write_only; /* Perform the write tests only */
+ int verify; /* Verify data correctness */
+};
+
+typedef struct _minmax {
+ double min;
+ double max;
+ double sum;
+ int num;
+} minmax;
+
+/* local functions */
+static off_t parse_size_directive(const char *size);
+static struct options *parse_command_line(int argc, char *argv[]);
+static void run_test_loop(struct options *options);
+static int run_test(iotype iot, parameters parms, struct options *opts);
+static void output_all_info(minmax *mm, int count, int indent_level);
+static void get_minmax(minmax *mm, double val);
+static minmax accumulate_minmax_stuff(minmax *mm, int count);
+static int create_comm_world(int num_procs, int *doing_pio);
+static int destroy_comm_world(void);
+static void output_results(const struct options *options, const char *name, minmax *table, int table_size,
+ off_t data_size);
+static void output_times(const struct options *options, const char *name, minmax *table, int table_size);
+static void output_report(const char *fmt, ...);
+static void print_indent(register int indent);
+static void usage(const char *prog);
+static void report_parameters(struct options *opts);
+static off_t squareo(off_t);
+
+/*
+ * Function: main
+ * Purpose: Start things up. Initialize MPI and then call the test looping
+ * function.
+ * Return: EXIT_SUCCESS or EXIT_FAILURE
+ * Programmer: Bill Wendling, 30. October 2001
+ * Modifications:
+ */
+int
+main(int argc, char *argv[])
+{
+ int ret;
+ int exit_value = EXIT_SUCCESS;
+ struct options *opts = NULL;
+
+#ifndef STANDALONE
+ /* Initialize h5tools lib */
+ h5tools_init();
+#endif
+
+ output = stdout;
+
+ /* initialize MPI and get the maximum num of processors we started with */
+ MPI_Init(&argc, &argv);
+ ret = MPI_Comm_size(MPI_COMM_WORLD, &comm_world_nprocs_g);
+
+ if (ret != MPI_SUCCESS) {
+ HDfprintf(stderr, "%s: MPI_Comm_size call failed\n", progname);
+
+ if (ret == MPI_ERR_COMM)
+ HDfprintf(stderr, "invalid MPI communicator\n");
+ else
+ HDfprintf(stderr, "invalid argument\n");
+
+ exit_value = EXIT_FAILURE;
+ goto finish;
+ }
+
+ ret = MPI_Comm_rank(MPI_COMM_WORLD, &comm_world_rank_g);
+
+ if (ret != MPI_SUCCESS) {
+ HDfprintf(stderr, "%s: MPI_Comm_rank call failed\n", progname);
+
+ if (ret == MPI_ERR_COMM)
+ HDfprintf(stderr, "invalid MPI communicator\n");
+ else
+ HDfprintf(stderr, "invalid argument\n");
+
+ exit_value = EXIT_FAILURE;
+ goto finish;
+ }
+
+ pio_comm_g = MPI_COMM_WORLD;
+
+ h5_set_info_object();
+ opts = parse_command_line(argc, argv);
+
+ if (!opts) {
+ exit_value = EXIT_FAILURE;
+ goto finish;
+ }
+
+ if (opts->output_file) {
+ if ((output = HDfopen(opts->output_file, "w")) == NULL) {
+ HDfprintf(stderr, "%s: cannot open output file\n", progname);
+ perror(opts->output_file);
+ goto finish;
+ }
+ }
+
+ if ((pio_debug_level == 0 && comm_world_rank_g == 0) || pio_debug_level > 0)
+ report_parameters(opts);
+
+ run_test_loop(opts);
+
+finish:
+ MPI_Finalize();
+ free(opts);
+ return exit_value;
+}
+
+off_t
+squareo(off_t x)
+{
+ return x * x;
+}
+
+/*
+ * Function: run_test_loop
+ * Purpose: Run the I/O tests. Write the results to OUTPUT.
+ *
+ * - The slowest changing part of the test is the number of
+ * processors to use. For each loop iteration, we divide that
+ * number by 2 and rerun the test.
+ *
+ * - The second slowest is what type of IO API to perform. We have
+ * three choices: POSIXIO, MPI-IO, and PHDF5.
+ *
+ * - Then we change the size of the buffer. This information is
+ * inferred from the number of datasets to create and the number
+ * of integers to put into each dataset. The backend code figures
+ * this out.
+ *
+ * Return: Nothing
+ * Programmer: Bill Wendling, 30. October 2001
+ * Modifications:
+ * Added 2D testing (Christian Chilan, 10. August 2005)
+ */
+static void
+run_test_loop(struct options *opts)
+{
+ parameters parms;
+ int num_procs;
+ int doing_pio; /* if this process is doing PIO */
+
+ parms.num_files = opts->num_files;
+ parms.num_dsets = opts->num_dsets;
+ parms.num_iters = opts->num_iters;
+ parms.blk_size = opts->blk_size;
+ parms.interleaved = opts->interleaved;
+ parms.collective = opts->collective;
+ parms.dim2d = opts->dim2d;
+ parms.h5_align = (hsize_t)opts->h5_alignment;
+ parms.h5_thresh = (hsize_t)opts->h5_threshold;
+ parms.h5_use_chunks = opts->h5_use_chunks;
+ parms.h5_write_only = opts->h5_write_only;
+ parms.verify = opts->verify;
+
+ /* start with max_num_procs and decrement it by half for each loop. */
+ /* if performance needs restart, fewer processes may be needed. */
+ for (num_procs = opts->max_num_procs; num_procs >= opts->min_num_procs; num_procs >>= 1) {
+ register size_t buf_size;
+
+ parms.num_procs = num_procs;
+
+ if (create_comm_world(parms.num_procs, &doing_pio) != SUCCESS) {
+ /* do something harsh */
+ }
+
+ /* only processes doing PIO will run the tests */
+ if (doing_pio) {
+ output_report("Number of processors = %ld\n", parms.num_procs);
+
+ /* multiply the xfer buffer size by 2 for each loop iteration */
+ for (buf_size = opts->min_xfer_size; buf_size <= opts->max_xfer_size; buf_size <<= 1) {
+ parms.buf_size = buf_size;
+
+ if (parms.dim2d) {
+ parms.num_bytes = squareo(opts->num_bpp * parms.num_procs);
+ if (parms.interleaved)
+ output_report("Transfer Buffer Size: %ldx%ld bytes, File size: %.2f MB\n", buf_size,
+ opts->blk_size,
+ ((double)parms.num_dsets * (double)parms.num_bytes) / ONE_MB);
+ else
+ output_report("Transfer Buffer Size: %ldx%ld bytes, File size: %.2f MB\n",
+ opts->blk_size, buf_size,
+ ((double)parms.num_dsets * (double)parms.num_bytes) / ONE_MB);
+
+ print_indent(1);
+ output_report(" # of files: %ld, # of datasets: %ld, dataset size: %.2fx%.2f KB\n",
+ parms.num_files, parms.num_dsets,
+ (double)(opts->num_bpp * parms.num_procs) / ONE_KB,
+ (double)(opts->num_bpp * parms.num_procs) / ONE_KB);
+ }
+ else {
+ parms.num_bytes = (off_t)opts->num_bpp * parms.num_procs;
+ output_report("Transfer Buffer Size: %ld bytes, File size: %.2f MB\n", buf_size,
+ ((double)parms.num_dsets * (double)parms.num_bytes) / ONE_MB);
+
+ print_indent(1);
+ output_report(" # of files: %ld, # of datasets: %ld, dataset size: %.2f MB\n",
+ parms.num_files, parms.num_dsets,
+ (double)(opts->num_bpp * parms.num_procs) / ONE_MB);
+ }
+
+ if (opts->io_types & PIO_POSIX)
+ run_test(POSIXIO, parms, opts);
+
+ if (opts->io_types & PIO_MPI)
+ run_test(MPIO, parms, opts);
+
+ if (opts->io_types & PIO_HDF5)
+ run_test(PHDF5, parms, opts);
+
+ /* Run the tests once if buf_size==0, but then break out */
+ if (buf_size == 0)
+ break;
+ }
+
+ if (destroy_comm_world() != SUCCESS) {
+ /* do something harsh */
+ }
+ }
+ }
+}
+
+/*
+ * Function: run_test
+ * Purpose: Inner loop call to actually run the I/O test.
+ * Return: Nothing
+ * Programmer: Bill Wendling, 18. December 2001
+ * Modifications:
+ */
+static int
+run_test(iotype iot, parameters parms, struct options *opts)
+{
+ results res;
+ register int i, ret_value = SUCCESS;
+ int comm_size;
+ off_t raw_size;
+ minmax * write_mpi_mm_table = NULL;
+ minmax * write_mm_table = NULL;
+ minmax * write_gross_mm_table = NULL;
+ minmax * write_raw_mm_table = NULL;
+ minmax * read_mpi_mm_table = NULL;
+ minmax * read_mm_table = NULL;
+ minmax * read_gross_mm_table = NULL;
+ minmax * read_raw_mm_table = NULL;
+ minmax * read_open_mm_table = NULL;
+ minmax * read_close_mm_table = NULL;
+ minmax * write_open_mm_table = NULL;
+ minmax * write_close_mm_table = NULL;
+ minmax write_mpi_mm = {0.0, 0.0, 0.0, 0};
+ minmax write_mm = {0.0, 0.0, 0.0, 0};
+ minmax write_gross_mm = {0.0, 0.0, 0.0, 0};
+ minmax write_raw_mm = {0.0, 0.0, 0.0, 0};
+ minmax read_mpi_mm = {0.0, 0.0, 0.0, 0};
+ minmax read_mm = {0.0, 0.0, 0.0, 0};
+ minmax read_gross_mm = {0.0, 0.0, 0.0, 0};
+ minmax read_raw_mm = {0.0, 0.0, 0.0, 0};
+ minmax read_open_mm = {0.0, 0.0, 0.0, 0};
+ minmax read_close_mm = {0.0, 0.0, 0.0, 0};
+ minmax write_open_mm = {0.0, 0.0, 0.0, 0};
+ minmax write_close_mm = {0.0, 0.0, 0.0, 0};
+
+ raw_size = parms.num_files * (off_t)parms.num_dsets * (off_t)parms.num_bytes;
+ parms.io_type = iot;
+ print_indent(2);
+ output_report("IO API = ");
+
+ switch (iot) {
+ case POSIXIO:
+ output_report("POSIX\n");
+ break;
+ case MPIO:
+ output_report("MPIO\n");
+ break;
+ case PHDF5:
+ output_report("PHDF5 (w/MPI-IO driver)\n");
+ break;
+ default:
+ break;
+ }
+
+ MPI_Comm_size(pio_comm_g, &comm_size);
+
+ /* allocate space for tables minmax and that it is sufficient */
+ /* to initialize all elements to zeros by calloc. */
+ write_mpi_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax));
+ write_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax));
+ write_gross_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax));
+ write_raw_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax));
+ write_open_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax));
+ write_close_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax));
+ if (!parms.h5_write_only) {
+ read_mpi_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax));
+ read_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax));
+ read_gross_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax));
+ read_raw_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax));
+ read_open_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax));
+ read_close_mm_table = calloc((size_t)parms.num_iters, sizeof(minmax));
+ }
+
+ /* Do IO iteration times, collecting statistics each time */
+ for (i = 0; i < parms.num_iters; ++i) {
+ double t;
+
+ MPI_Barrier(pio_comm_g);
+ res = do_pio(parms);
+
+ /* gather all of the "mpi write" times */
+ t = io_time_get(res.timers, HDF5_MPI_WRITE);
+ get_minmax(&write_mpi_mm, t);
+
+ write_mpi_mm_table[i] = write_mpi_mm;
+
+ /* gather all of the "write" times */
+ t = io_time_get(res.timers, HDF5_FINE_WRITE_FIXED_DIMS);
+ get_minmax(&write_mm, t);
+
+ write_mm_table[i] = write_mm;
+
+ /* gather all of the "write" times from open to close */
+ t = io_time_get(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS);
+ get_minmax(&write_gross_mm, t);
+
+ write_gross_mm_table[i] = write_gross_mm;
+
+ /* gather all of the raw "write" times */
+ t = io_time_get(res.timers, HDF5_RAW_WRITE_FIXED_DIMS);
+ get_minmax(&write_raw_mm, t);
+
+ write_raw_mm_table[i] = write_raw_mm;
+
+ /* gather all of the file open times (time from open to first write) */
+ t = io_time_get(res.timers, HDF5_FILE_WRITE_OPEN);
+ get_minmax(&write_open_mm, t);
+
+ write_open_mm_table[i] = write_open_mm;
+
+ /* gather all of the file close times (time from last write to close) */
+ t = io_time_get(res.timers, HDF5_FILE_WRITE_CLOSE);
+ get_minmax(&write_close_mm, t);
+
+ write_close_mm_table[i] = write_close_mm;
+
+ if (!parms.h5_write_only) {
+ /* gather all of the "mpi read" times */
+ t = io_time_get(res.timers, HDF5_MPI_READ);
+ get_minmax(&read_mpi_mm, t);
+
+ read_mpi_mm_table[i] = read_mpi_mm;
+
+ /* gather all of the "read" times */
+ t = io_time_get(res.timers, HDF5_FINE_READ_FIXED_DIMS);
+ get_minmax(&read_mm, t);
+
+ read_mm_table[i] = read_mm;
+
+ /* gather all of the "read" times from open to close */
+ t = io_time_get(res.timers, HDF5_GROSS_READ_FIXED_DIMS);
+ get_minmax(&read_gross_mm, t);
+
+ read_gross_mm_table[i] = read_gross_mm;
+
+ /* gather all of the raw "read" times */
+ t = io_time_get(res.timers, HDF5_RAW_READ_FIXED_DIMS);
+ get_minmax(&read_raw_mm, t);
+
+ read_raw_mm_table[i] = read_raw_mm;
+
+ /* gather all of the file open times (time from open to first read) */
+ t = io_time_get(res.timers, HDF5_FILE_READ_OPEN);
+ get_minmax(&read_open_mm, t);
+
+ read_open_mm_table[i] = read_open_mm;
+
+ /* gather all of the file close times (time from last read to close) */
+ t = io_time_get(res.timers, HDF5_FILE_READ_CLOSE);
+ get_minmax(&read_close_mm, t);
+
+ read_close_mm_table[i] = read_close_mm;
+ }
+
+ io_time_destroy(res.timers);
+ }
+
+ /*
+ * Show various statistics
+ */
+ /* Write statistics */
+ /* Print the raw data throughput if desired */
+ if (opts->print_raw) {
+ /* accumulate and output the max, min, and average "raw write" times */
+ if (pio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("Raw Data Write details:\n");
+ output_all_info(write_raw_mm_table, parms.num_iters, 4);
+ }
+
+ output_results(opts, "Raw Data Write", write_raw_mm_table, parms.num_iters, raw_size);
+ } /* end if */
+
+ /* show mpi write statics */
+ if (pio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("MPI Write details:\n");
+ output_all_info(write_mpi_mm_table, parms.num_iters, 4);
+ }
+
+ /* We don't currently output the MPI write results */
+
+ /* accumulate and output the max, min, and average "write" times */
+ if (pio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("Write details:\n");
+ output_all_info(write_mm_table, parms.num_iters, 4);
+ }
+
+ output_results(opts, "Write", write_mm_table, parms.num_iters, raw_size);
+
+ /* accumulate and output the max, min, and average "gross write" times */
+ if (pio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("Write Open-Close details:\n");
+ output_all_info(write_gross_mm_table, parms.num_iters, 4);
+ }
+
+ output_results(opts, "Write Open-Close", write_gross_mm_table, parms.num_iters, raw_size);
+
+ if (opts->print_times) {
+ output_times(opts, "Write File Open", write_open_mm_table, parms.num_iters);
+ output_times(opts, "Write File Close", write_close_mm_table, parms.num_iters);
+ }
+
+ /* Print out time from open to first write */
+ if (pio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("Write file open details:\n");
+ output_all_info(write_open_mm_table, parms.num_iters, 4);
+ }
+
+ /* Print out time from last write to close */
+ if (pio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("Write file close details:\n");
+ output_all_info(write_close_mm_table, parms.num_iters, 4);
+ }
+
+ if (!parms.h5_write_only) {
+ /* Read statistics */
+ /* Print the raw data throughput if desired */
+ if (opts->print_raw) {
+ /* accumulate and output the max, min, and average "raw read" times */
+ if (pio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("Raw Data Read details:\n");
+ output_all_info(read_raw_mm_table, parms.num_iters, 4);
+ }
+
+ output_results(opts, "Raw Data Read", read_raw_mm_table, parms.num_iters, raw_size);
+ } /* end if */
+
+ /* show mpi read statics */
+ if (pio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("MPI Read details:\n");
+ output_all_info(read_mpi_mm_table, parms.num_iters, 4);
+ }
+
+ /* We don't currently output the MPI read results */
+
+ /* accumulate and output the max, min, and average "read" times */
+ if (pio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("Read details:\n");
+ output_all_info(read_mm_table, parms.num_iters, 4);
+ }
+
+ output_results(opts, "Read", read_mm_table, parms.num_iters, raw_size);
+
+ /* accumulate and output the max, min, and average "gross read" times */
+ if (pio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("Read Open-Close details:\n");
+ output_all_info(read_gross_mm_table, parms.num_iters, 4);
+ }
+
+ output_results(opts, "Read Open-Close", read_gross_mm_table, parms.num_iters, raw_size);
+
+ if (opts->print_times) {
+ output_times(opts, "Read File Open", read_open_mm_table, parms.num_iters);
+ output_times(opts, "Read File Close", read_close_mm_table, parms.num_iters);
+ }
+
+ /* Print out time from open to first read */
+ if (pio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("Read file open details:\n");
+ output_all_info(read_open_mm_table, parms.num_iters, 4);
+ }
+
+ /* Print out time from last read to close */
+ if (pio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("Read file close details:\n");
+ output_all_info(read_close_mm_table, parms.num_iters, 4);
+ }
+ }
+
+ /* clean up our mess */
+ free(write_mpi_mm_table);
+ free(write_mm_table);
+ free(write_gross_mm_table);
+ free(write_raw_mm_table);
+ free(write_open_mm_table);
+ free(write_close_mm_table);
+
+ if (!parms.h5_write_only) {
+ free(read_mpi_mm_table);
+ free(read_mm_table);
+ free(read_gross_mm_table);
+ free(read_raw_mm_table);
+ free(read_open_mm_table);
+ free(read_close_mm_table);
+ }
+
+ return ret_value;
+}
+
+/*
+ * Function: output_all_info
+ * Purpose:
+ * Return: Nothing
+ * Programmer: Bill Wendling, 29. January 2002
+ * Modifications:
+ */
+static void
+output_all_info(minmax *mm, int count, int indent_level)
+{
+ int i;
+
+ for (i = 0; i < count; ++i) {
+ print_indent(indent_level);
+ output_report("Iteration %d:\n", i + 1);
+ print_indent(indent_level + 1);
+ output_report("Minimum Time: %.2fs\n", mm[i].min);
+ print_indent(indent_level + 1);
+ output_report("Maximum Time: %.2fs\n", mm[i].max);
+ }
+}
+
+/*
+ * Function: h5_set_info_object
+ * Purpose: Process environment variables setting to set up MPI Info
+ * object.
+ * Return: 0 if all is fine; otherwise non-zero.
+ * Programmer: Albert Cheng, 2002/05/21.
+ * Modifications:
+ * Bill Wendling, 2002/05/31
+ * Modified so that the HDF5_MPI_INFO environment variable can
+ * be a semicolon separated list of "key=value" pairings. Most
+ * of the code is to remove any whitespaces which might be
+ * surrounding the "key=value" pairs.
+ */
+int
+h5_set_info_object(void)
+{
+ char *envp; /* environment pointer */
+ int ret_value = 0;
+
+ /* handle any MPI INFO hints via $HDF5_MPI_INFO */
+ if ((envp = HDgetenv("HDF5_MPI_INFO")) != NULL) {
+ char *next, *valp;
+
+ valp = envp = next = HDstrdup(envp);
+
+ if (!valp)
+ return 0;
+
+ /* create an INFO object if not created yet */
+ if (h5_io_info_g == MPI_INFO_NULL)
+ MPI_Info_create(&h5_io_info_g);
+
+ do {
+ size_t len;
+ char * key_val, *endp, *namep;
+
+ if (*valp == ';')
+ valp++;
+
+ /* copy key/value pair into temporary buffer */
+ len = strcspn(valp, ";");
+ next = &valp[len];
+ key_val = (char *)HDcalloc(1, len + 1);
+
+ /* increment the next pointer past the terminating semicolon */
+ if (*next == ';')
+ ++next;
+
+ namep = HDstrncpy(key_val, valp, len);
+
+ /* pass up any beginning whitespaces */
+ while (*namep && (*namep == ' ' || *namep == '\t'))
+ namep++;
+
+ if (!*namep)
+ continue; /* was all white space, so move to next k/v pair */
+
+ /* eat up any ending white spaces */
+ endp = &namep[HDstrlen(namep) - 1];
+
+ while (endp && (*endp == ' ' || *endp == '\t'))
+ *endp-- = '\0';
+
+ /* find the '=' */
+ valp = HDstrchr(namep, '=');
+
+ if (valp != NULL) { /* it's a valid key/value pairing */
+ char *tmp_val = valp + 1;
+
+ /* change '=' to \0, move valp down one */
+ *valp-- = '\0';
+
+ /* eat up ending whitespace on the "key" part */
+ while (*valp == ' ' || *valp == '\t')
+ *valp-- = '\0';
+
+ valp = tmp_val;
+
+ /* eat up beginning whitespace on the "value" part */
+ while (*valp == ' ' || *valp == '\t')
+ *valp++ = '\0';
+
+ /* actually set the darned thing */
+ if (MPI_SUCCESS != MPI_Info_set(h5_io_info_g, namep, valp)) {
+ HDprintf("MPI_Info_set failed\n");
+ ret_value = -1;
+ }
+ }
+
+ valp = next;
+ HDfree(key_val);
+ } while (next && *next);
+
+ HDfree(envp);
+ }
+
+ return ret_value;
+}
+
+/*
+ * Function: h5_dump_info_object
+ * Purpose: Display content of an MPI Info object
+ * Return: void
+ * Programmer: Albert Cheng 2002/05/21
+ * Modifications:
+ */
+void
+h5_dump_info_object(MPI_Info info)
+{
+ char key[MPI_MAX_INFO_KEY + 1];
+ char value[MPI_MAX_INFO_VAL + 1];
+ int flag;
+ int i, nkeys;
+
+ HDprintf("Dumping MPI Info Object (up to %d bytes per item):\n", MPI_MAX_INFO_VAL);
+ if (info == MPI_INFO_NULL) {
+ HDprintf("object is MPI_INFO_NULL\n");
+ }
+ else {
+ MPI_Info_get_nkeys(info, &nkeys);
+ HDprintf("object has %d items\n", nkeys);
+ for (i = 0; i < nkeys; i++) {
+ MPI_Info_get_nthkey(info, i, key);
+ MPI_Info_get(info, key, MPI_MAX_INFO_VAL, value, &flag);
+ HDprintf("%s=%s\n", key, value);
+ }
+ }
+}
+
+/*
+ * Function: get_minmax
+ * Purpose: Gather all the min, max and total of val.
+ * Return: Nothing
+ * Programmer: Bill Wendling, 21. December 2001
+ * Modifications:
+ * Use MPI_Allreduce to do it. -akc, 2002/01/11
+ */
+static void
+get_minmax(minmax *mm, double val)
+{
+ int myrank;
+
+ MPI_Comm_rank(pio_comm_g, &myrank);
+ MPI_Comm_size(pio_comm_g, &mm->num);
+
+ MPI_Allreduce(&val, &mm->max, 1, MPI_DOUBLE, MPI_MAX, pio_comm_g);
+ MPI_Allreduce(&val, &mm->min, 1, MPI_DOUBLE, MPI_MIN, pio_comm_g);
+ MPI_Allreduce(&val, &mm->sum, 1, MPI_DOUBLE, MPI_SUM, pio_comm_g);
+}
+
+/*
+ * Function: accumulate_minmax_stuff
+ * Purpose: Accumulate the minimum, maximum, and average of the times
+ * across all processes.
+ * Return: TOTAL_MM - the total of all of these.
+ * Programmer: Bill Wendling, 21. December 2001
+ * Modifications:
+ * Changed to use seconds instead of MB/s - QAK, 5/9/02
+ */
+static minmax
+accumulate_minmax_stuff(minmax *mm, int count)
+{
+ int i;
+ minmax total_mm;
+
+ total_mm.sum = 0.0f;
+ total_mm.max = -DBL_MAX;
+ total_mm.min = DBL_MAX;
+ total_mm.num = count;
+
+ for (i = 0; i < count; ++i) {
+ double m = mm[i].max;
+
+ total_mm.sum += m;
+
+ if (m < total_mm.min)
+ total_mm.min = m;
+
+ if (m > total_mm.max)
+ total_mm.max = m;
+ }
+
+ return total_mm;
+}
+
+/*
+ * Function: create_comm_world
+ * Purpose: Create an MPI Comm world and store it in pio_comm_g, which
+ * is a global variable.
+ * Return: SUCCESS on success.
+ * FAIL otherwise.
+ * Programmer: Bill Wendling, 19. December 2001
+ * Modifications:
+ */
+static int
+create_comm_world(int num_procs, int *doing_pio)
+{
+ /* MPI variables */
+ int mrc; /* return values */
+ int color; /* for communicator creation */
+ int myrank, nprocs;
+
+ pio_comm_g = MPI_COMM_NULL;
+
+ /*
+ * Create a sub communicator for this PIO run. Easier to use the first N
+ * processes.
+ */
+ MPI_Comm_size(MPI_COMM_WORLD, &nprocs);
+
+ if (num_procs > nprocs) {
+ HDfprintf(stderr, "number of process(%d) must be <= number of processes in MPI_COMM_WORLD(%d)\n",
+ num_procs, nprocs);
+ goto error_done;
+ }
+
+ MPI_Comm_rank(MPI_COMM_WORLD, &myrank);
+ color = (myrank < num_procs);
+ mrc = MPI_Comm_split(MPI_COMM_WORLD, color, myrank, &pio_comm_g);
+
+ if (mrc != MPI_SUCCESS) {
+ HDfprintf(stderr, "MPI_Comm_split failed\n");
+ goto error_done;
+ }
+
+ if (!color) {
+ /* not involved in this run */
+ mrc = destroy_comm_world();
+ goto done;
+ }
+
+ /* determine the MPI rank in the PIO communicator */
+ MPI_Comm_size(pio_comm_g, &pio_mpi_nprocs_g);
+ MPI_Comm_rank(pio_comm_g, &pio_mpi_rank_g);
+
+done:
+ *doing_pio = color;
+ return SUCCESS;
+
+error_done:
+ destroy_comm_world();
+ return FAIL;
+}
+
+/*
+ * Function: destroy_comm_world
+ * Purpose: Destroy the created MPI Comm world which is stored in the
+ * pio_comm_g global variable.
+ * Return: SUCCESS on success.
+ * FAIL otherwise.
+ * Programmer: Bill Wendling, 19. December 2001
+ * Modifications:
+ */
+static int
+destroy_comm_world(void)
+{
+ int mrc = SUCCESS; /* return code */
+
+ /* release MPI resources */
+ if (pio_comm_g != MPI_COMM_NULL)
+ mrc = (MPI_Comm_free(&pio_comm_g) == MPI_SUCCESS ? SUCCESS : FAIL);
+
+ return mrc;
+}
+
+/*
+ * Function: output_results
+ * Purpose: Print information about the time & bandwidth for a given
+ * minmax & # of iterations.
+ * Return: Nothing
+ * Programmer: Quincey Koziol, 9. May 2002
+ * Modifications:
+ */
+static void
+output_results(const struct options *opts, const char *name, minmax *table, int table_size, off_t data_size)
+{
+ minmax total_mm;
+
+ total_mm = accumulate_minmax_stuff(table, table_size);
+
+ print_indent(3);
+ output_report("%s (%d iteration(s)):\n", name, table_size);
+
+ /* Note: The maximum throughput uses the minimum amount of time & vice versa */
+
+ print_indent(4);
+ output_report("Maximum Throughput: %6.2f MB/s", MB_PER_SEC(data_size, total_mm.min));
+ if (opts->print_times)
+ output_report(" (%7.3f s)\n", total_mm.min);
+ else
+ output_report("\n");
+
+ print_indent(4);
+ output_report("Average Throughput: %6.2f MB/s", MB_PER_SEC(data_size, total_mm.sum / total_mm.num));
+ if (opts->print_times)
+ output_report(" (%7.3f s)\n", (total_mm.sum / total_mm.num));
+ else
+ output_report("\n");
+
+ print_indent(4);
+ output_report("Minimum Throughput: %6.2f MB/s", MB_PER_SEC(data_size, total_mm.max));
+ if (opts->print_times)
+ output_report(" (%7.3f s)\n", total_mm.max);
+ else
+ output_report("\n");
+}
+
+static void
+output_times(const struct options *opts, const char *name, minmax *table, int table_size)
+{
+ minmax total_mm;
+
+ total_mm = accumulate_minmax_stuff(table, table_size);
+
+ print_indent(3);
+ output_report("%s (%d iteration(s)):\n", name, table_size);
+
+ /* Note: The maximum throughput uses the minimum amount of time & vice versa */
+
+ print_indent(4);
+ output_report("Minimum Accumulated Time using %d file(s): %7.5f s\n", opts->num_files, (total_mm.min));
+
+ print_indent(4);
+ output_report("Average Accumulated Time using %d file(s): %7.5f s\n", opts->num_files,
+ (total_mm.sum / total_mm.num));
+
+ print_indent(4);
+ output_report("Maximum Accumulated Time using %d file(s): %7.5f s\n", opts->num_files, (total_mm.max));
+}
+
+/*
+ * Function: output_report
+ * Purpose: Print a line of the report. Only do so if I'm the 0 process.
+ * Return: Nothing
+ * Programmer: Bill Wendling, 19. December 2001
+ * Modifications:
+ */
+static void
+output_report(const char *fmt, ...)
+{
+ int myrank;
+
+ MPI_Comm_rank(pio_comm_g, &myrank);
+
+ if (myrank == 0) {
+ va_list ap;
+
+ HDva_start(ap, fmt);
+ HDvfprintf(output, fmt, ap);
+ HDva_end(ap);
+ }
+}
+
+/*
+ * Function: print_indent
+ * Purpose: Print spaces to indent a new line of text for pretty printing
+ * things.
+ * Return: Nothing
+ * Programmer: Bill Wendling, 29. October 2001
+ * Modifications:
+ */
+static void
+print_indent(register int indent)
+{
+ int myrank;
+
+ MPI_Comm_rank(pio_comm_g, &myrank);
+
+ if (myrank == 0) {
+ indent *= TAB_SPACE;
+
+ for (; indent > 0; --indent)
+ HDfputc(' ', output);
+ }
+}
+
+static void
+recover_size_and_print(long long val, const char *end)
+{
+ if (val >= ONE_KB && (val % ONE_KB) == 0) {
+ if (val >= ONE_MB && (val % ONE_MB) == 0) {
+ if (val >= ONE_GB && (val % ONE_GB) == 0)
+ HDfprintf(output,
+ "%" H5_PRINTF_LL_WIDTH "d"
+ "GB%s",
+ val / ONE_GB, end);
+ else
+ HDfprintf(output,
+ "%" H5_PRINTF_LL_WIDTH "d"
+ "MB%s",
+ val / ONE_MB, end);
+ }
+ else {
+ HDfprintf(output,
+ "%" H5_PRINTF_LL_WIDTH "d"
+ "KB%s",
+ val / ONE_KB, end);
+ }
+ }
+ else {
+ HDfprintf(output,
+ "%" H5_PRINTF_LL_WIDTH "d"
+ "%s",
+ val, end);
+ }
+}
+
+static void
+print_io_api(long io_types)
+{
+ if (io_types & PIO_POSIX)
+ HDfprintf(output, "posix ");
+ if (io_types & PIO_MPI)
+ HDfprintf(output, "mpiio ");
+ if (io_types & PIO_HDF5)
+ HDfprintf(output, "phdf5 ");
+ HDfprintf(output, "\n");
+}
+
+static void
+report_parameters(struct options *opts)
+{
+ int rank = comm_world_rank_g;
+
+ print_version("HDF5 Library"); /* print library version */
+ HDfprintf(output, "rank %d: ==== Parameters ====\n", rank);
+
+ HDfprintf(output, "rank %d: IO API=", rank);
+ print_io_api(opts->io_types);
+
+ HDfprintf(output, "rank %d: Number of files=%ld\n", rank, opts->num_files);
+ HDfprintf(output, "rank %d: Number of datasets=%ld\n", rank, opts->num_dsets);
+ HDfprintf(output, "rank %d: Number of iterations=%d\n", rank, opts->num_iters);
+ HDfprintf(output, "rank %d: Number of processes=%d:%d\n", rank, opts->min_num_procs, opts->max_num_procs);
+
+ if (opts->dim2d) {
+ HDfprintf(output, "rank %d: Number of bytes per process per dataset=", rank);
+ recover_size_and_print((long long)(opts->num_bpp * opts->num_bpp * opts->min_num_procs), ":");
+ recover_size_and_print((long long)(opts->num_bpp * opts->num_bpp * opts->max_num_procs), "\n");
+
+ HDfprintf(output, "rank %d: Size of dataset(s)=", rank);
+ recover_size_and_print((long long)(opts->num_bpp * opts->min_num_procs), "x");
+ recover_size_and_print((long long)(opts->num_bpp * opts->min_num_procs), ":");
+ recover_size_and_print((long long)(opts->num_bpp * opts->max_num_procs), "x");
+ recover_size_and_print((long long)(opts->num_bpp * opts->max_num_procs), "\n");
+
+ HDfprintf(output, "rank %d: File size=", rank);
+ recover_size_and_print((long long)(squareo(opts->num_bpp * opts->min_num_procs) * opts->num_dsets),
+ ":");
+ recover_size_and_print((long long)(squareo(opts->num_bpp * opts->max_num_procs) * opts->num_dsets),
+ "\n");
+
+ HDfprintf(output, "rank %d: Transfer buffer size=", rank);
+ if (opts->interleaved) {
+ recover_size_and_print((long long)opts->min_xfer_size, "x");
+ recover_size_and_print((long long)opts->blk_size, ":");
+ recover_size_and_print((long long)opts->max_xfer_size, "x");
+ recover_size_and_print((long long)opts->blk_size, "\n");
+ }
+ else {
+ recover_size_and_print((long long)opts->blk_size, "x");
+ recover_size_and_print((long long)opts->min_xfer_size, ":");
+ recover_size_and_print((long long)opts->blk_size, "x");
+ recover_size_and_print((long long)opts->max_xfer_size, "\n");
+ }
+ HDfprintf(output, "rank %d: Block size=", rank);
+ recover_size_and_print((long long)opts->blk_size, "x");
+ recover_size_and_print((long long)opts->blk_size, "\n");
+ }
+ else {
+ HDfprintf(output, "rank %d: Number of bytes per process per dataset=", rank);
+ recover_size_and_print((long long)opts->num_bpp, "\n");
+
+ HDfprintf(output, "rank %d: Size of dataset(s)=", rank);
+ recover_size_and_print((long long)(opts->num_bpp * opts->min_num_procs), ":");
+ recover_size_and_print((long long)(opts->num_bpp * opts->max_num_procs), "\n");
+
+ HDfprintf(output, "rank %d: File size=", rank);
+ recover_size_and_print((long long)(opts->num_bpp * opts->min_num_procs * opts->num_dsets), ":");
+ recover_size_and_print((long long)(opts->num_bpp * opts->max_num_procs * opts->num_dsets), "\n");
+
+ HDfprintf(output, "rank %d: Transfer buffer size=", rank);
+ recover_size_and_print((long long)opts->min_xfer_size, ":");
+ recover_size_and_print((long long)opts->max_xfer_size, "\n");
+ HDfprintf(output, "rank %d: Block size=", rank);
+ recover_size_and_print((long long)opts->blk_size, "\n");
+ }
+
+ HDfprintf(output, "rank %d: Block Pattern in Dataset=", rank);
+ if (opts->interleaved)
+ HDfprintf(output, "Interleaved\n");
+ else
+ HDfprintf(output, "Contiguous\n");
+
+ HDfprintf(output, "rank %d: I/O Method for MPI and HDF5=", rank);
+ if (opts->collective)
+ HDfprintf(output, "Collective\n");
+ else
+ HDfprintf(output, "Independent\n");
+
+ HDfprintf(output, "rank %d: Geometry=", rank);
+ if (opts->dim2d)
+ HDfprintf(output, "2D\n");
+ else
+ HDfprintf(output, "1D\n");
+
+ HDfprintf(output, "rank %d: VFL used for HDF5 I/O=%s\n", rank, "MPI-IO driver");
+
+ HDfprintf(output, "rank %d: Data storage method in HDF5=", rank);
+ if (opts->h5_use_chunks)
+ HDfprintf(output, "Chunked\n");
+ else
+ HDfprintf(output, "Contiguous\n");
+
+ {
+ char *prefix = HDgetenv("HDF5_PARAPREFIX");
+
+ HDfprintf(output, "rank %d: Env HDF5_PARAPREFIX=%s\n", rank, (prefix ? prefix : "not set"));
+ }
+
+ HDfprintf(output, "rank %d: ", rank);
+ h5_dump_info_object(h5_io_info_g);
+
+ HDfprintf(output, "rank %d: ==== End of Parameters ====\n", rank);
+ HDfprintf(output, "\n");
+}
+
+/*
+ * Function: parse_command_line
+ * Purpose: Parse the command line options and return a STRUCT OPTIONS
+ * structure which will need to be freed by the calling function.
+ * Return: Pointer to an OPTIONS structure
+ * Programmer: Bill Wendling, 31. October 2001
+ * Modifications:
+ * Added 2D testing (Christian Chilan, 10. August 2005)
+ */
+static struct options *
+parse_command_line(int argc, char *argv[])
+{
+ register int opt;
+ struct options *cl_opts;
+
+ cl_opts = (struct options *)malloc(sizeof(struct options));
+
+ cl_opts->output_file = NULL;
+ cl_opts->io_types = 0; /* will set default after parsing options */
+ cl_opts->num_dsets = 1;
+ cl_opts->num_files = 1;
+ cl_opts->num_bpp = 0;
+ cl_opts->num_iters = 1;
+ cl_opts->max_num_procs = comm_world_nprocs_g;
+ cl_opts->min_num_procs = 1;
+ cl_opts->max_xfer_size = 0;
+ cl_opts->min_xfer_size = 0;
+ cl_opts->blk_size = 0;
+ cl_opts->interleaved = 0; /* Default to contiguous blocks in dataset */
+ cl_opts->collective = 0; /* Default to independent I/O access */
+ cl_opts->dim2d = 0; /* Default to 1D */
+ cl_opts->print_times = FALSE; /* Printing times is off by default */
+ cl_opts->print_raw = FALSE; /* Printing raw data throughput is off by default */
+ cl_opts->h5_alignment = 1; /* No alignment for HDF5 objects by default */
+ cl_opts->h5_threshold = 1; /* No threshold for aligning HDF5 objects by default */
+ cl_opts->h5_use_chunks = FALSE; /* Don't chunk the HDF5 dataset by default */
+ cl_opts->h5_write_only = FALSE; /* Do both read and write by default */
+ cl_opts->verify = FALSE; /* No Verify data correctness by default */
+
+ while ((opt = H5_get_option(argc, (const char **)argv, s_opts, l_opts)) != EOF) {
+ switch ((char)opt) {
+ case 'a':
+ cl_opts->h5_alignment = parse_size_directive(H5_optarg);
+ break;
+ case 'A': {
+ const char *end = H5_optarg;
+
+ while (end && *end != '\0') {
+ char buf[10];
+ int i;
+
+ HDmemset(buf, '\0', sizeof(buf));
+
+ for (i = 0; *end != '\0' && *end != ','; ++end)
+ if (isalnum(*end) && i < 10)
+ buf[i++] = *end;
+
+ if (!HDstrcasecmp(buf, "phdf5")) {
+ cl_opts->io_types |= PIO_HDF5;
+ }
+ else if (!HDstrcasecmp(buf, "mpiio")) {
+ cl_opts->io_types |= PIO_MPI;
+ }
+ else if (!HDstrcasecmp(buf, "posix")) {
+ cl_opts->io_types |= PIO_POSIX;
+ }
+ else {
+ HDfprintf(stderr, "pio_perf: invalid --api option %s\n", buf);
+ HDexit(EXIT_FAILURE);
+ }
+
+ if (*end == '\0')
+ break;
+
+ end++;
+ }
+ }
+
+ break;
+#if 0
+ case 'b':
+ /* the future "binary" option */
+ break;
+#endif /* 0 */
+ case 'B':
+ cl_opts->blk_size = (size_t)parse_size_directive(H5_optarg);
+ break;
+ case 'c':
+ /* Turn on chunked HDF5 dataset creation */
+ cl_opts->h5_use_chunks = TRUE;
+ break;
+ case 'C':
+ cl_opts->collective = 1;
+ break;
+ case 'd':
+ cl_opts->num_dsets = atoi(H5_optarg);
+ break;
+ case 'D': {
+ const char *end = H5_optarg;
+
+ while (end && *end != '\0') {
+ char buf[10];
+ int i;
+
+ HDmemset(buf, '\0', sizeof(buf));
+
+ for (i = 0; *end != '\0' && *end != ','; ++end)
+ if (HDisalnum(*end) && i < 10)
+ buf[i++] = *end;
+
+ if (HDstrlen(buf) > 1 || HDisdigit(buf[0])) {
+ size_t j;
+
+ for (j = 0; j < 10 && buf[j] != '\0'; ++j)
+ if (!isdigit(buf[j])) {
+ HDfprintf(stderr, "pio_perf: invalid --debug option %s\n", buf);
+ HDexit(EXIT_FAILURE);
+ }
+
+ pio_debug_level = atoi(buf);
+
+ if (pio_debug_level > 4)
+ pio_debug_level = 4;
+ else if (pio_debug_level < 0)
+ pio_debug_level = 0;
+ }
+ else {
+ switch (*buf) {
+ case 'r':
+ /* Turn on raw data throughput info */
+ cl_opts->print_raw = TRUE;
+ break;
+ case 't':
+ /* Turn on time printing */
+ cl_opts->print_times = TRUE;
+ break;
+ case 'v':
+ /* Turn on verify data correctness*/
+ cl_opts->verify = TRUE;
+ break;
+ default:
+ HDfprintf(stderr, "pio_perf: invalid --debug option %s\n", buf);
+ HDexit(EXIT_FAILURE);
+ }
+ }
+
+ if (*end == '\0')
+ break;
+
+ end++;
+ }
+ }
+
+ break;
+ case 'e':
+ cl_opts->num_bpp = parse_size_directive(H5_optarg);
+ break;
+ case 'F':
+ cl_opts->num_files = HDatoi(H5_optarg);
+ break;
+ case 'g':
+ cl_opts->dim2d = 1;
+ break;
+ case 'i':
+ cl_opts->num_iters = HDatoi(H5_optarg);
+ break;
+ case 'I':
+ cl_opts->interleaved = 1;
+ break;
+ case 'o':
+ cl_opts->output_file = H5_optarg;
+ break;
+ case 'p':
+ cl_opts->min_num_procs = HDatoi(H5_optarg);
+ break;
+ case 'P':
+ cl_opts->max_num_procs = HDatoi(H5_optarg);
+ break;
+ case 'T':
+ cl_opts->h5_threshold = parse_size_directive(H5_optarg);
+ break;
+ case 'w':
+ cl_opts->h5_write_only = TRUE;
+ break;
+ case 'x':
+ cl_opts->min_xfer_size = (size_t)parse_size_directive(H5_optarg);
+ break;
+ case 'X':
+ cl_opts->max_xfer_size = (size_t)parse_size_directive(H5_optarg);
+ break;
+ case 'h':
+ case '?':
+ default:
+ usage(progname);
+ HDfree(cl_opts);
+ return NULL;
+ }
+ }
+
+ if (cl_opts->num_bpp == 0) {
+ if (cl_opts->dim2d == 0)
+ cl_opts->num_bpp = 256 * ONE_KB;
+ else
+ cl_opts->num_bpp = 8 * ONE_KB;
+ }
+
+ if (cl_opts->max_xfer_size == 0)
+ cl_opts->max_xfer_size = (size_t)cl_opts->num_bpp;
+
+ if (cl_opts->min_xfer_size == 0)
+ cl_opts->min_xfer_size = (size_t)(cl_opts->num_bpp) / 2;
+
+ if (cl_opts->blk_size == 0)
+ cl_opts->blk_size = (size_t)(cl_opts->num_bpp) / 2;
+
+ /* set default if none specified yet */
+ if (!cl_opts->io_types)
+ cl_opts->io_types = PIO_HDF5 | PIO_MPI | PIO_POSIX; /* run all API */
+
+ /* verify parameters sanity. Adjust if needed. */
+ /* cap xfer_size with bytes per process */
+ if (!cl_opts->dim2d) {
+ if (cl_opts->min_xfer_size > (size_t)cl_opts->num_bpp)
+ cl_opts->min_xfer_size = (size_t)cl_opts->num_bpp;
+ if (cl_opts->max_xfer_size > (size_t)cl_opts->num_bpp)
+ cl_opts->max_xfer_size = (size_t)cl_opts->num_bpp;
+ }
+ if (cl_opts->min_xfer_size > cl_opts->max_xfer_size)
+ cl_opts->min_xfer_size = cl_opts->max_xfer_size;
+ if (cl_opts->blk_size > (size_t)cl_opts->num_bpp)
+ cl_opts->blk_size = (size_t)cl_opts->num_bpp;
+ /* check range of number of processes */
+ if (cl_opts->min_num_procs <= 0)
+ cl_opts->min_num_procs = 1;
+ if (cl_opts->max_num_procs <= 0)
+ cl_opts->max_num_procs = 1;
+ if (cl_opts->min_num_procs > cl_opts->max_num_procs)
+ cl_opts->min_num_procs = cl_opts->max_num_procs;
+ /* check iteration */
+ if (cl_opts->num_iters <= 0)
+ cl_opts->num_iters = 1;
+
+ return cl_opts;
+}
+
+/*
+ * Function: parse_size_directive
+ * Purpose: Parse the size directive passed on the commandline. The size
+ * directive is an integer followed by a size indicator:
+ *
+ * K, k - Kilobyte
+ * M, m - Megabyte
+ * G, g - Gigabyte
+ *
+ * Return: The size as a off_t because this is related to file size.
+ * If an unknown size indicator is used, then the program will
+ * exit with EXIT_FAILURE as the return value.
+ * Programmer: Bill Wendling, 18. December 2001
+ * Modifications:
+ */
+static off_t
+parse_size_directive(const char *size)
+{
+ off_t s;
+ char *endptr;
+
+ s = HDstrtol(size, &endptr, 10);
+
+ if (endptr && *endptr) {
+ while (*endptr != '\0' && (*endptr == ' ' || *endptr == '\t'))
+ ++endptr;
+
+ switch (*endptr) {
+ case 'K':
+ case 'k':
+ s *= ONE_KB;
+ break;
+ case 'M':
+ case 'm':
+ s *= ONE_MB;
+ break;
+ case 'G':
+ case 'g':
+ s *= ONE_GB;
+ break;
+ default:
+ HDfprintf(stderr, "Illegal size specifier '%c'\n", *endptr);
+ HDexit(EXIT_FAILURE);
+ }
+ }
+
+ return s;
+}
+
+/*
+ * Function: usage
+ * Purpose: Print a usage message and then exit.
+ * Return: Nothing
+ * Programmer: Bill Wendling, 31. October 2001
+ * Modifications:
+ * Added 2D testing (Christian Chilan, 10. August 2005)
+ */
+static void
+usage(const char *prog)
+{
+ int myrank;
+
+ MPI_Comm_rank(pio_comm_g, &myrank);
+
+ if (myrank == 0) {
+ print_version(prog);
+ HDprintf("usage: %s [OPTIONS]\n", prog);
+ HDprintf(" OPTIONS\n");
+ HDprintf(" -h, --help Print a usage message and exit\n");
+ HDprintf(" -a S, --align=S Alignment of objects in HDF5 file [default: 1]\n");
+ HDprintf(" -A AL, --api=AL Which APIs to test [default: all of them]\n");
+#if 0
+ HDprintf(" -b, --binary The elusive binary option\n");
+#endif /* 0 */
+ HDprintf(" -B S, --block-size=S Block size within transfer buffer\n");
+ HDprintf(" (see below for description)\n");
+ HDprintf(" [default: half the number of bytes per process\n");
+ HDprintf(" per dataset]\n");
+ HDprintf(" -c, --chunk Create HDF5 datasets using chunked storage\n");
+ HDprintf(" [default: contiguous storage]\n");
+ HDprintf(" -C, --collective Use collective I/O for MPI and HDF5 APIs\n");
+ HDprintf(" [default: independent I/O)\n");
+ HDprintf(" -d N, --num-dsets=N Number of datasets per file [default: 1]\n");
+ HDprintf(" -D DL, --debug=DL Indicate the debugging level\n");
+ HDprintf(" [default: no debugging]\n");
+ HDprintf(" -e S, --num-bytes=S Number of bytes per process per dataset\n");
+ HDprintf(" (see below for description)\n");
+ HDprintf(" [default: 256K for 1D, 8K for 2D]\n");
+ HDprintf(" -F N, --num-files=N Number of files [default: 1]\n");
+ HDprintf(" -g, --geometry Use 2D geometry [default: 1D geometry]\n");
+ HDprintf(" -i N, --num-iterations=N Number of iterations to perform [default: 1]\n");
+ HDprintf(" -I, --interleaved Interleaved access pattern\n");
+ HDprintf(" (see below for example)\n");
+ HDprintf(" [default: Contiguous access pattern]\n");
+ HDprintf(" -o F, --output=F Output raw data into file F [default: none]\n");
+ HDprintf(" -p N, --min-num-processes=N Minimum number of processes to use [default: 1]\n");
+ HDprintf(" -P N, --max-num-processes=N Maximum number of processes to use\n");
+ HDprintf(" [default: all MPI_COMM_WORLD processes ]\n");
+ HDprintf(" -T S, --threshold=S Threshold for alignment of objects in HDF5 file\n");
+ HDprintf(" [default: 1]\n");
+ HDprintf(" -w, --write-only Perform write tests not the read tests\n");
+ HDprintf(" -x S, --min-xfer-size=S Minimum transfer buffer size\n");
+ HDprintf(" (see below for description)\n");
+ HDprintf(" [default: half the number of bytes per process\n");
+ HDprintf(" per dataset]\n");
+ HDprintf(" -X S, --max-xfer-size=S Maximum transfer buffer size\n");
+ HDprintf(" [default: the number of bytes per process per\n");
+ HDprintf(" dataset]\n");
+ HDprintf("\n");
+ HDprintf(" F - is a filename.\n");
+ HDprintf(" N - is an integer >=0.\n");
+ HDprintf(" S - is a size specifier, an integer >=0 followed by a size indicator:\n");
+ HDprintf(" K - Kilobyte (%d)\n", ONE_KB);
+ HDprintf(" M - Megabyte (%d)\n", ONE_MB);
+ HDprintf(" G - Gigabyte (%d)\n", ONE_GB);
+ HDprintf("\n");
+ HDprintf(" Example: '37M' is 37 megabytes or %d bytes\n", 37 * ONE_MB);
+ HDprintf("\n");
+ HDprintf(" AL - is an API list. Valid values are:\n");
+ HDprintf(" phdf5 - Parallel HDF5\n");
+ HDprintf(" mpiio - MPI-I/O\n");
+ HDprintf(" posix - POSIX\n");
+ HDprintf("\n");
+ HDprintf(" Example: --api=mpiio,phdf5\n");
+ HDprintf("\n");
+ HDprintf(" Dataset size:\n");
+ HDprintf(" Depending on the selected geometry, each test dataset is either a linear\n");
+ HDprintf(" array of size bytes-per-process * num-processes, or a square array of size\n");
+ HDprintf(" (bytes-per-process * num-processes) x (bytes-per-process * num-processes).\n");
+ HDprintf("\n");
+ HDprintf(" Block size vs. Transfer buffer size:\n");
+ HDprintf(" buffer-size controls the size of the memory buffer, which is broken into\n");
+ HDprintf(" blocks and written to the file. Depending on the selected geometry, each\n");
+ HDprintf(" block can be a linear array of size block-size or a square array of size\n");
+ HDprintf(" block-size x block-size. The arrangement in which blocks are written is\n");
+ HDprintf(" determined by the access pattern.\n");
+ HDprintf("\n");
+ HDprintf(" In 1D geometry, the transfer buffer is a linear array of size buffer-size.\n");
+ HDprintf(" In 2D geometry, it is a rectangular array of size block-size x buffer-size\n");
+ HDprintf(" or buffer-size x block-size if interleaved pattern is selected.\n");
+ HDprintf("\n");
+ HDprintf(" Interleaved and Contiguous patterns in 1D geometry:\n");
+ HDprintf(" When contiguous access pattern is chosen, the dataset is evenly divided\n");
+ HDprintf(" into num-processes regions and each process writes data to its own region.\n");
+ HDprintf(" When interleaved blocks are written to a dataset, space for the first\n");
+ HDprintf(" block of the first process is allocated in the dataset, then space is\n");
+ HDprintf(" allocated for the first block of the second process, etc. until space is\n");
+ HDprintf(" allocated for the first block of each process, then space is allocated for\n");
+ HDprintf(" the second block of the first process, the second block of the second\n");
+ HDprintf(" process, etc.\n");
+ HDprintf("\n");
+ HDprintf(" For example, with a 3 process run, 512KB bytes-per-process, 256KB transfer\n");
+ HDprintf(" buffer size, and 64KB block size, each process must issue 2 transfer\n");
+ HDprintf(" requests to complete access to the dataset.\n");
+ HDprintf(" Contiguous blocks of the first transfer request are written like so:\n");
+ HDprintf(" 1111----2222----3333----\n");
+ HDprintf(" Interleaved blocks of the first transfer request are written like so:\n");
+ HDprintf(" 123123123123------------\n");
+ HDprintf(" The actual number of I/O operations involved in a transfer request\n");
+ HDprintf(" depends on the access pattern and communication mode.\n");
+ HDprintf(" When using independent I/O with interleaved pattern, each process\n");
+ HDprintf(" performs 4 small non-contiguous I/O operations per transfer request.\n");
+ HDprintf(" If collective I/O is turned on, the combined content of the buffers of\n");
+ HDprintf(" the 3 processes will be written using one collective I/O operation\n");
+ HDprintf(" per transfer request.\n");
+ HDprintf("\n");
+ HDprintf(" For information about access patterns in 2D geometry, please refer to the\n");
+ HDprintf(" HDF5 Reference Manual.\n");
+ HDprintf("\n");
+ HDprintf(" DL - is a list of debugging flags. Valid values are:\n");
+ HDprintf(" 1 - Minimal\n");
+ HDprintf(" 2 - Not quite everything\n");
+ HDprintf(" 3 - Everything\n");
+ HDprintf(" 4 - The kitchen sink\n");
+ HDprintf(" r - Raw data I/O throughput information\n");
+ HDprintf(" t - Times as well as throughputs\n");
+ HDprintf(" v - Verify data correctness\n");
+ HDprintf("\n");
+ HDprintf(" Example: --debug=2,r,t\n");
+ HDprintf("\n");
+ HDprintf(" Environment variables:\n");
+ HDprintf(" HDF5_NOCLEANUP Do not remove data files if set [default remove]\n");
+ HDprintf(" HDF5_MPI_INFO MPI INFO object key=value separated by ;\n");
+ HDprintf(" HDF5_PARAPREFIX Paralllel data files prefix\n");
+ fflush(stdout);
+ } /* end if */
+} /* end usage() */
+
+#else /* H5_HAVE_PARALLEL */
+
+/*
+ * Function: main
+ * Purpose: Dummy main() function for if HDF5 was configured without
+ * parallel stuff.
+ * Return: EXIT_SUCCESS
+ * Programmer: Bill Wendling, 14. November 2001
+ */
+int
+main(void)
+{
+ HDprintf("No parallel IO performance because parallel is not configured\n");
+ return EXIT_SUCCESS;
+} /* end main */
+
+#endif /* !H5_HAVE_PARALLEL */
diff --git a/tools/src/h5perf/pio_perf.h b/tools/src/h5perf/pio_perf.h
new file mode 100644
index 0000000..8924c20
--- /dev/null
+++ b/tools/src/h5perf/pio_perf.h
@@ -0,0 +1,109 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the COPYING file, which can be found at the root of the source code *
+ * distribution tree, or in https://www.hdfgroup.org/licenses. *
+ * If you do not have access to either file, you may request a copy from *
+ * help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#ifndef PIO_PERF_H
+#define PIO_PERF_H
+
+#ifndef STANDALONE
+#include "io_timer.h"
+#include "H5private.h"
+#include "h5tools.h"
+#include "h5tools_utils.h"
+#else
+#include "io_timer.h"
+#include "pio_standalone.h"
+#endif
+
+#ifdef H5_HAVE_PARALLEL
+extern MPI_Info h5_io_info_g; /* MPI INFO object for IO */
+#endif
+
+#ifdef H5_HAVE_PARALLEL
+int h5_set_info_object(void);
+void h5_dump_info_object(MPI_Info info);
+#endif
+
+/* setup the dataset no fill option if this is v1.5 or more */
+#if H5_VERS_MAJOR > 1 || H5_VERS_MINOR > 4
+#define H5_HAVE_NOFILL 1
+#endif
+
+typedef enum iotype_ {
+ POSIXIO,
+ MPIO,
+ PHDF5
+ /*NUM_TYPES*/
+} iotype;
+
+typedef struct parameters_ {
+ iotype io_type; /* The type of IO test to perform */
+ int num_procs; /* Maximum number of processes to use */
+ long num_files; /* Number of files to create */
+ long num_dsets; /* Number of datasets to create */
+ off_t num_bytes; /* Number of bytes in each dset */
+ int num_iters; /* Number of times to loop doing the IO */
+ size_t buf_size; /* Buffer size */
+ size_t blk_size; /* Block size */
+ unsigned interleaved; /* Interleaved vs. contiguous blocks */
+ unsigned collective; /* Collective vs. independent I/O */
+ unsigned dim2d; /* 1D vs. 2D */
+ hsize_t h5_align; /* HDF5 object alignment */
+ hsize_t h5_thresh; /* HDF5 object alignment threshold */
+ int h5_use_chunks; /* Make HDF5 dataset chunked */
+ int h5_write_only; /* Perform the write tests only */
+ int verify; /* Verify data correctness */
+} parameters;
+
+typedef struct results_ {
+ herr_t ret_code;
+ io_time_t *timers;
+} results;
+
+#ifndef SUCCESS
+#define SUCCESS 0
+#endif /* !SUCCESS */
+
+#ifndef FAIL
+#define FAIL -1
+#endif /* !FAIL */
+
+extern FILE * output; /* output file */
+extern io_time_t *timer_g; /* timer: global for stub functions */
+extern int comm_world_rank_g; /* my rank in MPI_COMM_RANK */
+extern int comm_world_nprocs_g; /* num. of processes of MPI_COMM_WORLD */
+extern MPI_Comm pio_comm_g; /* Communicator to run the PIO */
+extern int pio_mpi_rank_g; /* MPI rank of pio_comm_g */
+extern int pio_mpi_nprocs_g; /* number of processes of pio_comm_g */
+extern int pio_debug_level; /* The debug level:
+ * 0 - Off
+ * 1 - Minimal
+ * 2 - Some more
+ * 3 - Maximal
+ * 4 - Even More Debugging (timer stuff)
+ */
+
+#define HDprint_rank(f) /* print rank in MPI_COMM_WORLD */ HDfprintf(f, "%d: ", comm_world_rank_g);
+#define HDprint_size(f) /* print size of MPI_COMM_WORLD */ HDfprintf(f, "%d", comm_world_nprocs_g);
+#define HDprint_rank_size(f) /* print rank/size of MPI_COMM_WORLD */ \
+ HDfprintf(f, "%d/%d: ", comm_world_rank_g, comm_world_nprocs_g);
+
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+extern results do_pio(parameters param);
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+
+#endif /* PIO_PERF_H */
diff --git a/tools/src/h5perf/sio_engine.c b/tools/src/h5perf/sio_engine.c
new file mode 100644
index 0000000..dc2c68e
--- /dev/null
+++ b/tools/src/h5perf/sio_engine.c
@@ -0,0 +1,1330 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the COPYING file, which can be found at the root of the source code *
+ * distribution tree, or in https://www.hdfgroup.org/licenses. *
+ * If you do not have access to either file, you may request a copy from *
+ * help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * Author: Christian Chilan, April 2008
+ */
+
+#include "hdf5.h"
+
+#ifdef H5_STDC_HEADERS
+#include <errno.h>
+#include <fcntl.h>
+#include <stdio.h>
+#include <stdlib.h>
+#endif
+
+#ifdef H5_HAVE_UNISTD_H
+#include <sys/types.h>
+#include <unistd.h>
+#endif
+
+#ifdef H5_HAVE_SYS_STAT_H
+#include <sys/stat.h>
+#endif
+
+#include "sio_perf.h"
+
+/* Macro definitions */
+
+/* sizes of various items. these sizes won't change during program execution */
+#define ELMT_H5_TYPE H5T_NATIVE_UCHAR
+
+#define GOTOERROR(errcode) \
+ { \
+ ret_code = errcode; \
+ goto done; \
+ }
+#define ERRMSG(mesg) \
+ { \
+ HDfprintf(stderr, "*** Assertion failed (%s) at line %4d in %s\n", mesg, (int)__LINE__, __FILE__); \
+ }
+
+/* verify: if val is false (0), print mesg. */
+#define VRFY(val, mesg) \
+ do { \
+ if (!val) { \
+ ERRMSG(mesg); \
+ GOTOERROR(FAIL); \
+ } \
+ } while (0)
+
+/* POSIX I/O macros */
+#ifdef H5_HAVE_WIN32_API
+/* Can't link against the library, so this test will use the older, non-Unicode
+ * _open() call on Windows.
+ */
+#define HDopen(S, F, ...) _open(S, F | _O_BINARY, __VA_ARGS__)
+#endif /* H5_HAVE_WIN32_API */
+#define POSIXCREATE(fn) HDopen(fn, O_CREAT | O_TRUNC | O_RDWR, 0600)
+#define POSIXOPEN(fn, F) HDopen(fn, F, 0600)
+#define POSIXCLOSE(F) HDclose(F)
+#define POSIXSEEK(F, L) HDlseek(F, L, SEEK_SET)
+#define POSIXWRITE(F, B, S) HDwrite(F, B, S)
+#define POSIXREAD(F, B, S) HDread(F, B, S)
+
+enum { SIO_CREATE = 1, SIO_WRITE = 2, SIO_READ = 4 };
+
+/* Global variables */
+static int clean_file_g = -1; /*whether to cleanup temporary test */
+/*files. -1 is not defined; */
+/*0 is no cleanup; 1 is do cleanup */
+
+/* the different types of file descriptors we can expect */
+typedef union {
+ int posixfd; /* POSIX file handle*/
+ hid_t h5fd; /* HDF5 file */
+} file_descr;
+
+/* local functions */
+static char * sio_create_filename(iotype iot, const char *base_name, char *fullname, size_t size,
+ parameters *param);
+static herr_t do_write(results *res, file_descr *fd, parameters *parms, void *buffer);
+static herr_t do_read(results *res, file_descr *fd, parameters *parms, void *buffer);
+static herr_t dset_write(int local_dim, file_descr *fd, parameters *parms, void *buffer);
+static herr_t posix_buffer_write(int local_dim, file_descr *fd, parameters *parms, void *buffer);
+static herr_t dset_read(int localrank, file_descr *fd, parameters *parms, void *buffer, const char *buffer2);
+static herr_t posix_buffer_read(int local_dim, file_descr *fd, parameters *parms, void *buffer);
+static herr_t do_fopen(parameters *param, char *fname, file_descr *fd /*out*/, int flags);
+hid_t set_vfd(parameters *param);
+static herr_t do_fclose(iotype iot, file_descr *fd);
+static void do_cleanupfile(iotype iot, char *fname);
+
+/* global variables */
+static HDoff_t offset[MAX_DIMS]; /* dataset size in bytes */
+static size_t buf_offset[MAX_DIMS]; /* dataset size in bytes */
+static int order[MAX_DIMS]; /* dimension access order */
+static size_t linear_buf_size; /* linear buffer size */
+static int cont_dim; /* lowest dimension for contiguous POSIX
+ access */
+static size_t cont_size; /* size of contiguous POSIX access */
+static hid_t fapl; /* file access list */
+static unsigned char *buf_p; /* buffer pointer */
+static const char * multi_letters = "msbrglo"; /* string for multi driver */
+
+/* HDF5 global variables */
+static hsize_t h5count[MAX_DIMS]; /*selection count */
+static hssize_t h5offset[MAX_DIMS]; /* Selection offset within dataspace */
+static hid_t h5dset_space_id = H5I_INVALID_HID; /*dataset space ID */
+static hid_t h5mem_space_id = H5I_INVALID_HID; /*memory dataspace ID */
+static hid_t h5ds_id = H5I_INVALID_HID; /*dataset handle */
+static hid_t h5dcpl = H5I_INVALID_HID; /* Dataset creation property list */
+static hid_t h5dxpl = H5I_INVALID_HID; /* Dataset transfer property list */
+
+/*
+ * Function: do_sio
+ * Purpose: SIO Engine where IO are executed.
+ * Return: results
+ * Programmer: Christian Chilan, April, 2008
+ * Modifications:
+ */
+void
+do_sio(parameters param, results *res)
+{
+ char * buffer = NULL; /*data buffer pointer */
+ size_t buf_size[MAX_DIMS]; /* general buffer size in bytes */
+ file_descr fd; /* file handles */
+ iotype iot; /* API type */
+ char base_name[256]; /* test file base name */
+ /* return codes */
+ herr_t ret_code = 0; /*return code */
+
+ char fname[FILENAME_MAX]; /* test file name */
+ int i;
+ /* HDF5 variables */
+ herr_t hrc; /*HDF5 return code */
+
+ /* Sanity check parameters */
+
+ /* IO type */
+ iot = param.io_type;
+
+ switch (iot) {
+ case POSIXIO:
+ fd.posixfd = -1;
+ res->timers = io_time_new(SYS_CLOCK);
+ break;
+ case HDF5:
+ fd.h5fd = -1;
+ res->timers = io_time_new(SYS_CLOCK);
+ break;
+ default:
+ /* unknown request */
+ HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)iot);
+ GOTOERROR(FAIL);
+ }
+
+ linear_buf_size = 1;
+
+ for (i = 0; i < param.rank; i++) {
+ buf_size[i] = param.buf_size[i];
+ order[i] = param.order[i];
+ linear_buf_size *= buf_size[i];
+ buf_offset[i] = 0;
+ offset[i] = 0;
+
+ /* Validate transfer buffer size */
+ if (param.buf_size[i] <= 0) {
+ HDfprintf(stderr, "Transfer buffer size[%d] (%zu) must be > 0\n", i, buf_size[i]);
+ GOTOERROR(FAIL);
+ }
+
+ if ((param.dset_size[i] % param.buf_size[i]) != 0) {
+ HDfprintf(stderr,
+ "Dataset size[%d] (%" H5_PRINTF_LL_WIDTH "d) must be a multiple of the "
+ "trasfer buffer size[%d] (%zu)\n",
+ param.rank, (long long)param.dset_size[i], param.rank, param.buf_size[i]);
+ GOTOERROR(FAIL);
+ }
+ }
+
+ /* Allocate transfer buffer */
+ if ((buffer = (char *)malloc(linear_buf_size)) == NULL) {
+ HDfprintf(stderr, "malloc for transfer buffer size (%zu) failed\n", linear_buf_size);
+ GOTOERROR(FAIL);
+ }
+
+ if (sio_debug_level >= 4)
+
+ /* output all of the times for all iterations */
+ HDfprintf(output, "Timer details:\n");
+
+ /*
+ * Write performance measurement
+ */
+ /* Open file for write */
+
+ HDstrcpy(base_name, "#sio_tmp");
+ sio_create_filename(iot, base_name, fname, sizeof(fname), &param);
+
+ if (sio_debug_level > 0)
+ HDfprintf(output, "data filename=%s\n", fname);
+
+ io_time_set(res->timers, HDF5_GROSS_WRITE_FIXED_DIMS, TSTART);
+ hrc = do_fopen(&param, fname, &fd, SIO_CREATE | SIO_WRITE);
+ VRFY((hrc == SUCCESS), "do_fopen failed");
+
+ io_time_set(res->timers, HDF5_FINE_WRITE_FIXED_DIMS, TSTART);
+ hrc = do_write(res, &fd, &param, buffer);
+ io_time_set(res->timers, HDF5_FINE_WRITE_FIXED_DIMS, TSTOP);
+ VRFY((hrc == SUCCESS), "do_write failed");
+
+ /* Close file for write */
+ hrc = do_fclose(iot, &fd);
+ io_time_set(res->timers, HDF5_GROSS_WRITE_FIXED_DIMS, TSTOP);
+ VRFY((hrc == SUCCESS), "do_fclose failed");
+
+ if (!param.h5_write_only) {
+ /*
+ * Read performance measurement
+ */
+
+ /* Open file for read */
+ io_time_set(res->timers, HDF5_GROSS_READ_FIXED_DIMS, TSTART);
+ hrc = do_fopen(&param, fname, &fd, SIO_READ);
+ VRFY((hrc == SUCCESS), "do_fopen failed");
+
+ io_time_set(res->timers, HDF5_FINE_READ_FIXED_DIMS, TSTART);
+ hrc = do_read(res, &fd, &param, buffer);
+ io_time_set(res->timers, HDF5_FINE_READ_FIXED_DIMS, TSTOP);
+ VRFY((hrc == SUCCESS), "do_read failed");
+
+ /* Close file for read */
+ hrc = do_fclose(iot, &fd);
+
+ io_time_set(res->timers, HDF5_GROSS_READ_FIXED_DIMS, TSTOP);
+ VRFY((hrc == SUCCESS), "do_fclose failed");
+ }
+
+ do_cleanupfile(iot, fname);
+
+done:
+ /* clean up */
+ /* release HDF5 objects */
+
+ /* close any opened files */
+ /* no remove(fname) because that should have happened normally. */
+ switch (iot) {
+ case POSIXIO:
+ if (fd.posixfd != -1)
+ hrc = do_fclose(iot, &fd);
+ break;
+ case HDF5:
+ if (fd.h5fd != -1)
+ hrc = do_fclose(iot, &fd);
+ break;
+ default:
+ /* unknown request */
+ HDassert(0 && "Unknown IO type");
+ break;
+ }
+
+ /* release generic resources */
+ if (buffer)
+ free(buffer);
+
+ res->ret_code = ret_code;
+}
+
+/*
+ * Function: sio_create_filename
+ * Purpose: Create a new filename to write to. Determine the correct
+ * suffix to append to the filename by the type of I/O we're
+ * doing. Also, place in the /tmp/{$USER,$LOGIN} directory if
+ * USER or LOGIN are specified in the environment.
+ * Return: Pointer to filename or NULL
+ * Programmer: Bill Wendling, 21. November 2001
+ * Modifications: Support for file drivers. Christian Chilan, April, 2008
+ */
+static char *
+sio_create_filename(iotype iot, const char *base_name, char *fullname, size_t size, parameters *param)
+{
+ const char *prefix, *suffix = "";
+ char * ptr, last = '\0';
+ size_t i, j;
+ vfdtype vfd;
+ vfd = param->vfd;
+
+ if (!base_name || !fullname || size < 1)
+ return NULL;
+
+ memset(fullname, 0, size);
+
+ switch (iot) {
+ case POSIXIO:
+ suffix = ".posix";
+ break;
+ case HDF5:
+ suffix = ".h5";
+ if (vfd == family)
+ suffix = "%05d.h5";
+ else if (vfd == multi)
+ suffix = NULL;
+ break;
+ default:
+ /* unknown request */
+ HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)iot);
+ HDassert(0 && "Unknown IO type");
+ break;
+ }
+
+ /* First use the environment variable and then try the constant */
+ prefix = HDgetenv("HDF5_PREFIX");
+
+#ifdef HDF5_PREFIX
+ if (!prefix)
+ prefix = HDF5_PREFIX;
+#endif /* HDF5_PREFIX */
+
+ /* Prepend the prefix value to the base name */
+ if (prefix && *prefix) {
+ /* If the prefix specifies the HDF5_PREFIX directory, then
+ * default to using the "/tmp/$USER" or "/tmp/$LOGIN"
+ * directory instead. */
+ register char *user, *login, *subdir;
+
+ user = HDgetenv("USER");
+ login = HDgetenv("LOGIN");
+ subdir = (user ? user : login);
+
+ if (subdir) {
+ for (i = 0; i < size - 1 && prefix[i]; i++)
+ fullname[i] = prefix[i];
+
+ fullname[i++] = '/';
+
+ for (j = 0; i < size && subdir[j]; i++, j++)
+ fullname[i] = subdir[j];
+ }
+ else {
+ /* We didn't append the prefix yet */
+ HDstrncpy(fullname, prefix, size);
+ fullname[size - 1] = '\0';
+ }
+
+ if ((HDstrlen(fullname) + HDstrlen(base_name) + 1) < size) {
+ /* Append the base_name with a slash first. Multiple slashes are
+ * handled below. */
+ h5_stat_t buf;
+
+ if (HDstat(fullname, &buf) < 0)
+ /* The directory doesn't exist just yet */
+ if (HDmkdir(fullname, 0755) < 0 && errno != EEXIST) {
+ /* We couldn't make the "/tmp/${USER,LOGIN}" subdirectory.
+ * Default to PREFIX's original prefix value. */
+ HDstrcpy(fullname, prefix);
+ }
+
+ HDstrcat(fullname, "/");
+ HDstrcat(fullname, base_name);
+ }
+ else {
+ /* Buffer is too small */
+ return NULL;
+ }
+ }
+ else if (strlen(base_name) >= size) {
+ /* Buffer is too small */
+ return NULL;
+ }
+ else {
+ HDstrcpy(fullname, base_name);
+ }
+
+ /* Append a suffix */
+ if (suffix) {
+ if (HDstrlen(fullname) + HDstrlen(suffix) >= size)
+ return NULL;
+
+ HDstrcat(fullname, suffix);
+ }
+
+ /* Remove any double slashes in the filename */
+ for (ptr = fullname, i = j = 0; ptr && (i < size); i++, ptr++) {
+ if (*ptr != '/' || last != '/')
+ fullname[j++] = *ptr;
+
+ last = *ptr;
+ }
+
+ return fullname;
+}
+
+/*
+ * Function: do_write
+ * Purpose: Write the required amount of data to the file.
+ * Return: SUCCESS or FAIL
+ * Programmer: Christian Chilan, April, 2008
+ * Modifications:
+ */
+static herr_t
+do_write(results *res, file_descr *fd, parameters *parms, void *buffer)
+{
+ int ret_code = SUCCESS;
+ char dname[64];
+ int i;
+ size_t u;
+ /* HDF5 variables */
+ herr_t hrc; /*HDF5 return code */
+ hsize_t h5dims[MAX_DIMS]; /*dataset dim sizes */
+ hsize_t h5chunk[MAX_DIMS]; /*dataset dim sizes */
+ hsize_t h5block[MAX_DIMS]; /*dataspace selection */
+ hsize_t h5stride[MAX_DIMS]; /*selection stride */
+ hsize_t h5start[MAX_DIMS]; /*selection start */
+ hsize_t h5maxdims[MAX_DIMS];
+ int rank; /*rank of dataset */
+
+ /* Prepare buffer for verifying data */
+ /* if (parms->verify)
+ memset(buffer,1,linear_buf_size); */
+
+ buf_p = (unsigned char *)buffer;
+
+ for (u = 0; u < linear_buf_size; u++)
+ buf_p[u] = u % 128;
+
+ rank = parms->rank;
+
+ for (i = 0; i < rank; i++)
+ h5offset[i] = offset[i] = 0;
+
+ /* I/O Access specific setup */
+ switch (parms->io_type) {
+ case POSIXIO:
+
+ /* determine lowest dimension for contiguous POSIX access */
+ cont_dim = rank;
+
+ for (i = rank - 1; i >= 0; i--) {
+ if (parms->buf_size[i] == parms->dset_size[i])
+ cont_dim = i;
+ else
+ break;
+ }
+
+ /* determine size of the contiguous POSIX access */
+ cont_size = (!cont_dim) ? 1 : parms->buf_size[cont_dim - 1];
+ for (i = cont_dim; i < rank; i++)
+ cont_size *= parms->buf_size[i];
+
+ break;
+
+ case HDF5: /* HDF5 setup */
+
+ for (i = 0; i < rank; i++) {
+ h5dims[i] = parms->dset_size[i];
+ h5start[i] = 0;
+ h5stride[i] = 1;
+ h5block[i] = 1;
+ h5count[i] = parms->buf_size[i];
+ h5chunk[i] = parms->chk_size[i];
+ h5maxdims[i] = H5S_UNLIMITED;
+ }
+
+ if (parms->h5_use_chunks && parms->h5_extendable) {
+ h5dset_space_id = H5Screate_simple(rank, h5count, h5maxdims);
+ VRFY((h5dset_space_id >= 0), "H5Screate_simple");
+ }
+ else {
+ h5dset_space_id = H5Screate_simple(rank, h5dims, NULL);
+ VRFY((h5dset_space_id >= 0), "H5Screate_simple");
+ }
+
+ hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, h5start, h5stride, h5count, h5block);
+ VRFY((hrc >= 0), "H5Sselect_hyperslab");
+
+ /* Create the memory dataspace that corresponds to the xfer buffer */
+ h5mem_space_id = H5Screate_simple(rank, h5count, NULL);
+ VRFY((h5mem_space_id >= 0), "H5Screate_simple");
+
+ /* Create the dataset transfer property list */
+ h5dxpl = H5Pcreate(H5P_DATASET_XFER);
+ if (h5dxpl < 0) {
+ HDfprintf(stderr, "HDF5 Property List Create failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ break;
+
+ default:
+ HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)parms->io_type);
+ GOTOERROR(FAIL);
+ break;
+ } /* end switch */
+
+ /* create dataset */
+ switch (parms->io_type) {
+ case POSIXIO:
+ break;
+
+ case HDF5:
+ h5dcpl = H5Pcreate(H5P_DATASET_CREATE);
+
+ if (h5dcpl < 0) {
+ HDfprintf(stderr, "HDF5 Property List Create failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ if (parms->h5_use_chunks) {
+ /* Set the chunk size to be the same as the buffer size */
+ hrc = H5Pset_chunk(h5dcpl, rank, h5chunk);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Property List Set failed\n");
+ GOTOERROR(FAIL);
+ } /* end if */
+ } /* end if */
+
+ HDsprintf(dname, "Dataset_%ld", (unsigned long)parms->num_bytes);
+ h5ds_id =
+ H5Dcreate2(fd->h5fd, dname, ELMT_H5_TYPE, h5dset_space_id, H5P_DEFAULT, h5dcpl, H5P_DEFAULT);
+
+ if (h5ds_id < 0) {
+ HDfprintf(stderr, "HDF5 Dataset Create failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ hrc = H5Pclose(h5dcpl);
+ /* verifying the close of the dcpl */
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Property List Close failed\n");
+ GOTOERROR(FAIL);
+ }
+ break;
+
+ default:
+ /* unknown request */
+ HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)parms->io_type);
+ GOTOERROR(FAIL);
+ break;
+ }
+
+ /* Start "raw data" write timer */
+ io_time_set(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, TSTART);
+
+ /* Perform write */
+ hrc = dset_write(rank - 1, fd, parms, buffer);
+
+ if (hrc < 0) {
+ HDfprintf(stderr, "Error in dataset write\n");
+ GOTOERROR(FAIL);
+ }
+
+ /* Stop "raw data" write timer */
+ io_time_set(res->timers, HDF5_RAW_WRITE_FIXED_DIMS, TSTOP);
+
+ /* Calculate write time */
+
+ /* Close dataset. Only HDF5 needs to do an explicit close. */
+ if (parms->io_type == HDF5) {
+ hrc = H5Dclose(h5ds_id);
+
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Dataset Close failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ h5ds_id = H5I_INVALID_HID;
+ } /* end if */
+
+done:
+
+ /* release HDF5 objects */
+ if (h5dset_space_id != -1) {
+ hrc = H5Sclose(h5dset_space_id);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Dataset Space Close failed\n");
+ ret_code = FAIL;
+ }
+ else {
+ h5dset_space_id = H5I_INVALID_HID;
+ }
+ }
+
+ if (h5mem_space_id != -1) {
+ hrc = H5Sclose(h5mem_space_id);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Memory Space Close failed\n");
+ ret_code = FAIL;
+ }
+ else {
+ h5mem_space_id = H5I_INVALID_HID;
+ }
+ }
+
+ if (h5dxpl != -1) {
+ hrc = H5Pclose(h5dxpl);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Dataset Transfer Property List Close failed\n");
+ ret_code = FAIL;
+ }
+ else {
+ h5dxpl = H5I_INVALID_HID;
+ }
+ }
+
+ return ret_code;
+}
+
+/*
+ * Function: dset_write
+ * Purpose: Write buffer into the dataset.
+ * Return: SUCCESS or FAIL
+ * Programmer: Christian Chilan, April, 2008
+ * Modifications:
+ */
+static herr_t
+dset_write(int local_dim, file_descr *fd, parameters *parms, void *buffer)
+{
+ int cur_dim = order[local_dim] - 1;
+ int ret_code = SUCCESS;
+ int k;
+ hsize_t dims[MAX_DIMS], maxdims[MAX_DIMS];
+ hsize_t i;
+ int j;
+ herr_t hrc;
+
+ /* iterates according to the dimensions in order array */
+ for (i = 0; i < parms->dset_size[cur_dim]; i += parms->buf_size[cur_dim]) {
+
+ h5offset[cur_dim] = (hssize_t)i;
+ offset[cur_dim] = (HDoff_t)i;
+
+ if (local_dim > 0) {
+
+ dset_write(local_dim - 1, fd, parms, buffer);
+ }
+ else {
+
+ switch (parms->io_type) {
+
+ case POSIXIO:
+ /* initialize POSIX offset in the buffer */
+ for (j = 0; j < parms->rank; j++)
+ buf_offset[j] = 0;
+ buf_p = (unsigned char *)buffer;
+ /* write POSIX buffer */
+ posix_buffer_write(0, fd, parms, buffer);
+ break;
+
+ case HDF5:
+ /* if dimensions are extendable, extend them as needed during access */
+ if (parms->h5_use_chunks && parms->h5_extendable) {
+
+ hrc = H5Sget_simple_extent_dims(h5dset_space_id, dims, maxdims);
+ VRFY((hrc >= 0), "H5Sget_simple_extent_dims");
+
+ for (k = 0; k < parms->rank; k++) {
+
+ HDassert(h5offset[k] >= 0);
+ if (dims[k] <= (hsize_t)h5offset[k]) {
+ dims[k] = dims[k] + h5count[k];
+ hrc = H5Sset_extent_simple(h5dset_space_id, parms->rank, dims, maxdims);
+ VRFY((hrc >= 0), "H5Sset_extent_simple");
+ hrc = H5Dset_extent(h5ds_id, dims);
+ VRFY((hrc >= 0), "H5Dextend");
+ }
+ }
+ }
+ /* applies offset */
+ hrc = H5Soffset_simple(h5dset_space_id, h5offset);
+ VRFY((hrc >= 0), "H5Soffset_simple");
+
+ /* Write the buffer out */
+ hrc = H5Sget_simple_extent_dims(h5dset_space_id, dims, maxdims);
+ hrc = H5Dwrite(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, h5dset_space_id, h5dxpl, buffer);
+ VRFY((hrc >= 0), "H5Dwrite");
+
+ break;
+
+ default:
+ /* unknown request */
+ HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)parms->io_type);
+ HDassert(0 && "Unknown IO type");
+ break;
+ } /* switch (parms->io_type) */
+ }
+ }
+done:
+ return ret_code;
+}
+
+/*
+ * Function: posix_buffer_write
+ * Purpose: Write buffer into the POSIX file considering contiguity.
+ * Return: SUCCESS or FAIL
+ * Programmer: Christian Chilan, April, 2008
+ * Modifications:
+ */
+
+static herr_t
+posix_buffer_write(int local_dim, file_descr *fd, parameters *parms, void *buffer)
+{
+ int ret_code = SUCCESS;
+
+ /* if dimension is not contiguous, call recursively */
+ if (local_dim < parms->rank - 1 && local_dim != cont_dim) {
+ size_t u;
+
+ for (u = 0; u < parms->buf_size[local_dim]; u++) {
+ buf_offset[local_dim] = u;
+ posix_buffer_write(local_dim + 1, fd, parms, buffer);
+
+ /* if next dimension is cont_dim, it will fill out the buffer
+ traversing the entire dimension local_dim without the need
+ of performing iteration */
+ if (local_dim + 1 == cont_dim)
+ break;
+ }
+ /* otherwise, perform contiguous POSIX access */
+ }
+ else {
+ HDoff_t d_offset;
+ HDoff_t linear_dset_offset = 0;
+ int i, j, rc;
+
+ buf_offset[local_dim] = 0;
+
+ /* determine offset in the buffer */
+ for (i = 0; i < parms->rank; i++) {
+ d_offset = 1;
+
+ for (j = i + 1; j < parms->rank; j++)
+ d_offset *= (HDoff_t)parms->dset_size[j];
+
+ linear_dset_offset += (offset[i] + (HDoff_t)buf_offset[i]) * d_offset;
+ }
+
+ /* only care if seek returns error */
+ rc = POSIXSEEK(fd->posixfd, linear_dset_offset) < 0 ? -1 : 0;
+ VRFY((rc == 0), "POSIXSEEK");
+ /* check if all bytes are written */
+ rc = ((ssize_t)cont_size == POSIXWRITE(fd->posixfd, buf_p, cont_size));
+ VRFY((rc != 0), "POSIXWRITE");
+
+ /* Advance location in buffer */
+ buf_p += cont_size;
+ }
+
+done:
+ return ret_code;
+}
+
+/*
+ * Function: do_read
+ * Purpose: Read the required amount of data to the file.
+ * Return: SUCCESS or FAIL
+ * Programmer: Christian Chilan, April, 2008
+ * Modifications:
+ */
+static herr_t
+do_read(results *res, file_descr *fd, parameters *parms, void *buffer)
+{
+ char * buffer2 = NULL; /* Buffer for data verification */
+ int ret_code = SUCCESS;
+ char dname[64];
+ int i;
+ size_t u;
+ /* HDF5 variables */
+ herr_t hrc; /*HDF5 return code */
+ hsize_t h5dims[MAX_DIMS]; /*dataset dim sizes */
+ hsize_t h5block[MAX_DIMS]; /*dataspace selection */
+ hsize_t h5stride[MAX_DIMS]; /*selection stride */
+ hsize_t h5start[MAX_DIMS]; /*selection start */
+ int rank;
+
+ /* Allocate data verification buffer */
+ if (NULL == (buffer2 = (char *)malloc(linear_buf_size))) {
+ HDfprintf(stderr, "malloc for data verification buffer size (%zu) failed\n", linear_buf_size);
+ GOTOERROR(FAIL);
+ } /* end if */
+
+ /* Prepare buffer for verifying data */
+ for (u = 0; u < linear_buf_size; u++)
+ buffer2[u] = (char)(u % 128);
+
+ rank = parms->rank;
+ for (i = 0; i < rank; i++)
+ h5offset[i] = offset[i] = 0;
+
+ /* I/O Access specific setup */
+ switch (parms->io_type) {
+ case POSIXIO:
+ cont_dim = rank;
+
+ for (i = rank - 1; i >= 0; i--) {
+ if (parms->buf_size[i] == parms->dset_size[i])
+ cont_dim = i;
+ else
+ break;
+ }
+ cont_size = (!cont_dim) ? 1 : parms->buf_size[cont_dim - 1];
+ for (i = cont_dim; i < rank; i++)
+ cont_size *= parms->buf_size[i];
+
+ break;
+
+ case HDF5: /* HDF5 setup */
+ for (i = 0; i < rank; i++) {
+ h5dims[i] = parms->dset_size[i];
+ h5start[i] = 0;
+ h5stride[i] = 1;
+ h5block[i] = 1;
+ h5count[i] = parms->buf_size[i];
+ }
+
+ h5dset_space_id = H5Screate_simple(rank, h5dims, NULL);
+ VRFY((h5dset_space_id >= 0), "H5Screate_simple");
+
+ hrc = H5Sselect_hyperslab(h5dset_space_id, H5S_SELECT_SET, h5start, h5stride, h5count, h5block);
+ VRFY((hrc >= 0), "H5Sselect_hyperslab");
+
+ /* Create the memory dataspace that corresponds to the xfer buffer */
+ h5mem_space_id = H5Screate_simple(rank, h5count, NULL);
+ VRFY((h5mem_space_id >= 0), "H5Screate_simple");
+
+ /* Create the dataset transfer property list */
+ h5dxpl = H5Pcreate(H5P_DATASET_XFER);
+ if (h5dxpl < 0) {
+ HDfprintf(stderr, "HDF5 Property List Create failed\n");
+ GOTOERROR(FAIL);
+ }
+ break;
+
+ default:
+ /* unknown request */
+ HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)parms->io_type);
+ GOTOERROR(FAIL);
+ break;
+ } /* end switch */
+
+ /* create dataset */
+ switch (parms->io_type) {
+ case POSIXIO:
+ break;
+
+ case HDF5:
+ HDsprintf(dname, "Dataset_%ld", (long)parms->num_bytes);
+ h5ds_id = H5Dopen2(fd->h5fd, dname, H5P_DEFAULT);
+ if (h5ds_id < 0) {
+ HDfprintf(stderr, "HDF5 Dataset open failed\n");
+ GOTOERROR(FAIL);
+ }
+ break;
+
+ default:
+ /* unknown request */
+ HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)parms->io_type);
+ GOTOERROR(FAIL);
+ break;
+ } /* end switch */
+
+ /* Start "raw data" read timer */
+ io_time_set(res->timers, HDF5_RAW_READ_FIXED_DIMS, TSTART);
+ hrc = dset_read(rank - 1, fd, parms, buffer, buffer2);
+
+ if (hrc < 0) {
+ HDfprintf(stderr, "Error in dataset read\n");
+ GOTOERROR(FAIL);
+ }
+
+ /* Stop "raw data" read timer */
+ io_time_set(res->timers, HDF5_RAW_READ_FIXED_DIMS, TSTOP);
+
+ /* Calculate read time */
+
+ /* Close dataset. Only HDF5 needs to do an explicit close. */
+ if (parms->io_type == HDF5) {
+ hrc = H5Dclose(h5ds_id);
+
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Dataset Close failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ h5ds_id = H5I_INVALID_HID;
+ } /* end if */
+
+done:
+
+ /* release HDF5 objects */
+ if (h5dset_space_id != -1) {
+ hrc = H5Sclose(h5dset_space_id);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Dataset Space Close failed\n");
+ ret_code = FAIL;
+ }
+ else {
+ h5dset_space_id = H5I_INVALID_HID;
+ }
+ }
+
+ if (h5mem_space_id != -1) {
+ hrc = H5Sclose(h5mem_space_id);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Memory Space Close failed\n");
+ ret_code = FAIL;
+ }
+ else {
+ h5mem_space_id = H5I_INVALID_HID;
+ }
+ }
+
+ if (h5dxpl != -1) {
+ hrc = H5Pclose(h5dxpl);
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 Dataset Transfer Property List Close failed\n");
+ ret_code = FAIL;
+ }
+ else {
+ h5dxpl = H5I_INVALID_HID;
+ }
+ }
+
+ /* release generic resources */
+ if (buffer2)
+ free(buffer2);
+
+ return ret_code;
+}
+
+/*
+ * Function: dset_read
+ * Purpose: Read buffer into the dataset.
+ * Return: SUCCESS or FAIL
+ * Programmer: Christian Chilan, April, 2008
+ * Modifications:
+ */
+
+static herr_t
+dset_read(int local_dim, file_descr *fd, parameters *parms, void *buffer, const char *buffer2)
+{
+ int cur_dim = order[local_dim] - 1;
+ hsize_t i;
+ int j;
+ herr_t hrc;
+ int ret_code = SUCCESS;
+
+ /* iterate on the current dimension */
+ for (i = 0; i < parms->dset_size[cur_dim]; i += parms->buf_size[cur_dim]) {
+
+ h5offset[cur_dim] = (hssize_t)i;
+ offset[cur_dim] = (HDoff_t)i;
+
+ /* if traverse in order array is incomplete, recurse */
+ if (local_dim > 0) {
+
+ ret_code = dset_read(local_dim - 1, fd, parms, buffer, buffer2);
+
+ /* otherwise, write buffer into dataset */
+ }
+ else {
+
+ switch (parms->io_type) {
+
+ case POSIXIO:
+ for (j = 0; j < parms->rank; j++) {
+ buf_offset[j] = 0;
+ }
+ buf_p = (unsigned char *)buffer;
+ posix_buffer_read(0, fd, parms, buffer);
+ break;
+
+ case HDF5:
+ hrc = H5Soffset_simple(h5dset_space_id, h5offset);
+ VRFY((hrc >= 0), "H5Soffset_simple");
+ /* Read the buffer out */
+ hrc = H5Dread(h5ds_id, ELMT_H5_TYPE, h5mem_space_id, h5dset_space_id, h5dxpl, buffer);
+ VRFY((hrc >= 0), "H5Dread");
+ break;
+
+ default:
+ /* unknown request */
+ HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)parms->io_type);
+ HDassert(0 && "Unknown IO type");
+ break;
+ } /* switch (parms->io_type) */
+ }
+ }
+done:
+ return ret_code;
+}
+
+/*
+ * Function: posix_buffer_read
+ * Purpose: Read buffer into the POSIX file considering contiguity.
+ * Return: SUCCESS or FAIL
+ * Programmer: Christian Chilan, April, 2008
+ * Modifications:
+ */
+
+static herr_t
+posix_buffer_read(int local_dim, file_descr *fd, parameters *parms, void *buffer)
+{
+ int ret_code = SUCCESS;
+
+ /* if local dimension is not contiguous, recurse */
+ if (local_dim < parms->rank - 1 && local_dim != cont_dim) {
+ size_t u;
+
+ for (u = 0; u < parms->buf_size[local_dim]; u++) {
+ buf_offset[local_dim] = u;
+ ret_code = posix_buffer_read(local_dim + 1, fd, parms, buffer);
+ if (local_dim + 1 == cont_dim)
+ break;
+ }
+ /* otherwise, perform contiguous POSIX access */
+ }
+ else {
+ HDoff_t d_offset;
+ HDoff_t linear_dset_offset = 0;
+ int i, j, rc;
+
+ buf_offset[local_dim] = 0;
+ /* determine offset in buffer */
+ for (i = 0; i < parms->rank; i++) {
+ d_offset = 1;
+
+ for (j = i + 1; j < parms->rank; j++)
+ d_offset *= (HDoff_t)parms->dset_size[j];
+
+ linear_dset_offset += (offset[i] + (HDoff_t)buf_offset[i]) * d_offset;
+ }
+
+ /* only care if seek returns error */
+ rc = POSIXSEEK(fd->posixfd, linear_dset_offset) < 0 ? -1 : 0;
+ VRFY((rc == 0), "POSIXSEEK");
+ /* check if all bytes are read */
+ rc = ((ssize_t)cont_size == POSIXREAD(fd->posixfd, buf_p, cont_size));
+ VRFY((rc != 0), "POSIXREAD");
+
+ /* Advance location in buffer */
+ buf_p += cont_size;
+ }
+done:
+ return ret_code;
+}
+
+/*
+ * Function: do_fopen
+ * Purpose: Open the specified file.
+ * Return: SUCCESS or FAIL
+ * Programmer: Albert Cheng, Bill Wendling, 2001/12/13
+ * Modifications: Support for file drivers, Christian Chilan, April, 2008
+ */
+static herr_t
+do_fopen(parameters *param, char *fname, file_descr *fd /*out*/, int flags)
+{
+ int ret_code = SUCCESS;
+ hid_t fcpl;
+
+ switch (param->io_type) {
+ case POSIXIO:
+ if (flags & (SIO_CREATE | SIO_WRITE))
+ fd->posixfd = POSIXCREATE(fname);
+ else
+ fd->posixfd = POSIXOPEN(fname, O_RDONLY);
+
+ if (fd->posixfd < 0) {
+ HDfprintf(stderr, "POSIX File Open failed(%s)\n", fname);
+ GOTOERROR(FAIL);
+ }
+
+ break;
+
+ case HDF5:
+
+ fapl = set_vfd(param);
+
+ if (fapl < 0) {
+ HDfprintf(stderr, "HDF5 Property List Create failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ fcpl = H5Pcreate(H5P_FILE_CREATE);
+ if (param->page_size) {
+ H5Pset_file_space_strategy(fcpl, H5F_FSPACE_STRATEGY_PAGE, 0, (hsize_t)1);
+ H5Pset_file_space_page_size(fcpl, param->page_size);
+ if (param->page_buffer_size)
+ H5Pset_page_buffer_size(fapl, param->page_buffer_size, 0, 0);
+ }
+
+ /* create the parallel file */
+ if (flags & (SIO_CREATE | SIO_WRITE)) {
+ fd->h5fd = H5Fcreate(fname, H5F_ACC_TRUNC, fcpl, fapl);
+ }
+ else {
+ fd->h5fd = H5Fopen(fname, H5F_ACC_RDONLY, fapl);
+ }
+
+ if (fd->h5fd < 0) {
+ HDfprintf(stderr, "HDF5 File Create failed(%s)\n", fname);
+ GOTOERROR(FAIL);
+ }
+ break;
+
+ default:
+ /* unknown request */
+ HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)param->io_type);
+ GOTOERROR(FAIL);
+ break;
+ }
+
+done:
+ return ret_code;
+}
+
+/*
+ * Function: set_vfd
+ * Purpose: Sets file driver.
+ * Return: SUCCESS or FAIL
+ * Programmer: Christian Chilan, April, 2008
+ * Modifications:
+ */
+
+hid_t
+set_vfd(parameters *param)
+{
+ hid_t my_fapl = H5I_INVALID_HID;
+ vfdtype vfd;
+
+ vfd = param->vfd;
+
+ if ((my_fapl = H5Pcreate(H5P_FILE_ACCESS)) < 0)
+ return -1;
+
+ if (vfd == sec2) {
+ /* Unix read() and write() system calls */
+ if (H5Pset_fapl_sec2(my_fapl) < 0)
+ return -1;
+ }
+ else if (vfd == stdio) {
+ /* Standard C fread() and fwrite() system calls */
+ if (H5Pset_fapl_stdio(my_fapl) < 0)
+ return -1;
+ }
+ else if (vfd == core) {
+ /* In-core temporary file with 1MB increment */
+ if (H5Pset_fapl_core(my_fapl, (size_t)1024 * 1024, TRUE) < 0)
+ return -1;
+ }
+ else if (vfd == split) {
+ /* Split meta data and raw data each using default driver */
+ if (H5Pset_fapl_split(my_fapl, "-m.h5", H5P_DEFAULT, "-r.h5", H5P_DEFAULT) < 0)
+ return -1;
+ }
+ else if (vfd == multi) {
+ /* Multi-file driver, general case of the split driver */
+ H5FD_mem_t memb_map[H5FD_MEM_NTYPES];
+ hid_t memb_fapl[H5FD_MEM_NTYPES];
+ const char *memb_name[H5FD_MEM_NTYPES];
+ char sv[H5FD_MEM_NTYPES][1024];
+ haddr_t memb_addr[H5FD_MEM_NTYPES];
+ H5FD_mem_t mt;
+
+ HDmemset(memb_map, 0, sizeof memb_map);
+ HDmemset(memb_fapl, 0, sizeof memb_fapl);
+ HDmemset(memb_name, 0, sizeof memb_name);
+ HDmemset(memb_addr, 0, sizeof memb_addr);
+
+ HDassert(HDstrlen(multi_letters) == H5FD_MEM_NTYPES);
+ for (mt = H5FD_MEM_DEFAULT; mt < H5FD_MEM_NTYPES; mt++) {
+ memb_fapl[mt] = H5P_DEFAULT;
+ HDsprintf(sv[mt], "%%s-%c.h5", multi_letters[mt]);
+ memb_name[mt] = sv[mt];
+ memb_addr[mt] = (haddr_t)MAX(mt - 1, 0) * (HADDR_MAX / 10);
+ }
+
+ if (H5Pset_fapl_multi(my_fapl, memb_map, memb_fapl, memb_name, memb_addr, FALSE) < 0) {
+ return -1;
+ }
+ }
+ else if (vfd == family) {
+ hsize_t fam_size = 1 * 1024 * 1024; /*100 MB*/
+
+ /* Family of files, each 1MB and using the default driver */
+ /* if ((val=HDstrtok(NULL, " \t\n\r")))
+ fam_size = (hsize_t)(HDstrtod(val, NULL) * 1024*1024); */
+ if (H5Pset_fapl_family(my_fapl, fam_size, H5P_DEFAULT) < 0)
+ return -1;
+ }
+ else if (vfd == direct) {
+#ifdef H5_HAVE_DIRECT
+ /* Linux direct read() and write() system calls. Set memory boundary, file block size,
+ * and copy buffer size to the default values. */
+ if (H5Pset_fapl_direct(my_fapl, 1024, 4096, 8 * 4096) < 0)
+ return -1;
+#endif
+ }
+ else {
+ /* Unknown driver */
+ return -1;
+ }
+
+ return my_fapl;
+}
+
+/*
+ * Function: do_fclose
+ * Purpose: Close the specified file descriptor.
+ * Return: SUCCESS or FAIL
+ * Programmer: Albert Cheng, Bill Wendling, 2001/12/13
+ * Modifications:
+ */
+static herr_t
+do_fclose(iotype iot, file_descr *fd /*out*/)
+{
+ herr_t ret_code = SUCCESS, hrc;
+ int rc = 0;
+
+ switch (iot) {
+ case POSIXIO:
+ rc = POSIXCLOSE(fd->posixfd);
+
+ if (rc != 0) {
+ HDfprintf(stderr, "POSIX File Close failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ fd->posixfd = -1;
+ break;
+
+ case HDF5:
+ hrc = H5Fclose(fd->h5fd);
+
+ if (hrc < 0) {
+ HDfprintf(stderr, "HDF5 File Close failed\n");
+ GOTOERROR(FAIL);
+ }
+
+ fd->h5fd = -1;
+ break;
+
+ default:
+ /* unknown request */
+ HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)iot);
+ GOTOERROR(FAIL);
+ break;
+ }
+
+done:
+ return ret_code;
+}
+
+/*
+ * Function: do_cleanupfile
+ * Purpose: Cleanup temporary file unless HDF5_NOCLEANUP is set.
+ * Return: void
+ * Programmer: Albert Cheng 2001/12/12
+ * Modifications: Support for file drivers. Christian Chilan, April, 2008
+ */
+static void
+do_cleanupfile(iotype iot, char *filename)
+{
+ char temp[2048];
+ int j;
+ hid_t driver;
+
+ if (clean_file_g == -1)
+ clean_file_g = (HDgetenv("HDF5_NOCLEANUP") == NULL) ? 1 : 0;
+
+ if (clean_file_g) {
+
+ switch (iot) {
+ case POSIXIO:
+ HDremove(filename);
+ break;
+
+ case HDF5:
+ driver = H5Pget_driver(fapl);
+
+ if (driver == H5FD_FAMILY) {
+ for (j = 0; /*void*/; j++) {
+ HDsnprintf(temp, sizeof temp, filename, j);
+
+ if (HDaccess(temp, F_OK) < 0)
+ break;
+
+ HDremove(temp);
+ }
+ }
+ else if (driver == H5FD_CORE) {
+ hbool_t backing; /* Whether the core file has backing store */
+
+ H5Pget_fapl_core(fapl, NULL, &backing);
+
+ /* If the file was stored to disk with bacing store, remove it */
+ if (backing)
+ HDremove(filename);
+ }
+ else if (driver == H5FD_MULTI) {
+ H5FD_mem_t mt;
+ assert(HDstrlen(multi_letters) == H5FD_MEM_NTYPES);
+
+ for (mt = H5FD_MEM_DEFAULT; mt < H5FD_MEM_NTYPES; mt++) {
+ HDsnprintf(temp, sizeof temp, "%s-%c.h5", filename, multi_letters[mt]);
+ HDremove(temp); /*don't care if it fails*/
+ }
+ }
+ else {
+ HDremove(filename);
+ }
+ H5Pclose(fapl);
+ break;
+
+ default:
+ /* unknown request */
+ HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)iot);
+ HDassert(0 && "Unknown IO type");
+ break;
+ }
+ }
+}
diff --git a/tools/src/h5perf/sio_perf.c b/tools/src/h5perf/sio_perf.c
new file mode 100644
index 0000000..7bd58d8
--- /dev/null
+++ b/tools/src/h5perf/sio_perf.c
@@ -0,0 +1,1301 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the COPYING file, which can be found at the root of the source code *
+ * distribution tree, or in https://www.hdfgroup.org/licenses. *
+ * If you do not have access to either file, you may request a copy from *
+ * help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+/*
+ * Serial HDF5 Performance Testing Code
+ * --------------------------------------
+ *
+ * Portable code to test performance on the different platforms we support.
+ * This is what the report should look like:
+ *
+ * nprocs = Max#Procs
+ * IO API = POSIXIO
+ * # Files = 1, # of dsets = 1000, Elements per dset = 37000
+ * Write Results = x MB/s
+ * Read Results = x MB/s
+ * # Files = 1, # of dsets = 3000, Elements per dset = 37000
+ * Write Results = x MB/s
+ * Read Results = x MB/s
+ *
+ * . . .
+ *
+ *
+ * IO API = HDF5
+ * # Files = 1, # of dsets = 1000, Elements per dset = 37000
+ * Write Results = x MB/s
+ * Read Results = x MB/s
+ * # Files = 1, # of dsets = 3000, Elements per dset = 37000
+ * Write Results = x MB/s
+ * Read Results = x MB/s
+ *
+ * . . .
+ *
+ *
+ * . . .
+ *
+ */
+
+/* system header files */
+#include <stdarg.h>
+#include <stdio.h>
+#include <stdlib.h>
+
+#include "hdf5.h"
+
+/* our header files */
+#include "sio_perf.h"
+
+/* useful macros */
+#define TAB_SPACE 4
+
+#define ONE_KB 1024
+#define ONE_MB (ONE_KB * ONE_KB)
+#define ONE_GB (ONE_MB * ONE_KB)
+
+#define SIO_POSIX 0x1
+#define SIO_HDF5 0x4
+
+/* report 0.0 in case t is zero too */
+#define MB_PER_SEC(bytes, t) (H5_DBL_ABS_EQUAL(t, 0.0) ? 0.0 : ((((double)bytes) / (double)ONE_MB) / (t)))
+
+#ifndef TRUE
+#define TRUE 1
+#endif /* TRUE */
+#ifndef FALSE
+#define FALSE (!TRUE)
+#endif /* FALSE */
+
+/* global variables */
+FILE *output; /* output file */
+int sio_debug_level = 0; /* The debug level:
+ * 0 - Off
+ * 1 - Minimal
+ * 2 - Some more
+ * 3 - Maximal
+ * 4 - Maximal & then some
+ */
+
+/* local variables */
+static const char *progname = "h5perf_serial";
+
+/*
+ * Command-line options: The user can specify short or long-named
+ * parameters. The long-named ones can be partially spelled. When
+ * adding more, make sure that they don't clash with each other.
+ */
+
+/*
+ * It seems that only the options that accept additional information
+ * such as dataset size (-e) require the colon next to it.
+ */
+static const char * s_opts = "a:A:B:c:Cd:D:e:F:ghi:Imno:p:P:r:stT:v:wx:X:";
+static struct h5_long_options l_opts[] = {{"align", require_arg, 'a'},
+ {"api", require_arg, 'A'},
+#if 0
+ /* a sighting of the elusive binary option */
+ { "binary", no_arg, 'b' },
+#endif /* 0 */
+ {"block-size", require_arg, 'B'},
+ {"chunk", no_arg, 'c'},
+ {"collective", no_arg, 'C'},
+ {"debug", require_arg, 'D'},
+ {"file-driver", require_arg, 'v'},
+ {"geometry", no_arg, 'g'},
+ {"help", no_arg, 'h'},
+ {"interleaved", require_arg, 'I'},
+ {"max-num-processes", require_arg, 'P'},
+ {"min-num-processes", require_arg, 'p'},
+ {"max-xfer-size", require_arg, 'X'},
+ {"min-xfer-size", require_arg, 'x'},
+ {"num-bytes", require_arg, 'e'},
+ {"num-dsets", require_arg, 'd'},
+ {"num-files", require_arg, 'F'},
+ {"num-iterations", require_arg, 'i'},
+ {"order", require_arg, 'r'},
+ {"output", require_arg, 'o'},
+ {"extendable", no_arg, 't'},
+ {"threshold", require_arg, 'T'},
+ {"write-only", require_arg, 'w'},
+ {NULL, 0, '\0'}};
+
+struct options {
+ long io_types; /* bitmask of which I/O types to test */
+ const char *output_file; /* file to print report to */
+ long num_dsets; /* number of datasets */
+ long num_files; /* number of files */
+ off_t num_bpp; /* number of bytes per proc per dset */
+ int num_iters; /* number of iterations */
+ hsize_t dset_size[MAX_DIMS]; /* Dataset size */
+ size_t buf_size[MAX_DIMS]; /* Buffer size */
+ size_t chk_size[MAX_DIMS]; /* Chunk size */
+ int order[MAX_DIMS]; /* Dimension access order */
+ int dset_rank; /* Rank */
+ int buf_rank; /* Rank */
+ int order_rank; /* Rank */
+ int chk_rank; /* Rank */
+ int print_times; /* print times as well as throughputs */
+ int print_raw; /* print raw data throughput info */
+ hsize_t h5_alignment; /* alignment in HDF5 file */
+ hsize_t h5_threshold; /* threshold for alignment in HDF5 file */
+ int h5_use_chunks; /* Make HDF5 dataset chunked */
+ int h5_write_only; /* Perform the write tests only */
+ int h5_extendable; /* Perform the write tests only */
+ int verify; /* Verify data correctness */
+ vfdtype vfd; /* File driver */
+ size_t page_buffer_size;
+ size_t page_size;
+};
+
+typedef struct {
+ double min;
+ double max;
+ double sum;
+ int num;
+} minmax;
+
+/* local functions */
+static hsize_t parse_size_directive(const char *size);
+static struct options *parse_command_line(int argc, const char *argv[]);
+static void run_test_loop(struct options *options);
+static int run_test(iotype iot, parameters parms, struct options *opts);
+static void output_all_info(minmax *mm, int count, int indent_level);
+static void get_minmax(minmax *mm, double val);
+static void accumulate_minmax_stuff(const minmax *mm, int count, minmax *total_mm);
+static void output_results(const struct options *options, const char *name, minmax *table, int table_size,
+ off_t data_size);
+static void output_report(const char *fmt, ...);
+static void print_indent(register int indent);
+static void usage(const char *prog);
+static void report_parameters(struct options *opts);
+
+/*
+ * Function: main
+ * Purpose: Start things up.
+ * Return: EXIT_SUCCESS or EXIT_FAILURE
+ * Programmer: Bill Wendling, 30. October 2001
+ * Modifications:
+ */
+int
+main(int argc, const char *argv[])
+{
+ int exit_value = EXIT_SUCCESS;
+ struct options *opts = NULL;
+
+#ifndef STANDALONE
+ /* Initialize h5tools lib */
+ h5tools_init();
+#endif
+
+ output = stdout;
+
+ opts = parse_command_line(argc, argv);
+
+ if (!opts) {
+ exit_value = EXIT_FAILURE;
+ goto finish;
+ }
+
+ if (opts->output_file) {
+ if ((output = HDfopen(opts->output_file, "w")) == NULL) {
+ HDfprintf(stderr, "%s: cannot open output file\n", progname);
+ HDperror(opts->output_file);
+ goto finish;
+ }
+ }
+
+ report_parameters(opts);
+
+ run_test_loop(opts);
+
+finish:
+ HDfree(opts);
+ return exit_value;
+}
+
+/*
+ * Function: run_test_loop
+ * Purpose: Run the I/O tests. Write the results to OUTPUT.
+ *
+ * - The slowest changing part of the test is the number of
+ * processors to use. For each loop iteration, we divide that
+ * number by 2 and rerun the test.
+ *
+ * - The second slowest is what type of IO API to perform. We have
+ * three choices: POSIXIO, and HDF5.
+ *
+ * - Then we change the size of the buffer. This information is
+ * inferred from the number of datasets to create and the number
+ * of integers to put into each dataset. The backend code figures
+ * this out.
+ *
+ * Return: Nothing
+ * Programmer: Bill Wendling, 30. October 2001
+ * Modifications:
+ * Added multidimensional testing (Christian Chilan, April, 2008)
+ */
+static void
+run_test_loop(struct options *opts)
+{
+ parameters parms;
+ int i;
+ size_t buf_bytes;
+
+ /* load options into parameter structure */
+ parms.num_files = opts->num_files;
+ parms.num_dsets = opts->num_dsets;
+ parms.num_iters = opts->num_iters;
+ parms.rank = opts->dset_rank;
+ parms.h5_align = opts->h5_alignment;
+ parms.h5_thresh = opts->h5_threshold;
+ parms.h5_use_chunks = opts->h5_use_chunks;
+ parms.h5_extendable = opts->h5_extendable;
+ parms.h5_write_only = opts->h5_write_only;
+ parms.verify = opts->verify;
+ parms.vfd = opts->vfd;
+ parms.page_buffer_size = opts->page_buffer_size;
+ parms.page_size = opts->page_size;
+
+ /* load multidimensional options */
+ parms.num_bytes = 1;
+ buf_bytes = 1;
+ for (i = 0; i < parms.rank; i++) {
+ parms.buf_size[i] = opts->buf_size[i];
+ parms.dset_size[i] = opts->dset_size[i];
+ parms.chk_size[i] = opts->chk_size[i];
+ parms.order[i] = opts->order[i];
+ parms.num_bytes *= opts->dset_size[i];
+ buf_bytes *= opts->buf_size[i];
+ }
+
+ /* print size information */
+ output_report("Transfer Buffer Size (bytes): %d\n", buf_bytes);
+ output_report("File Size(MB): %.2f\n", ((double)parms.num_bytes) / ONE_MB);
+
+ print_indent(0);
+ if (opts->io_types & SIO_POSIX)
+ run_test(POSIXIO, parms, opts);
+
+ print_indent(0);
+ if (opts->io_types & SIO_HDF5)
+ run_test(HDF5, parms, opts);
+}
+
+/*
+ * Function: run_test
+ * Purpose: Inner loop call to actually run the I/O test.
+ * Return: Nothing
+ * Programmer: Bill Wendling, 18. December 2001
+ * Modifications:
+ */
+static int
+run_test(iotype iot, parameters parms, struct options *opts)
+{
+ results res;
+ register int i, ret_value = SUCCESS;
+ off_t raw_size;
+ minmax * write_sys_mm_table = NULL;
+ minmax * write_mm_table = NULL;
+ minmax * write_gross_mm_table = NULL;
+ minmax * write_raw_mm_table = NULL;
+ minmax * read_sys_mm_table = NULL;
+ minmax * read_mm_table = NULL;
+ minmax * read_gross_mm_table = NULL;
+ minmax * read_raw_mm_table = NULL;
+ minmax write_sys_mm = {0.0F, 0.0F, 0.0F, 0};
+ minmax write_mm = {0.0F, 0.0F, 0.0F, 0};
+ minmax write_gross_mm = {0.0F, 0.0F, 0.0F, 0};
+ minmax write_raw_mm = {0.0F, 0.0F, 0.0F, 0};
+ minmax read_sys_mm = {0.0F, 0.0F, 0.0F, 0};
+ minmax read_mm = {0.0F, 0.0F, 0.0F, 0};
+ minmax read_gross_mm = {0.0F, 0.0F, 0.0F, 0};
+ minmax read_raw_mm = {0.0F, 0.0F, 0.0F, 0};
+
+ raw_size = (off_t)parms.num_bytes;
+ parms.io_type = iot;
+ print_indent(2);
+ output_report("IO API = ");
+
+ switch (iot) {
+ case POSIXIO:
+ output_report("POSIX\n");
+ break;
+ case HDF5:
+ output_report("HDF5\n");
+ break;
+ default:
+ /* unknown request */
+ HDfprintf(stderr, "Unknown IO type request (%d)\n", (int)iot);
+ HDassert(0 && "Unknown IO tpe");
+ break;
+ }
+
+ /* allocate space for tables minmax and that it is sufficient */
+ /* to initialize all elements to zeros by calloc. */
+ write_sys_mm_table = (minmax *)calloc((size_t)parms.num_iters, sizeof(minmax));
+ write_mm_table = (minmax *)calloc((size_t)parms.num_iters, sizeof(minmax));
+ write_gross_mm_table = (minmax *)calloc((size_t)parms.num_iters, sizeof(minmax));
+ write_raw_mm_table = (minmax *)calloc((size_t)parms.num_iters, sizeof(minmax));
+
+ if (!parms.h5_write_only) {
+ read_sys_mm_table = (minmax *)calloc((size_t)parms.num_iters, sizeof(minmax));
+ read_mm_table = (minmax *)calloc((size_t)parms.num_iters, sizeof(minmax));
+ read_gross_mm_table = (minmax *)calloc((size_t)parms.num_iters, sizeof(minmax));
+ read_raw_mm_table = (minmax *)calloc((size_t)parms.num_iters, sizeof(minmax));
+ }
+
+ /* Do IO iteration times, collecting statistics each time */
+ for (i = 0; i < parms.num_iters; ++i) {
+ double t;
+
+ do_sio(parms, &res);
+
+ /* gather all of the "sys write" times */
+ t = io_time_get(res.timers, HDF5_MPI_WRITE);
+ get_minmax(&write_sys_mm, t);
+
+ write_sys_mm_table[i] = write_sys_mm;
+
+ /* gather all of the "write" times */
+ t = io_time_get(res.timers, HDF5_FINE_WRITE_FIXED_DIMS);
+ get_minmax(&write_mm, t);
+
+ write_mm_table[i] = write_mm;
+
+ /* gather all of the "write" times from open to close */
+ t = io_time_get(res.timers, HDF5_GROSS_WRITE_FIXED_DIMS);
+ get_minmax(&write_gross_mm, t);
+
+ write_gross_mm_table[i] = write_gross_mm;
+
+ /* gather all of the raw "write" times */
+ t = io_time_get(res.timers, HDF5_RAW_WRITE_FIXED_DIMS);
+ get_minmax(&write_raw_mm, t);
+
+ write_raw_mm_table[i] = write_raw_mm;
+
+ if (!parms.h5_write_only) {
+ /* gather all of the "mpi read" times */
+ t = io_time_get(res.timers, HDF5_MPI_READ);
+ get_minmax(&read_sys_mm, t);
+
+ read_sys_mm_table[i] = read_sys_mm;
+
+ /* gather all of the "read" times */
+ t = io_time_get(res.timers, HDF5_FINE_READ_FIXED_DIMS);
+ get_minmax(&read_mm, t);
+
+ read_mm_table[i] = read_mm;
+
+ /* gather all of the "read" times from open to close */
+ t = io_time_get(res.timers, HDF5_GROSS_READ_FIXED_DIMS);
+ get_minmax(&read_gross_mm, t);
+
+ read_gross_mm_table[i] = read_gross_mm;
+
+ /* gather all of the raw "read" times */
+ t = io_time_get(res.timers, HDF5_RAW_READ_FIXED_DIMS);
+ get_minmax(&read_raw_mm, t);
+
+ read_raw_mm_table[i] = read_gross_mm;
+ }
+ io_time_destroy(res.timers);
+ }
+
+ /*
+ * Show various statistics
+ */
+ /* Write statistics */
+ /* Print the raw data throughput if desired */
+ if (opts->print_raw) {
+ /* accumulate and output the max, min, and average "raw write" times */
+ if (sio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("Raw Data Write details:\n");
+ output_all_info(write_raw_mm_table, parms.num_iters, 4);
+ }
+
+ output_results(opts, "Raw Data Write", write_raw_mm_table, parms.num_iters, raw_size);
+ } /* end if */
+
+ /* show sys write statics */
+#if 0
+ if (sio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("MPI Write details:\n");
+ output_all_info(write_sys_mm_table, parms.num_iters, 4);
+ }
+#endif
+ /* We don't currently output the MPI write results */
+
+ /* accumulate and output the max, min, and average "write" times */
+ if (sio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("Write details:\n");
+ output_all_info(write_mm_table, parms.num_iters, 4);
+ }
+
+ output_results(opts, "Write", write_mm_table, parms.num_iters, raw_size);
+
+ /* accumulate and output the max, min, and average "gross write" times */
+ if (sio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("Write Open-Close details:\n");
+ output_all_info(write_gross_mm_table, parms.num_iters, 4);
+ }
+
+ output_results(opts, "Write Open-Close", write_gross_mm_table, parms.num_iters, raw_size);
+
+ if (!parms.h5_write_only) {
+ /* Read statistics */
+ /* Print the raw data throughput if desired */
+ if (opts->print_raw) {
+ /* accumulate and output the max, min, and average "raw read" times */
+ if (sio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("Raw Data Read details:\n");
+ output_all_info(read_raw_mm_table, parms.num_iters, 4);
+ }
+
+ output_results(opts, "Raw Data Read", read_raw_mm_table, parms.num_iters, raw_size);
+ } /* end if */
+
+ /* show mpi read statics */
+#if 0
+ if (sio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("MPI Read details:\n");
+ output_all_info(read_sys_mm_table, parms.num_iters, 4);
+ }
+#endif
+ /* We don't currently output the MPI read results */
+
+ /* accumulate and output the max, min, and average "read" times */
+ if (sio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("Read details:\n");
+ output_all_info(read_mm_table, parms.num_iters, 4);
+ }
+
+ output_results(opts, "Read", read_mm_table, parms.num_iters, raw_size);
+
+ /* accumulate and output the max, min, and average "gross read" times */
+ if (sio_debug_level >= 3) {
+ /* output all of the times for all iterations */
+ print_indent(3);
+ output_report("Read Open-Close details:\n");
+ output_all_info(read_gross_mm_table, parms.num_iters, 4);
+ }
+
+ output_results(opts, "Read Open-Close", read_gross_mm_table, parms.num_iters, raw_size);
+ }
+
+ /* clean up our mess */
+ HDfree(write_sys_mm_table);
+ HDfree(write_mm_table);
+ HDfree(write_gross_mm_table);
+ HDfree(write_raw_mm_table);
+
+ if (!parms.h5_write_only) {
+ HDfree(read_sys_mm_table);
+ HDfree(read_mm_table);
+ HDfree(read_gross_mm_table);
+ HDfree(read_raw_mm_table);
+ }
+
+ return ret_value;
+}
+
+/*
+ * Function: output_all_info
+ * Purpose:
+ * Return: Nothing
+ * Programmer: Bill Wendling, 29. January 2002
+ * Modifications:
+ */
+static void
+output_all_info(minmax *mm, int count, int indent_level)
+{
+ int i;
+
+ for (i = 0; i < count; ++i) {
+ print_indent(indent_level);
+ output_report("Iteration %d:\n", i + 1);
+ print_indent(indent_level + 1);
+ output_report("Minimum Time: %.2fs\n", mm[i].min);
+ print_indent(indent_level + 1);
+ output_report("Maximum Time: %.2fs\n", mm[i].max);
+ }
+}
+
+/*
+ * Function: get_minmax
+ * Purpose: Gather all the min, max and total of val.
+ * Return: Nothing
+ * Programmer: Bill Wendling, 21. December 2001
+ * Modifications:
+ * Use MPI_Allreduce to do it. -akc, 2002/01/11
+ */
+
+static void
+get_minmax(minmax *mm, double val)
+{
+ mm->max = val;
+ mm->min = val;
+ mm->sum = val;
+}
+
+/*
+ * Function: accumulate_minmax_stuff
+ * Purpose: Accumulate the minimum, maximum, and average of the times
+ * across all processes.
+ * Return: TOTAL_MM - the total of all of these.
+ * Programmer: Bill Wendling, 21. December 2001
+ * Modifications:
+ * Changed to use seconds instead of MB/s - QAK, 5/9/02
+ */
+static void
+accumulate_minmax_stuff(const minmax *mm, int count, minmax *total_mm)
+{
+ int i;
+
+ total_mm->sum = 0.0F;
+ total_mm->max = -DBL_MAX;
+ total_mm->min = DBL_MAX;
+ total_mm->num = count;
+
+ for (i = 0; i < count; ++i) {
+ double m = mm[i].max;
+
+ total_mm->sum += m;
+
+ if (m < total_mm->min)
+ total_mm->min = m;
+
+ if (m > total_mm->max)
+ total_mm->max = m;
+ }
+}
+
+/*
+ * Function: output_results
+ * Purpose: Print information about the time & bandwidth for a given
+ * minmax & # of iterations.
+ * Return: Nothing
+ * Programmer: Quincey Koziol, 9. May 2002
+ * Modifications:
+ */
+static void
+output_results(const struct options *opts, const char *name, minmax *table, int table_size, off_t data_size)
+{
+ minmax total_mm;
+
+ accumulate_minmax_stuff(table, table_size, &total_mm);
+
+ print_indent(3);
+ output_report("%s (%d iteration(s)):\n", name, table_size);
+
+ /* Note: The maximum throughput uses the minimum amount of time & vice versa */
+
+ print_indent(4);
+ output_report("Maximum Throughput: %6.2f MB/s", MB_PER_SEC(data_size, total_mm.min));
+ if (opts->print_times)
+ output_report(" (%7.3f s)\n", total_mm.min);
+ else
+ output_report("\n");
+
+ print_indent(4);
+ output_report("Average Throughput: %6.2f MB/s", MB_PER_SEC(data_size, total_mm.sum / total_mm.num));
+ if (opts->print_times)
+ output_report(" (%7.3f s)\n", (total_mm.sum / total_mm.num));
+ else
+ output_report("\n");
+
+ print_indent(4);
+ output_report("Minimum Throughput: %6.2f MB/s", MB_PER_SEC(data_size, total_mm.max));
+ if (opts->print_times)
+ output_report(" (%7.3f s)\n", total_mm.max);
+ else
+ output_report("\n");
+}
+
+/*
+ * Function: output_report
+ * Purpose: Print a line of the report. Only do so if I'm the 0 process.
+ * Return: Nothing
+ * Programmer: Bill Wendling, 19. December 2001
+ * Modifications:
+ */
+static void
+output_report(const char *fmt, ...)
+{
+ va_list ap;
+
+ HDva_start(ap, fmt);
+ HDvfprintf(output, fmt, ap);
+ HDva_end(ap);
+}
+
+/*
+ * Function: print_indent
+ * Purpose: Print spaces to indent a new line of text for pretty printing
+ * things.
+ * Return: Nothing
+ * Programmer: Bill Wendling, 29. October 2001
+ * Modifications:
+ */
+static void
+print_indent(register int indent)
+{
+ indent *= TAB_SPACE;
+
+ for (; indent > 0; --indent)
+ HDfputc(' ', output);
+}
+
+static void
+recover_size_and_print(long long val, const char *end)
+{
+ if (val >= ONE_KB && (val % ONE_KB) == 0) {
+ if (val >= ONE_MB && (val % ONE_MB) == 0) {
+ if (val >= ONE_GB && (val % ONE_GB) == 0)
+ HDfprintf(output,
+ "%" H5_PRINTF_LL_WIDTH "d"
+ "GB%s",
+ val / ONE_GB, end);
+ else
+ HDfprintf(output,
+ "%" H5_PRINTF_LL_WIDTH "d"
+ "MB%s",
+ val / ONE_MB, end);
+ }
+ else {
+ HDfprintf(output,
+ "%" H5_PRINTF_LL_WIDTH "d"
+ "KB%s",
+ val / ONE_KB, end);
+ }
+ }
+ else {
+ HDfprintf(output,
+ "%" H5_PRINTF_LL_WIDTH "d"
+ "%s",
+ val, end);
+ }
+}
+
+static void
+print_io_api(long io_types)
+{
+ if (io_types & SIO_POSIX)
+ HDfprintf(output, "posix ");
+ if (io_types & SIO_HDF5)
+ HDfprintf(output, "hdf5 ");
+ HDfprintf(output, "\n");
+}
+
+static void
+report_parameters(struct options *opts)
+{
+ int i, rank;
+ rank = opts->dset_rank;
+
+ print_version("HDF5 Library"); /* print library version */
+ HDfprintf(output, "==== Parameters ====\n");
+
+ HDfprintf(output, "IO API=");
+ print_io_api(opts->io_types);
+
+ HDfprintf(output, "Number of iterations=%d\n", opts->num_iters);
+
+ HDfprintf(output, "Dataset size=");
+
+ for (i = 0; i < rank; i++)
+ recover_size_and_print((long long)opts->dset_size[i], " ");
+ HDfprintf(output, "\n");
+
+ HDfprintf(output, "Transfer buffer size=");
+ for (i = 0; i < rank; i++)
+ recover_size_and_print((long long)opts->buf_size[i], " ");
+ HDfprintf(output, "\n");
+
+ if (opts->page_size) {
+ HDfprintf(output, "Page Aggregation Enabled. Page size = %zu\n", opts->page_size);
+ if (opts->page_buffer_size)
+ HDfprintf(output, "Page Buffering Enabled. Page Buffer size = %zu\n", opts->page_buffer_size);
+ else
+ HDfprintf(output, "Page Buffering Disabled\n");
+ }
+ else
+ HDfprintf(output, "Page Aggregation Disabled\n");
+
+ HDfprintf(output, "Dimension access order=");
+ for (i = 0; i < rank; i++)
+ recover_size_and_print((long long)opts->order[i], " ");
+ HDfprintf(output, "\n");
+
+ if (opts->io_types & SIO_HDF5) {
+
+ HDfprintf(output, "HDF5 data storage method=");
+
+ if (opts->h5_use_chunks) {
+
+ HDfprintf(output, "Chunked\n");
+ HDfprintf(output, "HDF5 chunk size=");
+ for (i = 0; i < rank; i++)
+ recover_size_and_print((long long)opts->chk_size[i], " ");
+ HDfprintf(output, "\n");
+
+ HDfprintf(output, "HDF5 dataset dimensions=");
+ if (opts->h5_extendable) {
+ HDfprintf(output, "Extendable\n");
+ }
+ else {
+ HDfprintf(output, "Fixed\n");
+ }
+ }
+ else {
+ HDfprintf(output, "Contiguous\n");
+ }
+
+ HDfprintf(output, "HDF5 file driver=");
+ if (opts->vfd == sec2) {
+ HDfprintf(output, "sec2\n");
+ }
+ else if (opts->vfd == stdio) {
+ HDfprintf(output, "stdio\n");
+ }
+ else if (opts->vfd == core) {
+ HDfprintf(output, "core\n");
+ }
+ else if (opts->vfd == split) {
+ HDfprintf(output, "split\n");
+ }
+ else if (opts->vfd == multi) {
+ HDfprintf(output, "multi\n");
+ }
+ else if (opts->vfd == family) {
+ HDfprintf(output, "family\n");
+ }
+ else if (opts->vfd == direct) {
+ HDfprintf(output, "direct\n");
+ }
+ }
+
+ {
+ char *prefix = HDgetenv("HDF5_PREFIX");
+
+ HDfprintf(output, "Env HDF5_PREFIX=%s\n", (prefix ? prefix : "not set"));
+ }
+
+ HDfprintf(output, "==== End of Parameters ====\n");
+ HDfprintf(output, "\n");
+}
+
+/*
+ * Function: parse_command_line
+ * Purpose: Parse the command line options and return a STRUCT OPTIONS
+ * structure which will need to be freed by the calling function.
+ * Return: Pointer to an OPTIONS structure
+ * Programmer: Bill Wendling, 31. October 2001
+ * Modifications:
+ * Added multidimensional testing (Christian Chilan, April, 2008)
+ */
+static struct options *
+parse_command_line(int argc, const char *argv[])
+{
+ int opt;
+ struct options *cl_opts;
+ int i, default_rank, actual_rank, ranks[4];
+
+ cl_opts = (struct options *)HDmalloc(sizeof(struct options));
+
+ cl_opts->page_buffer_size = 0;
+ cl_opts->page_size = 0;
+
+ cl_opts->output_file = NULL;
+ cl_opts->io_types = 0; /* will set default after parsing options */
+ cl_opts->num_iters = 1;
+
+ default_rank = 2;
+
+ cl_opts->dset_rank = 0;
+ cl_opts->buf_rank = 0;
+ cl_opts->chk_rank = 0;
+ cl_opts->order_rank = 0;
+
+ for (i = 0; i < MAX_DIMS; i++) {
+ cl_opts->buf_size[i] = (size_t)((i + 1) * 10);
+ cl_opts->dset_size[i] = (hsize_t)((i + 1) * 100);
+ cl_opts->chk_size[i] = (size_t)((i + 1) * 10);
+ cl_opts->order[i] = i + 1;
+ }
+
+ cl_opts->vfd = sec2;
+
+ cl_opts->print_times = FALSE; /* Printing times is off by default */
+ cl_opts->print_raw = FALSE; /* Printing raw data throughput is off by default */
+ cl_opts->h5_alignment = 1; /* No alignment for HDF5 objects by default */
+ cl_opts->h5_threshold = 1; /* No threshold for aligning HDF5 objects by default */
+ cl_opts->h5_use_chunks = FALSE; /* Don't chunk the HDF5 dataset by default */
+ cl_opts->h5_write_only = FALSE; /* Do both read and write by default */
+ cl_opts->h5_extendable = FALSE; /* Use extendable dataset */
+ cl_opts->verify = FALSE; /* No Verify data correctness by default */
+
+ while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
+ switch ((char)opt) {
+ case 'a':
+ cl_opts->h5_alignment = parse_size_directive(H5_optarg);
+ break;
+ case 'G':
+ cl_opts->page_size = parse_size_directive(H5_optarg);
+ break;
+ case 'b':
+ cl_opts->page_buffer_size = parse_size_directive(H5_optarg);
+ break;
+ case 'A': {
+ const char *end = H5_optarg;
+ while (end && *end != '\0') {
+ char buf[10];
+
+ HDmemset(buf, '\0', sizeof(buf));
+
+ for (i = 0; *end != '\0' && *end != ','; ++end)
+ if (HDisalnum(*end) && i < 10)
+ buf[i++] = *end;
+
+ if (!HDstrcasecmp(buf, "hdf5")) {
+ cl_opts->io_types |= SIO_HDF5;
+ }
+ else if (!HDstrcasecmp(buf, "posix")) {
+ cl_opts->io_types |= SIO_POSIX;
+ }
+ else {
+ HDfprintf(stderr, "sio_perf: invalid --api option %s\n", buf);
+ HDexit(EXIT_FAILURE);
+ }
+
+ if (*end == '\0')
+ break;
+
+ end++;
+ }
+ }
+
+ break;
+#if 0
+ case 'b':
+ /* the future "binary" option */
+ break;
+#endif /* 0 */
+ case 'c':
+ /* Turn on chunked HDF5 dataset creation */
+ cl_opts->h5_use_chunks = 1;
+ {
+ const char *end = H5_optarg;
+ int j = 0;
+
+ while (end && *end != '\0') {
+ char buf[10];
+
+ HDmemset(buf, '\0', sizeof(buf));
+
+ for (i = 0; *end != '\0' && *end != ','; ++end)
+ if (HDisalnum(*end) && i < 10)
+ buf[i++] = *end;
+
+ cl_opts->chk_size[j] = parse_size_directive(buf);
+
+ j++;
+
+ if (*end == '\0')
+ break;
+
+ end++;
+ }
+ cl_opts->chk_rank = j;
+ }
+
+ break;
+
+ case 'D': {
+ const char *end = H5_optarg;
+
+ while (end && *end != '\0') {
+ char buf[10];
+
+ HDmemset(buf, '\0', sizeof(buf));
+
+ for (i = 0; *end != '\0' && *end != ','; ++end)
+ if (HDisalnum(*end) && i < 10)
+ buf[i++] = *end;
+
+ if (HDstrlen(buf) > 1 || HDisdigit(buf[0])) {
+ size_t j;
+
+ for (j = 0; j < 10 && buf[j] != '\0'; ++j)
+ if (!HDisdigit(buf[j])) {
+ HDfprintf(stderr, "sio_perf: invalid --debug option %s\n", buf);
+ HDexit(EXIT_FAILURE);
+ }
+
+ sio_debug_level = atoi(buf);
+
+ if (sio_debug_level > 4)
+ sio_debug_level = 4;
+ else if (sio_debug_level < 0)
+ sio_debug_level = 0;
+ }
+ else {
+ switch (*buf) {
+ case 'r':
+ /* Turn on raw data throughput info */
+ cl_opts->print_raw = TRUE;
+ break;
+ case 't':
+ /* Turn on time printing */
+ cl_opts->print_times = TRUE;
+ break;
+ case 'v':
+ /* Turn on verify data correctness*/
+ cl_opts->verify = TRUE;
+ break;
+ default:
+ HDfprintf(stderr, "sio_perf: invalid --debug option %s\n", buf);
+ HDexit(EXIT_FAILURE);
+ }
+ }
+
+ if (*end == '\0')
+ break;
+
+ end++;
+ }
+ }
+
+ break;
+ case 'e': {
+ const char *end = H5_optarg;
+ int j = 0;
+
+ while (end && *end != '\0') {
+ char buf[10];
+
+ HDmemset(buf, '\0', sizeof(buf));
+
+ for (i = 0; *end != '\0' && *end != ','; ++end)
+ if (HDisalnum(*end) && i < 10)
+ buf[i++] = *end;
+
+ cl_opts->dset_size[j] = parse_size_directive(buf);
+
+ j++;
+
+ if (*end == '\0')
+ break;
+
+ end++;
+ }
+ cl_opts->dset_rank = j;
+ }
+
+ break;
+
+ case 'i':
+ cl_opts->num_iters = HDatoi(H5_optarg);
+ break;
+ case 'o':
+ cl_opts->output_file = H5_optarg;
+ break;
+ case 'T':
+ cl_opts->h5_threshold = parse_size_directive(H5_optarg);
+ break;
+ case 'v':
+ if (!HDstrcasecmp(H5_optarg, "sec2")) {
+ cl_opts->vfd = sec2;
+ }
+ else if (!HDstrcasecmp(H5_optarg, "stdio")) {
+ cl_opts->vfd = stdio;
+ }
+ else if (!HDstrcasecmp(H5_optarg, "core")) {
+ cl_opts->vfd = core;
+ }
+ else if (!HDstrcasecmp(H5_optarg, "split")) {
+ cl_opts->vfd = split;
+ }
+ else if (!HDstrcasecmp(H5_optarg, "multi")) {
+ cl_opts->vfd = multi;
+ }
+ else if (!HDstrcasecmp(H5_optarg, "family")) {
+ cl_opts->vfd = family;
+ }
+ else if (!HDstrcasecmp(H5_optarg, "direct")) {
+ cl_opts->vfd = direct;
+ }
+ else {
+ HDfprintf(stderr, "sio_perf: invalid --api option %s\n", H5_optarg);
+ HDexit(EXIT_FAILURE);
+ }
+ break;
+ case 'w':
+ cl_opts->h5_write_only = TRUE;
+ break;
+ case 't':
+ cl_opts->h5_extendable = TRUE;
+ break;
+ case 'x': {
+ const char *end = H5_optarg;
+ int j = 0;
+
+ while (end && *end != '\0') {
+ char buf[10];
+
+ HDmemset(buf, '\0', sizeof(buf));
+
+ for (i = 0; *end != '\0' && *end != ','; ++end)
+ if (HDisalnum(*end) && i < 10)
+ buf[i++] = *end;
+
+ cl_opts->buf_size[j] = parse_size_directive(buf);
+
+ j++;
+
+ if (*end == '\0')
+ break;
+
+ end++;
+ }
+ cl_opts->buf_rank = j;
+ }
+
+ break;
+
+ case 'r': {
+ const char *end = H5_optarg;
+ int j = 0;
+
+ while (end && *end != '\0') {
+ char buf[10];
+
+ HDmemset(buf, '\0', sizeof(buf));
+
+ for (i = 0; *end != '\0' && *end != ','; ++end)
+ if (HDisalnum(*end) && i < 10)
+ buf[i++] = *end;
+
+ cl_opts->order[j] = (int)parse_size_directive(buf);
+
+ j++;
+
+ if (*end == '\0')
+ break;
+
+ end++;
+ }
+
+ cl_opts->order_rank = j;
+ }
+
+ break;
+
+ case 'h':
+ case '?':
+ default:
+ usage(progname);
+ HDfree(cl_opts);
+ return NULL;
+ }
+ }
+
+ /* perform rank consistency analysis */
+ actual_rank = 0;
+
+ ranks[0] = cl_opts->dset_rank;
+ ranks[1] = cl_opts->buf_rank;
+ ranks[2] = cl_opts->order_rank;
+ ranks[3] = cl_opts->chk_rank;
+
+ for (i = 0; i < 4; i++) {
+ if (ranks[i] > 0) {
+ if (!actual_rank) {
+ actual_rank = ranks[i];
+ }
+ else {
+ if (actual_rank != ranks[i])
+ exit(EXIT_FAILURE);
+ }
+ }
+ }
+
+ if (!actual_rank)
+ actual_rank = default_rank;
+
+ cl_opts->dset_rank = actual_rank;
+ cl_opts->buf_rank = actual_rank;
+ cl_opts->order_rank = actual_rank;
+ cl_opts->chk_rank = actual_rank;
+
+ for (i = 0; i < actual_rank; i++) {
+ if (cl_opts->order[i] > actual_rank) {
+ exit(EXIT_FAILURE);
+ }
+ }
+
+ /* set default if none specified yet */
+ if (!cl_opts->io_types)
+ cl_opts->io_types = SIO_HDF5 | SIO_POSIX; /* run all API */
+
+ /* verify parameters sanity. Adjust if needed. */
+ /* cap xfer_size with bytes per process */
+ if (cl_opts->num_iters <= 0)
+ cl_opts->num_iters = 1;
+
+ return cl_opts;
+}
+
+/*
+ * Function: parse_size_directive
+ * Purpose: Parse the size directive passed on the commandline. The size
+ * directive is an integer followed by a size indicator:
+ *
+ * K, k - Kilobyte
+ * M, m - Megabyte
+ * G, g - Gigabyte
+ *
+ * Return: The size as a off_t because this is related to file size.
+ * If an unknown size indicator is used, then the program will
+ * exit with EXIT_FAILURE as the return value.
+ * Programmer: Bill Wendling, 18. December 2001
+ * Modifications:
+ */
+
+static hsize_t
+parse_size_directive(const char *size)
+{
+ hsize_t s;
+ char * endptr;
+
+ s = HDstrtoull(size, &endptr, 10);
+
+ if (endptr && *endptr) {
+ while (*endptr != '\0' && (*endptr == ' ' || *endptr == '\t'))
+ ++endptr;
+
+ switch (*endptr) {
+ case 'K':
+ case 'k':
+ s *= ONE_KB;
+ break;
+
+ case 'M':
+ case 'm':
+ s *= ONE_MB;
+ break;
+
+ case 'G':
+ case 'g':
+ s *= ONE_GB;
+ break;
+
+ default:
+ HDfprintf(stderr, "Illegal size specifier '%c'\n", *endptr);
+ HDexit(EXIT_FAILURE);
+ }
+ }
+
+ return s;
+}
+
+/*
+ * Function: usage
+ * Purpose: Print a usage message and then exit.
+ * Return: Nothing
+ * Programmer: Bill Wendling, 31. October 2001
+ * Modifications:
+ */
+static void
+usage(const char *prog)
+{
+ print_version(prog);
+ HDprintf("usage: %s [OPTIONS]\n", prog);
+ HDprintf(" OPTIONS\n");
+ HDprintf(" -h Print an usage message and exit\n");
+ HDprintf(" -A AL Which APIs to test\n");
+ HDprintf(" [default: all of them]\n");
+ HDprintf(" -c SL Selects chunked storage and defines chunks dimensions\n");
+ HDprintf(" and sizes\n");
+ HDprintf(" [default: Off]\n");
+ HDprintf(" -e SL Dimensions and sizes of dataset\n");
+ HDprintf(" [default: 100,200]\n");
+ HDprintf(" -i N Number of iterations to perform\n");
+ HDprintf(" [default: 1]\n");
+ HDprintf(" -r NL Dimension access order (see below for description)\n");
+ HDprintf(" [default: 1,2]\n");
+ HDprintf(" -t Selects extendable dimensions for HDF5 dataset\n");
+ HDprintf(" [default: Off]\n");
+ HDprintf(" -v VFD Selects file driver for HDF5 access\n");
+ HDprintf(" [default: sec2]\n");
+ HDprintf(" -w Perform write tests, not the read tests\n");
+ HDprintf(" [default: Off]\n");
+ HDprintf(" -x SL Dimensions and sizes of the transfer buffer\n");
+ HDprintf(" [default: 10,20]\n");
+ HDprintf("\n");
+ HDprintf(" N - is an integer > 0.\n");
+ HDprintf("\n");
+ HDprintf(" S - is a size specifier, an integer > 0 followed by a size indicator:\n");
+ HDprintf(" K - Kilobyte (%d)\n", ONE_KB);
+ HDprintf(" M - Megabyte (%d)\n", ONE_MB);
+ HDprintf(" G - Gigabyte (%d)\n", ONE_GB);
+ HDprintf("\n");
+ HDprintf(" Example: '37M' is 37 megabytes or %d bytes\n", 37 * ONE_MB);
+ HDprintf("\n");
+ HDprintf(" AL - is an API list. Valid values are:\n");
+ HDprintf(" hdf5 - HDF5\n");
+ HDprintf(" posix - POSIX\n");
+ HDprintf("\n");
+ HDprintf(" Example: -A posix,hdf5\n");
+ HDprintf("\n");
+ HDprintf(" NL - is list of integers (N) separated by commas.\n");
+ HDprintf("\n");
+ HDprintf(" Example: 1,2,3\n");
+ HDprintf("\n");
+ HDprintf(" SL - is list of size specifiers (S) separated by commas.\n");
+ HDprintf("\n");
+ HDprintf(" Example: 2K,2K,3K\n");
+ HDprintf("\n");
+ HDprintf(" The example defines an object (dataset, tranfer buffer) with three\n");
+ HDprintf(" dimensions. Be aware that as the number of dimensions increases, the\n");
+ HDprintf(" the total size of the object increases exponentially.\n");
+ HDprintf("\n");
+ HDprintf(" VFD - is an HDF5 file driver specifier. Valid values are:\n");
+ HDprintf(" sec2, stdio, core, split, multi, family, direct\n");
+ HDprintf("\n");
+ HDprintf(" Dimension access order:\n");
+ HDprintf(" Data access starts at the cardinal origin of the dataset using the\n");
+ HDprintf(" transfer buffer. The next access occurs on a dataset region next to\n");
+ HDprintf(" the previous one. For a multidimensional dataset, there are several\n");
+ HDprintf(" directions as to where to proceed. This can be specified in the dimension\n");
+ HDprintf(" access order. For example, -r 1,2 states that the tool should traverse\n");
+ HDprintf(" dimension 1 first, and then dimension 2.\n");
+ HDprintf("\n");
+ HDprintf(" Environment variables:\n");
+ HDprintf(" HDF5_NOCLEANUP Do not remove data files if set [default remove]\n");
+ HDprintf(" HDF5_PREFIX Data file prefix\n");
+ HDprintf("\n");
+ HDfflush(stdout);
+} /* end usage() */
diff --git a/tools/src/h5perf/sio_perf.h b/tools/src/h5perf/sio_perf.h
new file mode 100644
index 0000000..d998377
--- /dev/null
+++ b/tools/src/h5perf/sio_perf.h
@@ -0,0 +1,104 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * Copyright by The HDF Group. *
+ * All rights reserved. *
+ * *
+ * This file is part of HDF5. The full HDF5 copyright notice, including *
+ * terms governing use, modification, and redistribution, is contained in *
+ * the COPYING file, which can be found at the root of the source code *
+ * distribution tree, or in https://www.hdfgroup.org/licenses. *
+ * If you do not have access to either file, you may request a copy from *
+ * help@hdfgroup.org. *
+ * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
+
+#ifndef SIO_PERF_H
+#define SIO_PERF_H
+
+#ifndef STANDALONE
+#include "io_timer.h"
+#include "H5private.h"
+#include "h5tools.h"
+#include "h5tools_utils.h"
+#else
+#include "io_timer.h"
+#include "sio_standalone.h"
+#endif
+
+/* setup the dataset no fill option if this is v1.5 or more */
+#if H5_VERS_MAJOR > 1 || H5_VERS_MINOR > 4
+#define H5_HAVE_NOFILL 1
+#endif
+
+#define MAX_DIMS 32
+
+typedef enum iotype_ {
+ POSIXIO,
+ HDF5
+ /*NUM_TYPES*/
+} iotype;
+
+typedef enum vfdtype_ {
+ sec2,
+ stdio,
+ core,
+ split,
+ multi,
+ family,
+ direct
+ /*NUM_TYPES*/
+} vfdtype;
+
+typedef struct parameters_ {
+ iotype io_type; /* The type of IO test to perform */
+ vfdtype vfd;
+ long num_files; /* Number of files to create */
+ long num_dsets; /* Number of datasets to create */
+ hsize_t num_bytes; /* Number of bytes in each dset */
+ int num_iters; /* Number of times to loop doing the IO */
+ int rank; /* Rank of dataset */
+ hsize_t dset_size[MAX_DIMS]; /* Dataset size */
+ size_t buf_size[MAX_DIMS]; /* Buffer size */
+ size_t chk_size[MAX_DIMS]; /* Chunk size */
+ int order[MAX_DIMS]; /* Buffer size */
+ hsize_t h5_align; /* HDF5 object alignment */
+ hsize_t h5_thresh; /* HDF5 object alignment threshold */
+ int h5_use_chunks; /* Make HDF5 dataset chunked */
+ int h5_extendable; /* Make HDF5 dataset chunked */
+ int h5_write_only; /* Perform the write tests only */
+ int verify; /* Verify data correctness */
+ size_t page_size;
+ size_t page_buffer_size;
+} parameters;
+
+typedef struct results_ {
+ herr_t ret_code;
+ io_time_t *timers;
+} results;
+
+#ifndef SUCCESS
+#define SUCCESS 0
+#endif /* !SUCCESS */
+
+#ifndef FAIL
+#define FAIL -1
+#endif /* !FAIL */
+
+extern FILE * output; /* output file */
+extern io_time_t *timer_g; /* timer: global for stub functions */
+extern int sio_debug_level; /* The debug level:
+ * 0 - Off
+ * 1 - Minimal
+ * 2 - Some more
+ * 3 - Maximal
+ * 4 - Even More Debugging (timer stuff)
+ */
+#ifdef __cplusplus
+extern "C" {
+#endif /* __cplusplus */
+
+extern void do_sio(parameters param, results *res);
+
+#ifdef __cplusplus
+}
+#endif /* __cplusplus */
+
+#endif /* SIO_PERF_H */
diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c
index 1f1b821..3526268 100644
--- a/tools/src/h5repack/h5repack_main.c
+++ b/tools/src/h5repack/h5repack_main.c
@@ -31,44 +31,44 @@ const char *outfile = NULL;
* Command-line options: The user can specify short or long-named
* parameters.
*/
-static const char * s_opts = "a:b:c:d:e:f:hi:j:k:l:m:no:q:s:t:u:vz:EG:LM:P:S:T:VXW1:2:3:4:5:6:";
-static struct long_options l_opts[] = {{"alignment", require_arg, 'a'},
- {"block", require_arg, 'b'},
- {"compact", require_arg, 'c'},
- {"indexed", require_arg, 'd'},
- {"file", require_arg, 'e'},
- {"filter", require_arg, 'f'},
- {"help", no_arg, 'h'},
- {"infile", require_arg, 'i'}, /* for backward compability */
- {"low", require_arg, 'j'},
- {"high", require_arg, 'k'},
- {"layout", require_arg, 'l'},
- {"minimum", require_arg, 'm'},
- {"native", no_arg, 'n'},
- {"outfile", require_arg, 'o'}, /* for backward compability */
- {"sort_by", require_arg, 'q'},
- {"ssize", require_arg, 's'},
- {"threshold", require_arg, 't'},
- {"ublock", require_arg, 'u'},
- {"verbose", no_arg, 'v'},
- {"sort_order", require_arg, 'z'},
- {"enable-error-stack", no_arg, 'E'},
- {"fs_pagesize", require_arg, 'G'},
- {"latest", no_arg, 'L'},
- {"metadata_block_size", require_arg, 'M'},
- {"fs_persist", require_arg, 'P'},
- {"fs_strategy", require_arg, 'S'},
- {"fs_threshold", require_arg, 'T'},
- {"version", no_arg, 'V'},
- {"merge", no_arg, 'X'},
- {"prune", no_arg, 'W'},
- {"src-vol-value", require_arg, '1'},
- {"src-vol-name", require_arg, '2'},
- {"src-vol-info", require_arg, '3'},
- {"dst-vol-value", require_arg, '4'},
- {"dst-vol-name", require_arg, '5'},
- {"dst-vol-info", require_arg, '6'},
- {NULL, 0, '\0'}};
+static const char * s_opts = "a:b:c:d:e:f:hi:j:k:l:m:no:q:s:t:u:vz:EG:LM:P:S:T:VXW1:2:3:4:5:6:";
+static struct h5_long_options l_opts[] = {{"alignment", require_arg, 'a'},
+ {"block", require_arg, 'b'},
+ {"compact", require_arg, 'c'},
+ {"indexed", require_arg, 'd'},
+ {"file", require_arg, 'e'},
+ {"filter", require_arg, 'f'},
+ {"help", no_arg, 'h'},
+ {"infile", require_arg, 'i'}, /* for backward compability */
+ {"low", require_arg, 'j'},
+ {"high", require_arg, 'k'},
+ {"layout", require_arg, 'l'},
+ {"minimum", require_arg, 'm'},
+ {"native", no_arg, 'n'},
+ {"outfile", require_arg, 'o'}, /* for backward compability */
+ {"sort_by", require_arg, 'q'},
+ {"ssize", require_arg, 's'},
+ {"threshold", require_arg, 't'},
+ {"ublock", require_arg, 'u'},
+ {"verbose", no_arg, 'v'},
+ {"sort_order", require_arg, 'z'},
+ {"enable-error-stack", no_arg, 'E'},
+ {"fs_pagesize", require_arg, 'G'},
+ {"latest", no_arg, 'L'},
+ {"metadata_block_size", require_arg, 'M'},
+ {"fs_persist", require_arg, 'P'},
+ {"fs_strategy", require_arg, 'S'},
+ {"fs_threshold", require_arg, 'T'},
+ {"version", no_arg, 'V'},
+ {"merge", no_arg, 'X'},
+ {"prune", no_arg, 'W'},
+ {"src-vol-value", require_arg, '1'},
+ {"src-vol-name", require_arg, '2'},
+ {"src-vol-info", require_arg, '3'},
+ {"dst-vol-value", require_arg, '4'},
+ {"dst-vol-name", require_arg, '5'},
+ {"dst-vol-info", require_arg, '6'},
+ {NULL, 0, '\0'}};
/*-------------------------------------------------------------------------
* Function: usage
@@ -363,7 +363,7 @@ read_info(const char *filename, pack_opt_t *options)
/* cycle until end of file reached */
while (1) {
- if (EOF == fscanf(fp, "%9s", stype))
+ if (EOF == HDfscanf(fp, "%9s", stype))
break;
/* Info indicator must be for layout or filter */
@@ -378,7 +378,7 @@ read_info(const char *filename, pack_opt_t *options)
i = 0;
c = '0';
while (c != ' ') {
- if (fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
+ if (HDfscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
error_msg("fscanf error\n");
h5tools_setstatus(EXIT_FAILURE);
ret_value = EXIT_FAILURE;
@@ -390,7 +390,7 @@ read_info(const char *filename, pack_opt_t *options)
c = '0';
/* go until end */
while (c != ' ') {
- if (fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
+ if (HDfscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
error_msg("fscanf error\n");
h5tools_setstatus(EXIT_FAILURE);
ret_value = EXIT_FAILURE;
@@ -497,18 +497,18 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
HDmemset(&out_vol_info, 0, sizeof(h5tools_vol_info_t));
/* parse command line options */
- while (EOF != (opt = get_option(argc, argv, s_opts, l_opts))) {
+ while (EOF != (opt = H5_get_option(argc, argv, s_opts, l_opts))) {
switch ((char)opt) {
/* -i for backward compatibility */
case 'i':
- infile = opt_arg;
+ infile = H5_optarg;
has_i++;
break;
/* -o for backward compatibility */
case 'o':
- outfile = opt_arg;
+ outfile = H5_optarg;
has_o++;
break;
@@ -530,7 +530,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
case 'f':
/* parse the -f filter option */
- if (h5repack_addfilter(opt_arg, options) < 0) {
+ if (h5repack_addfilter(H5_optarg, options) < 0) {
error_msg("in parsing filter\n");
h5tools_setstatus(EXIT_FAILURE);
ret_value = -1;
@@ -540,7 +540,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
case 'l':
/* parse the -l layout option */
- if (h5repack_addlayout(opt_arg, options) < 0) {
+ if (h5repack_addlayout(H5_optarg, options) < 0) {
error_msg("in parsing layout\n");
h5tools_setstatus(EXIT_FAILURE);
ret_value = -1;
@@ -549,9 +549,9 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
break;
case 'm':
- options->min_comp = HDstrtoull(opt_arg, NULL, 0);
+ options->min_comp = HDstrtoull(H5_optarg, NULL, 0);
if ((int)options->min_comp <= 0) {
- error_msg("invalid minimum compress size <%s>\n", opt_arg);
+ error_msg("invalid minimum compress size <%s>\n", H5_optarg);
h5tools_setstatus(EXIT_FAILURE);
ret_value = -1;
goto done;
@@ -559,8 +559,8 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
break;
case 'e':
- if ((ret_value = read_info(opt_arg, options)) < 0) {
- error_msg("failed to read from repack options file <%s>\n", opt_arg);
+ if ((ret_value = read_info(H5_optarg, options)) < 0) {
+ error_msg("failed to read from repack options file <%s>\n", H5_optarg);
h5tools_setstatus(EXIT_FAILURE);
ret_value = -1;
goto done;
@@ -576,7 +576,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
break;
case 'j':
- bound = HDatoi(opt_arg);
+ bound = HDatoi(H5_optarg);
if (bound < H5F_LIBVER_EARLIEST || bound > H5F_LIBVER_LATEST) {
error_msg("in parsing low bound\n");
h5tools_setstatus(EXIT_FAILURE);
@@ -587,7 +587,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
break;
case 'k':
- bound = HDatoi(opt_arg);
+ bound = HDatoi(H5_optarg);
if (bound < H5F_LIBVER_EARLIEST || bound > H5F_LIBVER_LATEST) {
error_msg("in parsing high bound\n");
h5tools_setstatus(EXIT_FAILURE);
@@ -606,13 +606,13 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
break;
case 'c':
- options->grp_compact = HDatoi(opt_arg);
+ options->grp_compact = HDatoi(H5_optarg);
if (options->grp_compact > 0)
options->latest = TRUE; /* must use latest format */
break;
case 'd':
- options->grp_indexed = HDatoi(opt_arg);
+ options->grp_indexed = HDatoi(H5_optarg);
if (options->grp_indexed > 0)
options->latest = TRUE; /* must use latest format */
break;
@@ -620,10 +620,10 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
case 's': {
int idx = 0;
int ssize = 0;
- char *msgPtr = HDstrchr(opt_arg, ':');
+ char *msgPtr = HDstrchr(H5_optarg, ':');
options->latest = TRUE; /* must use latest format */
if (msgPtr == NULL) {
- ssize = HDatoi(opt_arg);
+ ssize = HDatoi(H5_optarg);
for (idx = 0; idx < 5; idx++)
options->msg_size[idx] = ssize;
}
@@ -632,7 +632,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
HDstrcpy(msgType, msgPtr + 1);
msgPtr[0] = '\0';
- ssize = HDatoi(opt_arg);
+ ssize = HDatoi(H5_optarg);
if (!HDstrncmp(msgType, "dspace", 6))
options->msg_size[0] = ssize;
else if (!HDstrncmp(msgType, "dtype", 5))
@@ -647,25 +647,25 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
} break;
case 'u':
- options->ublock_filename = opt_arg;
+ options->ublock_filename = H5_optarg;
break;
case 'b':
- options->ublock_size = (hsize_t)HDatol(opt_arg);
+ options->ublock_size = (hsize_t)HDatol(H5_optarg);
break;
case 'M':
- options->meta_block_size = (hsize_t)HDatol(opt_arg);
+ options->meta_block_size = (hsize_t)HDatol(H5_optarg);
break;
case 't':
- options->threshold = (hsize_t)HDatol(opt_arg);
+ options->threshold = (hsize_t)HDatol(H5_optarg);
break;
case 'a':
- options->alignment = HDstrtoull(opt_arg, NULL, 0);
+ options->alignment = HDstrtoull(H5_optarg, NULL, 0);
if (options->alignment < 1) {
- error_msg("invalid alignment size\n", opt_arg);
+ error_msg("invalid alignment size\n", H5_optarg);
h5tools_setstatus(EXIT_FAILURE);
ret_value = -1;
goto done;
@@ -675,7 +675,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
case 'S': {
char strategy[MAX_NC_NAME];
- HDstrcpy(strategy, opt_arg);
+ HDstrcpy(strategy, H5_optarg);
if (!HDstrcmp(strategy, "FSM_AGGR"))
options->fs_strategy = H5F_FSPACE_STRATEGY_FSM_AGGR;
else if (!HDstrcmp(strategy, "PAGE"))
@@ -685,7 +685,7 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
else if (!HDstrcmp(strategy, "NONE"))
options->fs_strategy = H5F_FSPACE_STRATEGY_NONE;
else {
- error_msg("invalid file space management strategy\n", opt_arg);
+ error_msg("invalid file space management strategy\n", H5_optarg);
h5tools_setstatus(EXIT_FAILURE);
ret_value = -1;
goto done;
@@ -696,29 +696,29 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
} break;
case 'P':
- options->fs_persist = HDatoi(opt_arg);
+ options->fs_persist = HDatoi(H5_optarg);
if (options->fs_persist == 0)
/* To distinguish the "specified" zero value */
options->fs_persist = -1;
break;
case 'T':
- options->fs_threshold = HDatol(opt_arg);
+ options->fs_threshold = HDatol(H5_optarg);
if (options->fs_threshold == 0)
/* To distinguish the "specified" zero value */
options->fs_threshold = -1;
break;
case 'G':
- options->fs_pagesize = HDstrtoll(opt_arg, NULL, 0);
+ options->fs_pagesize = HDstrtoll(H5_optarg, NULL, 0);
if (options->fs_pagesize == 0)
/* To distinguish the "specified" zero value */
options->fs_pagesize = -1;
break;
case 'q':
- if (H5_INDEX_UNKNOWN == (sort_by = set_sort_by(opt_arg))) {
- error_msg("failed to set sort by form <%s>\n", opt_arg);
+ if (H5_INDEX_UNKNOWN == (sort_by = set_sort_by(H5_optarg))) {
+ error_msg("failed to set sort by form <%s>\n", H5_optarg);
h5tools_setstatus(EXIT_FAILURE);
ret_value = -1;
goto done;
@@ -726,8 +726,8 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
break;
case 'z':
- if (H5_ITER_UNKNOWN == (sort_order = set_sort_order(opt_arg))) {
- error_msg("failed to set sort order form <%s>\n", opt_arg);
+ if (H5_ITER_UNKNOWN == (sort_order = set_sort_order(H5_optarg))) {
+ error_msg("failed to set sort order form <%s>\n", H5_optarg);
h5tools_setstatus(EXIT_FAILURE);
ret_value = -1;
goto done;
@@ -740,34 +740,34 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
case '1':
in_vol_info.type = VOL_BY_VALUE;
- in_vol_info.u.value = (H5VL_class_value_t)HDatoi(opt_arg);
+ in_vol_info.u.value = (H5VL_class_value_t)HDatoi(H5_optarg);
custom_in_fapl = TRUE;
break;
case '2':
in_vol_info.type = VOL_BY_NAME;
- in_vol_info.u.name = opt_arg;
+ in_vol_info.u.name = H5_optarg;
custom_in_fapl = TRUE;
break;
case '3':
- in_vol_info.info_string = opt_arg;
+ in_vol_info.info_string = H5_optarg;
break;
case '4':
out_vol_info.type = VOL_BY_VALUE;
- out_vol_info.u.value = (H5VL_class_value_t)HDatoi(opt_arg);
+ out_vol_info.u.value = (H5VL_class_value_t)HDatoi(H5_optarg);
custom_out_fapl = TRUE;
break;
case '5':
out_vol_info.type = VOL_BY_NAME;
- out_vol_info.u.name = opt_arg;
+ out_vol_info.u.name = H5_optarg;
custom_out_fapl = TRUE;
break;
case '6':
- out_vol_info.info_string = opt_arg;
+ out_vol_info.info_string = H5_optarg;
break;
default:
@@ -777,9 +777,9 @@ parse_command_line(int argc, const char **argv, pack_opt_t *options)
/* If neither -i nor -o given, get in and out files positionally */
if (0 == (has_i + has_o)) {
- if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) {
- infile = argv[opt_ind];
- outfile = argv[opt_ind + 1];
+ if (argv[H5_optind] != NULL && argv[H5_optind + 1] != NULL) {
+ infile = argv[H5_optind];
+ outfile = argv[H5_optind + 1];
if (!HDstrcmp(infile, outfile)) {
error_msg("file names cannot be the same\n");
diff --git a/tools/src/h5stat/h5stat.c b/tools/src/h5stat/h5stat.c
index 853f3ce..d97a628 100644
--- a/tools/src/h5stat/h5stat.c
+++ b/tools/src/h5stat/h5stat.c
@@ -171,106 +171,23 @@ struct handler_t {
static const char *s_opts = "Aa:Ddm:EFfhGgl:sSTO:Vw:H:";
/* e.g. "filemetadata" has to precede "file"; "groupmetadata" has to precede "group" etc. */
-static struct long_options l_opts[] = {{"help", no_arg, 'h'},
- {"hel", no_arg, 'h'},
- {"he", no_arg, 'h'},
- {"filemetadata", no_arg, 'F'},
- {"filemetadat", no_arg, 'F'},
- {"filemetada", no_arg, 'F'},
- {"filemetad", no_arg, 'F'},
- {"filemeta", no_arg, 'F'},
- {"filemet", no_arg, 'F'},
- {"fileme", no_arg, 'F'},
- {"filem", no_arg, 'F'},
- {"file", no_arg, 'f'},
- {"fil", no_arg, 'f'},
- {"fi", no_arg, 'f'},
- {"groupmetadata", no_arg, 'G'},
- {"groupmetadat", no_arg, 'G'},
- {"groupmetada", no_arg, 'G'},
- {"groupmetad", no_arg, 'G'},
- {"groupmeta", no_arg, 'G'},
- {"groupmet", no_arg, 'G'},
- {"groupme", no_arg, 'G'},
- {"groupm", no_arg, 'G'},
- {"group", no_arg, 'g'},
- {"grou", no_arg, 'g'},
- {"gro", no_arg, 'g'},
- {"gr", no_arg, 'g'},
- {"links", require_arg, 'l'},
- {"link", require_arg, 'l'},
- {"lin", require_arg, 'l'},
- {"li", require_arg, 'l'},
- {"dsetmetadata", no_arg, 'D'},
- {"dsetmetadat", no_arg, 'D'},
- {"dsetmetada", no_arg, 'D'},
- {"dsetmetad", no_arg, 'D'},
- {"dsetmeta", no_arg, 'D'},
- {"dsetmet", no_arg, 'D'},
- {"dsetme", no_arg, 'D'},
- {"dsetm", no_arg, 'D'},
- {"dset", no_arg, 'd'},
- {"dse", no_arg, 'd'},
- {"ds", no_arg, 'd'},
- {"dims", require_arg, 'm'},
- {"dim", require_arg, 'm'},
- {"di", require_arg, 'm'},
- {"dtypemetadata", no_arg, 'T'},
- {"dtypemetadat", no_arg, 'T'},
- {"dtypemetada", no_arg, 'T'},
- {"dtypemetad", no_arg, 'T'},
- {"dtypemeta", no_arg, 'T'},
- {"dtypemet", no_arg, 'T'},
- {"dtypeme", no_arg, 'T'},
- {"dtypem", no_arg, 'T'},
- {"dtype", no_arg, 'T'},
- {"dtyp", no_arg, 'T'},
- {"dty", no_arg, 'T'},
- {"dt", no_arg, 'T'},
- {"object", require_arg, 'O'},
- {"objec", require_arg, 'O'},
- {"obje", require_arg, 'O'},
- {"obj", require_arg, 'O'},
- {"ob", require_arg, 'O'},
- {"version", no_arg, 'V'},
- {"versio", no_arg, 'V'},
- {"versi", no_arg, 'V'},
- {"vers", no_arg, 'V'},
- {"ver", no_arg, 'V'},
- {"ve", no_arg, 'V'},
- {"attribute", no_arg, 'A'},
- {"attribut", no_arg, 'A'},
- {"attribu", no_arg, 'A'},
- {"attrib", no_arg, 'A'},
- {"attri", no_arg, 'A'},
- {"attr", no_arg, 'A'},
- {"att", no_arg, 'A'},
- {"at", no_arg, 'A'},
- {"enable-error-stack", no_arg, 'E'},
- {"numattrs", require_arg, 'a'},
- {"numattr", require_arg, 'a'},
- {"numatt", require_arg, 'a'},
- {"numat", require_arg, 'a'},
- {"numa", require_arg, 'a'},
- {"num", require_arg, 'a'},
- {"nu", require_arg, 'a'},
- {"freespace", no_arg, 's'},
- {"freespac", no_arg, 's'},
- {"freespa", no_arg, 's'},
- {"freesp", no_arg, 's'},
- {"frees", no_arg, 's'},
- {"free", no_arg, 's'},
- {"fre", no_arg, 's'},
- {"fr", no_arg, 's'},
- {"summary", no_arg, 'S'},
- {"summar", no_arg, 'S'},
- {"summa", no_arg, 'S'},
- {"summ", no_arg, 'S'},
- {"sum", no_arg, 'S'},
- {"su", no_arg, 'S'},
- {"s3-cred", require_arg, 'w'},
- {"hdfs-attrs", require_arg, 'H'},
- {NULL, 0, '\0'}};
+static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'},
+ {"filemetadata", no_arg, 'F'},
+ {"groupmetadata", no_arg, 'G'},
+ {"links", require_arg, 'l'},
+ {"dsetmetadata", no_arg, 'D'},
+ {"dims", require_arg, 'm'},
+ {"dtypemetadata", no_arg, 'T'},
+ {"object", require_arg, 'O'},
+ {"version", no_arg, 'V'},
+ {"attribute", no_arg, 'A'},
+ {"enable-error-stack", no_arg, 'E'},
+ {"numattrs", require_arg, 'a'},
+ {"freespace", no_arg, 's'},
+ {"summary", no_arg, 'S'},
+ {"s3-cred", require_arg, 'w'},
+ {"hdfs-attrs", require_arg, 'H'},
+ {NULL, 0, '\0'}};
static void
leave(int ret)
@@ -920,7 +837,7 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
struct handler_t *hand = NULL;
/* parse command line options */
- while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+ while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
switch ((char)opt) {
case 'h':
usage(h5tools_getprogname());
@@ -959,8 +876,8 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
break;
case 'l':
- if (opt_arg) {
- sgroups_threshold = HDatoi(opt_arg);
+ if (H5_optarg) {
+ sgroups_threshold = HDatoi(H5_optarg);
if (sgroups_threshold < 1) {
error_msg("Invalid threshold for small groups\n");
goto error;
@@ -982,8 +899,8 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
break;
case 'm':
- if (opt_arg) {
- sdsets_threshold = HDatoi(opt_arg);
+ if (H5_optarg) {
+ sdsets_threshold = HDatoi(H5_optarg);
if (sdsets_threshold < 1) {
error_msg("Invalid threshold for small datasets\n");
goto error;
@@ -1005,8 +922,8 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
break;
case 'a':
- if (opt_arg) {
- sattrs_threshold = HDatoi(opt_arg);
+ if (H5_optarg) {
+ sattrs_threshold = HDatoi(H5_optarg);
if (sattrs_threshold < 1) {
error_msg("Invalid threshold for small # of attributes\n");
goto error;
@@ -1046,7 +963,7 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
/* Store object names */
for (u = 0; u < hand->obj_count; u++)
- if (NULL == (hand->obj[u] = HDstrdup(opt_arg))) {
+ if (NULL == (hand->obj[u] = HDstrdup(H5_optarg))) {
error_msg("unable to allocate memory for object name\n");
goto error;
} /* end if */
@@ -1054,7 +971,7 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
case 'w':
#ifdef H5_HAVE_ROS3_VFD
- if (h5tools_parse_ros3_fapl_tuple(opt_arg, ',', &ros3_fa) < 0) {
+ if (h5tools_parse_ros3_fapl_tuple(H5_optarg, ',', &ros3_fa) < 0) {
error_msg("failed to parse S3 VFD credential info\n");
goto error;
}
@@ -1068,7 +985,7 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
case 'H':
#ifdef H5_HAVE_LIBHDFS
- if (h5tools_parse_hdfs_fapl_tuple(opt_arg, ',', &hdfs_fa) < 0) {
+ if (h5tools_parse_hdfs_fapl_tuple(H5_optarg, ',', &hdfs_fa) < 0) {
error_msg("failed to parse HDFS VFD configuration info\n");
goto error;
}
@@ -1087,7 +1004,7 @@ parse_command_line(int argc, const char *argv[], struct handler_t **hand_ret)
} /* end while */
/* check for file name to be processed */
- if (argc <= opt_ind) {
+ if (argc <= H5_optind) {
error_msg("missing file name\n");
usage(h5tools_getprogname());
goto error;
@@ -1811,7 +1728,7 @@ main(int argc, const char *argv[])
}
}
- fname = argv[opt_ind];
+ fname = argv[H5_optind];
/* Check for filename given */
if (fname) {
diff --git a/tools/src/misc/h5clear.c b/tools/src/misc/h5clear.c
index ac7c0ca..008dae3 100644
--- a/tools/src/misc/h5clear.c
+++ b/tools/src/misc/h5clear.c
@@ -44,40 +44,11 @@ static hsize_t increment = DEFAULT_INCREMENT;
/*
* Command-line options: only publicize long options
*/
-static const char * s_opts = "hVsmzi*";
-static struct long_options l_opts[] = {{"help", no_arg, 'h'},
- {"hel", no_arg, 'h'},
- {"he", no_arg, 'h'},
- {"version", no_arg, 'V'},
- {"version", no_arg, 'V'},
- {"versio", no_arg, 'V'},
- {"versi", no_arg, 'V'},
- {"vers", no_arg, 'V'},
- {"status", no_arg, 's'},
- {"statu", no_arg, 's'},
- {"stat", no_arg, 's'},
- {"sta", no_arg, 's'},
- {"st", no_arg, 's'},
- {"image", no_arg, 'm'},
- {"imag", no_arg, 'm'},
- {"ima", no_arg, 'm'},
- {"im", no_arg, 'm'},
- {"filesize", no_arg, 'z'},
- {"filesiz", no_arg, 'z'},
- {"filesi", no_arg, 'z'},
- {"files", no_arg, 'z'},
- {"file", no_arg, 'z'},
- {"fil", no_arg, 'z'},
- {"fi", no_arg, 'z'},
- {"increment", optional_arg, 'i'},
- {"incremen", optional_arg, 'i'},
- {"increme", optional_arg, 'i'},
- {"increm", optional_arg, 'i'},
- {"incre", optional_arg, 'i'},
- {"incr", optional_arg, 'i'},
- {"inc", optional_arg, 'i'},
- {"in", optional_arg, 'i'},
- {NULL, 0, '\0'}};
+static const char * s_opts = "hVsmzi*";
+static struct h5_long_options l_opts[] = {
+ {"help", no_arg, 'h'}, {"version", no_arg, 'V'}, {"status", no_arg, 's'},
+ {"image", no_arg, 'm'}, {"filesize", no_arg, 'z'}, {"increment", optional_arg, 'i'},
+ {NULL, 0, '\0'}};
/*-------------------------------------------------------------------------
* Function: usage
@@ -150,7 +121,7 @@ parse_command_line(int argc, const char **argv)
}
/* parse command line options */
- while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+ while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
switch ((char)opt) {
case 'h':
usage(h5tools_getprogname());
@@ -176,12 +147,12 @@ parse_command_line(int argc, const char **argv)
case 'i':
increment_eoa_eof = TRUE;
- if (opt_arg != NULL) {
- if (HDatoi(opt_arg) < 0) {
+ if (H5_optarg != NULL) {
+ if (HDatoi(H5_optarg) < 0) {
usage(h5tools_getprogname());
goto done;
}
- increment = (hsize_t)HDatoi(opt_arg);
+ increment = (hsize_t)HDatoi(H5_optarg);
}
break;
@@ -193,14 +164,14 @@ parse_command_line(int argc, const char **argv)
} /* end while */
/* check for file name to be processed */
- if (argc <= opt_ind) {
+ if (argc <= H5_optind) {
error_msg("missing file name\n");
usage(h5tools_getprogname());
h5tools_setstatus(EXIT_FAILURE);
goto error;
} /* end if */
- fname_g = HDstrdup(argv[opt_ind]);
+ fname_g = HDstrdup(argv[H5_optind]);
done:
return (0);
diff --git a/tools/src/misc/h5mkgrp.c b/tools/src/misc/h5mkgrp.c
index 516191c..a85ee4d 100644
--- a/tools/src/misc/h5mkgrp.c
+++ b/tools/src/misc/h5mkgrp.c
@@ -22,8 +22,8 @@
int d_status = EXIT_SUCCESS;
/* command-line options: short and long-named parameters */
-static const char * s_opts = "hlpvV";
-static struct long_options l_opts[] = {
+static const char * s_opts = "hlpvV";
+static struct h5_long_options l_opts[] = {
{"help", no_arg, 'h'}, {"latest", no_arg, 'l'}, {"parents", no_arg, 'p'},
{"verbose", no_arg, 'v'}, {"version", no_arg, 'V'}, {"vol-value", require_arg, '1'},
{"vol-name", require_arg, '2'}, {"vol-info", require_arg, '3'}, {NULL, 0, '\0'}};
@@ -140,7 +140,7 @@ parse_command_line(int argc, const char *argv[], mkgrp_opt_t *options)
HDmemset(&vol_info, 0, sizeof(h5tools_vol_info_t));
/* Parse command line options */
- while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+ while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
switch ((char)opt) {
/* Display 'help' */
case 'h':
@@ -171,18 +171,18 @@ parse_command_line(int argc, const char *argv[], mkgrp_opt_t *options)
case '1':
vol_info.type = VOL_BY_VALUE;
- vol_info.u.value = (H5VL_class_value_t)HDatoi(opt_arg);
+ vol_info.u.value = (H5VL_class_value_t)HDatoi(H5_optarg);
custom_fapl = TRUE;
break;
case '2':
vol_info.type = VOL_BY_NAME;
- vol_info.u.name = opt_arg;
+ vol_info.u.name = H5_optarg;
custom_fapl = TRUE;
break;
case '3':
- vol_info.info_string = opt_arg;
+ vol_info.info_string = H5_optarg;
break;
/* Bad command line argument */
@@ -193,33 +193,33 @@ parse_command_line(int argc, const char *argv[], mkgrp_opt_t *options)
} /* end while */
/* Check for file name to be processed */
- if (argc <= opt_ind) {
+ if (argc <= H5_optind) {
error_msg("missing file name\n");
usage(h5tools_getprogname());
leave(EXIT_FAILURE);
}
/* Retrieve file name */
- options->fname = HDstrdup(argv[opt_ind]);
- opt_ind++;
+ options->fname = HDstrdup(argv[H5_optind]);
+ H5_optind++;
/* Check for group(s) to be created */
- if (argc <= opt_ind) {
+ if (argc <= H5_optind) {
error_msg("missing group name(s)\n");
usage(h5tools_getprogname());
leave(EXIT_FAILURE);
}
/* Allocate space for the group name pointers */
- options->ngroups = (size_t)(argc - opt_ind);
+ options->ngroups = (size_t)(argc - H5_optind);
options->groups = (char **)HDmalloc(options->ngroups * sizeof(char *));
/* Retrieve the group names */
curr_group = 0;
- while (opt_ind < argc) {
- options->groups[curr_group] = HDstrdup(argv[opt_ind]);
+ while (H5_optind < argc) {
+ options->groups[curr_group] = HDstrdup(argv[H5_optind]);
curr_group++;
- opt_ind++;
+ H5_optind++;
}
/* Setup a custom fapl for file accesses */
generated by cgit v0.12 at 2024-12-27 13:55:58 (GMT)