Merge pull request #2203 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:1.10/master to 1.10/masterhdf5-1_10_6

* commit 'e0fa36bfe008c03365ce8ea94d705f8fdebccdf0': (166 commits)
  Update release date strings in README.txt and release_docs/RELEASE.txt
  Add release note about using ompio instead of romio when collective writes fail with OpenMPI.
  Fixed typos, grammatical errors, etc. Expanded entry for S3 and HDFS VFDs. Moved Mac 10.11 and 10.12 from Supported Platforms to More Platforms Tested.
  Add qualification to RELEASE.txt regarding performance improvements
  Standalone doesn't use h5test implementation.
  Add missing note
  Update COPYING file with new HDF5 license.
  Update bin/config.guess and config.sub to current version available from git.savannah.gnu.org.
  Fix include to correct memory calls - big-endian issue.
  Revert BLDLIBDIR value in junit.sh.in.
  Corrections to CMake functions
  Update version for HDF5 1.10.6 release. Remove autom4te.cache directory that shouldn't have been added.
  Remove duplicate instance
  Fix merge issue
  HDFFV-10979 - fix global name clash
  Correct clang search and java include
  Latest date first in RELEASE.txt
  Update RELEASE.txt with performance improvements and Steven Varga's bugfix.
  Update version numbers for shared lib files according to api compatibility report.
  Created hdf5_1_10_6 branch for HDF5 1.10.6 release preparation. Set version to 1.10.6-pre1. Switched default  maintainer mode to disabled and default build mode to production. Added files produced by autogen.sh to commit except for src/H5config.h.in~ and src/H5public.h~.
  ...

1 files changed, 119 insertions, 119 deletions

diff --git a/tools/test/perform/sio_perf.c b/tools/test/perform/sio_perf.c
index e77b99e..90030d8 100644
--- a/tools/test/perform/sio_perf.c
+++ b/tools/test/perform/sio_perf.c
@@ -98,7 +98,7 @@ static const char  *progname = "h5perf_serial";
  * 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:b:c:Cd:D:e:F:G:ghi:Imno:p:P:r:stT:v:wx:X:";
+static const char *s_opts = "a:A:B:c:Cd:D:e:F:ghi:Imno:p:P:r:stT:v:wx:X:";
 static struct long_options l_opts[] = {
     { "align", require_arg, 'a' },
     { "alig", require_arg, 'a' },
@@ -281,14 +281,14 @@ struct options {
     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       */
+    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              */
+    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;
@@ -333,7 +333,7 @@ main(int argc, char **argv)
     /* Initialize h5tools lib */
     h5tools_init();
 #endif
-    
+
     output = stdout;
 
     opts = parse_command_line(argc, argv);
@@ -345,8 +345,8 @@ main(int argc, char **argv)
 
     if (opts->output_file) {
         if ((output = HDfopen(opts->output_file, "w")) == NULL) {
-            fprintf(stderr, "%s: cannot open output file\n", progname);
-            perror(opts->output_file);
+            HDfprintf(stderr, "%s: cannot open output file\n", progname);
+            HDperror(opts->output_file);
             goto finish;
         }
     }
@@ -356,7 +356,7 @@ main(int argc, char **argv)
     run_test_loop(opts);
 
 finish:
-    free(opts);
+    HDfree(opts);
     return exit_value;
 }
 
@@ -385,8 +385,8 @@ static void
 run_test_loop(struct options *opts)
 {
     parameters parms;
-    int i;
-    size_t      buf_bytes;
+    int        i;
+    size_t     buf_bytes;
 
     /* load options into parameter structure */
     parms.num_files = opts->num_files;
@@ -552,7 +552,7 @@ run_test(iotype iot, parameters parms, struct options *opts)
     /*
      * Show various statistics
      */
-    /* Write 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 */
@@ -598,7 +598,7 @@ run_test(iotype iot, parameters parms, struct options *opts)
     output_results(opts,"Write Open-Close",write_gross_mm_table,parms.num_iters,raw_size);
 
     if (!parms.h5_write_only) {
-        /* Read statistics	*/
+        /* Read statistics    */
         /* Print the raw data throughput if desired */
         if (opts->print_raw) {
             /* accumulate and output the max, min, and average "raw read" times */
@@ -647,16 +647,16 @@ run_test(iotype iot, parameters parms, struct options *opts)
     }
 
     /* clean up our mess */
-    free(write_sys_mm_table);
-    free(write_mm_table);
-    free(write_gross_mm_table);
-    free(write_raw_mm_table);
+    HDfree(write_sys_mm_table);
+    HDfree(write_mm_table);
+    HDfree(write_gross_mm_table);
+    HDfree(write_raw_mm_table);
 
     if (!parms.h5_write_only) {
-        free(read_sys_mm_table);
-        free(read_mm_table);
-        free(read_gross_mm_table);
-        free(read_raw_mm_table);
+        HDfree(read_sys_mm_table);
+        HDfree(read_mm_table);
+        HDfree(read_gross_mm_table);
+        HDfree(read_raw_mm_table);
     }
 
     return ret_value;
@@ -790,9 +790,9 @@ output_report(const char *fmt, ...)
 {
         va_list ap;
 
-        va_start(ap, fmt);
-        vfprintf(output, fmt, ap);
-        va_end(ap);
+        HDva_start(ap, fmt);
+        HDvfprintf(output, fmt, ap);
+        HDva_end(ap);
 }
 
 /*
@@ -806,10 +806,10 @@ output_report(const char *fmt, ...)
 static void
 print_indent(register int indent)
 {
-	indent *= TAB_SPACE;
+    indent *= TAB_SPACE;
 
-	for (; indent > 0; --indent)
-	    fputc(' ', output);
+    for (; indent > 0; --indent)
+        HDfputc(' ', output);
 }
 
 static void
@@ -833,9 +833,9 @@ static void
 print_io_api(long io_types)
 {
     if (io_types & SIO_POSIX)
-	HDfprintf(output, "posix ");
+    HDfprintf(output, "posix ");
     if (io_types & SIO_HDF5)
-	HDfprintf(output, "hdf5 ");
+    HDfprintf(output, "hdf5 ");
     HDfprintf(output, "\n");
 }
 
@@ -845,7 +845,7 @@ report_parameters(struct options *opts)
     int i, rank;
     rank = opts->dset_rank;
 
-    print_version("HDF5 Library");	/* print library version */
+    print_version("HDF5 Library");    /* print library version */
     HDfprintf(output, "==== Parameters ====\n");
 
     HDfprintf(output, "IO API=");
@@ -1004,7 +1004,7 @@ parse_command_line(int argc, char *argv[])
                     HDmemset(buf, '\0', sizeof(buf));
 
                     for (i = 0; *end != '\0' && *end != ','; ++end)
-                        if (isalnum(*end) && i < 10)
+                        if (HDisalnum(*end) && i < 10)
                             buf[i++] = *end;
 
                     if (!HDstrcasecmp(buf, "hdf5")) {
@@ -1012,9 +1012,9 @@ parse_command_line(int argc, char *argv[])
                     } else if (!HDstrcasecmp(buf, "posix")) {
                         cl_opts->io_types |= SIO_POSIX;
                     } else {
-                        fprintf(stderr, "sio_perf: invalid --api option %s\n",
+                        HDfprintf(stderr, "sio_perf: invalid --api option %s\n",
                                 buf);
-                        exit(EXIT_FAILURE);
+                        HDexit(EXIT_FAILURE);
                     }
 
                     if (*end == '\0')
@@ -1043,7 +1043,7 @@ parse_command_line(int argc, char *argv[])
                     HDmemset(buf, '\0', sizeof(buf));
 
                     for (i = 0; *end != '\0' && *end != ','; ++end)
-                        if (isalnum(*end) && i < 10)
+                        if (HDisalnum(*end) && i < 10)
                             buf[i++] = *end;
 
                     cl_opts->chk_size[j] = parse_size_directive(buf);
@@ -1071,17 +1071,17 @@ parse_command_line(int argc, char *argv[])
                     HDmemset(buf, '\0', sizeof(buf));
 
                     for (i = 0; *end != '\0' && *end != ','; ++end)
-                        if (isalnum(*end) && i < 10)
+                        if (HDisalnum(*end) && i < 10)
                             buf[i++] = *end;
 
-                    if (strlen(buf) > 1 || isdigit(buf[0])) {
+                    if (HDstrlen(buf) > 1 || HDisdigit(buf[0])) {
                         size_t j;
 
                         for (j = 0; j < 10 && buf[j] != '\0'; ++j)
-                            if (!isdigit(buf[j])) {
-                                fprintf(stderr, "sio_perf: invalid --debug option %s\n",
+                            if (!HDisdigit(buf[j])) {
+                                HDfprintf(stderr, "sio_perf: invalid --debug option %s\n",
                                         buf);
-                                exit(EXIT_FAILURE);
+                                HDexit(EXIT_FAILURE);
                             }
 
                         sio_debug_level = atoi(buf);
@@ -1105,8 +1105,8 @@ parse_command_line(int argc, char *argv[])
                 cl_opts->verify = TRUE;
                 break;
                         default:
-                            fprintf(stderr, "sio_perf: invalid --debug option %s\n", buf);
-                            exit(EXIT_FAILURE);
+                            HDfprintf(stderr, "sio_perf: invalid --debug option %s\n", buf);
+                            HDexit(EXIT_FAILURE);
                         }
                     }
 
@@ -1129,7 +1129,7 @@ parse_command_line(int argc, char *argv[])
                     HDmemset(buf, '\0', sizeof(buf));
 
                     for (i = 0; *end != '\0' && *end != ','; ++end)
-                        if (isalnum(*end) && i < 10)
+                        if (HDisalnum(*end) && i < 10)
                             buf[i++] = *end;
 
                     cl_opts->dset_size[j] = parse_size_directive(buf);
@@ -1147,7 +1147,7 @@ parse_command_line(int argc, char *argv[])
             break;
 
         case 'i':
-            cl_opts->num_iters = atoi(opt_arg);
+            cl_opts->num_iters = HDatoi(opt_arg);
             break;
         case 'o':
             cl_opts->output_file = opt_arg;
@@ -1171,9 +1171,9 @@ parse_command_line(int argc, char *argv[])
             } else if (!HDstrcasecmp(opt_arg, "direct")) {
                 cl_opts->vfd=direct;
             } else {
-                fprintf(stderr, "sio_perf: invalid --api option %s\n",
+                HDfprintf(stderr, "sio_perf: invalid --api option %s\n",
                                 opt_arg);
-                exit(EXIT_FAILURE);
+                HDexit(EXIT_FAILURE);
             }
             break;
         case 'w':
@@ -1193,7 +1193,7 @@ parse_command_line(int argc, char *argv[])
                     HDmemset(buf, '\0', sizeof(buf));
 
                     for (i = 0; *end != '\0' && *end != ','; ++end)
-                        if (isalnum(*end) && i < 10)
+                        if (HDisalnum(*end) && i < 10)
                             buf[i++] = *end;
 
                     cl_opts->buf_size[j] = parse_size_directive(buf);
@@ -1221,7 +1221,7 @@ parse_command_line(int argc, char *argv[])
                     HDmemset(buf, '\0', sizeof(buf));
 
                     for (i = 0; *end != '\0' && *end != ','; ++end)
-                        if (isalnum(*end) && i < 10)
+                        if (HDisalnum(*end) && i < 10)
                             buf[i++] = *end;
 
                     cl_opts->order[j] = (int)parse_size_directive(buf);
@@ -1243,7 +1243,7 @@ parse_command_line(int argc, char *argv[])
         case '?':
         default:
             usage(progname);
-            free(cl_opts);
+            HDfree(cl_opts);
             return NULL;
         }
     }
@@ -1339,8 +1339,8 @@ parse_size_directive(const char *size)
                 break;
 
             default:
-                fprintf(stderr, "Illegal size specifier '%c'\n", *endptr);
-                exit(EXIT_FAILURE);
+                HDfprintf(stderr, "Illegal size specifier '%c'\n", *endptr);
+                HDexit(EXIT_FAILURE);
         }
     }
 
@@ -1357,72 +1357,72 @@ parse_size_directive(const char *size)
 static void
 usage(const char *prog)
 {
-	print_version(prog);
-        printf("usage: %s [OPTIONS]\n", prog);
-        printf("  OPTIONS\n");
-        printf("     -h                Print an usage message and exit\n");
-        printf("     -A AL             Which APIs to test\n");
-        printf("                       [default: all of them]\n");
-        printf("     -c SL             Selects chunked storage and defines chunks dimensions\n");
-        printf("                       and sizes\n");
-        printf("                       [default: Off]\n");
-        printf("     -e SL             Dimensions and sizes of dataset\n");
-        printf("                       [default: 100,200]\n");
-        printf("     -i N              Number of iterations to perform\n");
-        printf("                       [default: 1]\n");
-        printf("     -r NL             Dimension access order (see below for description)\n");
-        printf("                       [default: 1,2]\n");
-        printf("     -t                Selects extendable dimensions for HDF5 dataset\n");
-        printf("                       [default: Off]\n");
-        printf("     -v VFD            Selects file driver for HDF5 access\n");
-        printf("                       [default: sec2]\n");
-        printf("     -w                Perform write tests, not the read tests\n");
-        printf("                       [default: Off]\n");
-        printf("     -x SL             Dimensions and sizes of the transfer buffer\n");
-        printf("                       [default: 10,20]\n");
-        printf("\n");
-        printf("  N  - is an integer > 0.\n");
-        printf("\n");
-        printf("  S  - is a size specifier, an integer > 0 followed by a size indicator:\n");
-        printf("          K - Kilobyte (%d)\n", ONE_KB);
-        printf("          M - Megabyte (%d)\n", ONE_MB);
-        printf("          G - Gigabyte (%d)\n", ONE_GB);
-        printf("\n");
-        printf("      Example: '37M' is 37 megabytes or %d bytes\n", 37*ONE_MB);
-        printf("\n");
-        printf("  AL - is an API list. Valid values are:\n");
-        printf("          hdf5 - HDF5\n");
-        printf("          posix - POSIX\n");
-        printf("\n");
-        printf("      Example: -A posix,hdf5\n");
-        printf("\n");
-        printf("  NL - is list of integers (N) separated by commas.\n");
-        printf("\n");
-        printf("      Example: 1,2,3\n");
-        printf("\n");
-        printf("  SL - is list of size specifiers (S) separated by commas.\n");
-        printf("\n");
-        printf("      Example: 2K,2K,3K\n");
-        printf("\n");
-        printf("      The example defines an object (dataset, tranfer buffer) with three\n");
-        printf("      dimensions. Be aware that as the number of dimensions increases, the\n");
-        printf("      the total size of the object increases exponentially.\n");
-        printf("\n");
-        printf("  VFD  - is an HDF5 file driver specifier. Valid values are:\n");
-        printf("          sec2, stdio, core, split, multi, family, direct\n");
-        printf("\n");
-        printf("  Dimension access order:\n");
-        printf("      Data access starts at the cardinal origin of the dataset using the\n");
-        printf("      transfer buffer. The next access occurs on a dataset region next to\n");
-        printf("      the previous one. For a multidimensional dataset, there are several\n");
-        printf("      directions as to where to proceed. This can be specified in the dimension\n");
-        printf("      access order. For example, -r 1,2 states that the tool should traverse\n");
-        printf("      dimension 1 first, and then dimension 2.\n");
-        printf("\n");
-        printf("  Environment variables:\n");
-        printf("      HDF5_NOCLEANUP   Do not remove data files if set [default remove]\n");
-        printf("      HDF5_PREFIX      Data file prefix\n");
-        printf("\n");
-        fflush(stdout);
+    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() */