summaryrefslogtreecommitdiffstats
path: root/tools/src/h5repack
diff options
context:
space:
mode:
authorLarry Knox <lrknox@hdfgroup.org>2019-12-24 21:12:08 (GMT)
committerLarry Knox <lrknox@hdfgroup.org>2019-12-24 21:12:08 (GMT)
commit5b9cf732caab9daa6ed1e00f2df4f5a792340196 (patch)
tree4c01c9bd71ba5e7d8d11b474f6896e6ffbf0416d /tools/src/h5repack
parent646fc294078f560fc9bef784cb1c4e27cdc51f5b (diff)
parente0fa36bfe008c03365ce8ea94d705f8fdebccdf0 (diff)
downloadhdf5-5b9cf732caab9daa6ed1e00f2df4f5a792340196.zip
hdf5-5b9cf732caab9daa6ed1e00f2df4f5a792340196.tar.gz
hdf5-5b9cf732caab9daa6ed1e00f2df4f5a792340196.tar.bz2
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~. ...
Diffstat (limited to 'tools/src/h5repack')
-rw-r--r--tools/src/h5repack/CMakeLists.txt20
-rw-r--r--tools/src/h5repack/Makefile.am2
-rw-r--r--tools/src/h5repack/Makefile.in13
-rw-r--r--tools/src/h5repack/h5repack.c292
-rw-r--r--tools/src/h5repack/h5repack_copy.c181
-rw-r--r--tools/src/h5repack/h5repack_filters.c10
-rw-r--r--tools/src/h5repack/h5repack_main.c375
-rw-r--r--tools/src/h5repack/h5repack_refs.c52
8 files changed, 455 insertions, 490 deletions
diff --git a/tools/src/h5repack/CMakeLists.txt b/tools/src/h5repack/CMakeLists.txt
index c0cd558..4a1430e 100644
--- a/tools/src/h5repack/CMakeLists.txt
+++ b/tools/src/h5repack/CMakeLists.txt
@@ -14,18 +14,20 @@ set (REPACK_COMMON_SOURCES
${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack.c
)
-add_executable (h5repack ${REPACK_COMMON_SOURCES} ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_main.c)
-target_include_directories(h5repack PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
-TARGET_C_PROPERTIES (h5repack STATIC)
-target_link_libraries (h5repack PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
-set_target_properties (h5repack PROPERTIES FOLDER tools)
-set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5repack")
-
-set (H5_DEP_EXECUTABLES h5repack)
+if (NOT ONLY_SHARED_LIBS)
+ add_executable (h5repack ${REPACK_COMMON_SOURCES} ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_main.c)
+ target_include_directories (h5repack PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+ TARGET_C_PROPERTIES (h5repack STATIC)
+ target_link_libraries (h5repack PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
+ set_target_properties (h5repack PROPERTIES FOLDER tools)
+ set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5repack")
+
+ set (H5_DEP_EXECUTABLES h5repack)
+endif ()
if (BUILD_SHARED_LIBS)
add_executable (h5repack-shared ${REPACK_COMMON_SOURCES} ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_main.c)
- target_include_directories(h5repack-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+ target_include_directories (h5repack-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_DIR};${HDF5_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
TARGET_C_PROPERTIES (h5repack-shared SHARED)
target_link_libraries (h5repack-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
set_target_properties (h5repack-shared PROPERTIES FOLDER tools)
diff --git a/tools/src/h5repack/Makefile.am b/tools/src/h5repack/Makefile.am
index c71e65b..925b8a7 100644
--- a/tools/src/h5repack/Makefile.am
+++ b/tools/src/h5repack/Makefile.am
@@ -28,7 +28,7 @@ libh5repack_la_SOURCES=h5repack.c h5repack_copy.c h5repack_filters.c \
h5repack_opttable.c h5repack_parse.c h5repack_refs.c \
h5repack_verify.c
libh5repack_la_LDFLAGS = $(AM_LDFLAGS)
-libh5repack_la_LIBADD=$(LIBH5TOOLS) $(LIBH5TEST) $(LIBHDF5)
+libh5repack_la_LIBADD=$(LIBH5TOOLS) $(LIBHDF5)
# Our main target, h5repack tool
diff --git a/tools/src/h5repack/Makefile.in b/tools/src/h5repack/Makefile.in
index a1f4a02..a3a12c5 100644
--- a/tools/src/h5repack/Makefile.in
+++ b/tools/src/h5repack/Makefile.in
@@ -135,7 +135,7 @@ CONFIG_HEADER = $(top_builddir)/src/H5config.h \
CONFIG_CLEAN_FILES =
CONFIG_CLEAN_VPATH_FILES =
LTLIBRARIES = $(noinst_LTLIBRARIES)
-libh5repack_la_DEPENDENCIES = $(LIBH5TOOLS) $(LIBH5TEST) $(LIBHDF5)
+libh5repack_la_DEPENDENCIES = $(LIBH5TOOLS) $(LIBHDF5)
am_libh5repack_la_OBJECTS = h5repack.lo h5repack_copy.lo \
h5repack_filters.lo h5repack_opttable.lo h5repack_parse.lo \
h5repack_refs.lo h5repack_verify.lo
@@ -494,7 +494,6 @@ FC_VERSION = @FC_VERSION@
FGREP = @FGREP@
FORTRAN_C_LONG_DOUBLE_IS_UNIQUE = @FORTRAN_C_LONG_DOUBLE_IS_UNIQUE@
FORTRAN_HAVE_C_LONG_DOUBLE = @FORTRAN_HAVE_C_LONG_DOUBLE@
-FORTRAN_SIZEOF_LONG_DOUBLE = @FORTRAN_SIZEOF_LONG_DOUBLE@
FSEARCH_DIRS = @FSEARCH_DIRS@
Fortran_COMPILER_ID = @Fortran_COMPILER_ID@
GREP = @GREP@
@@ -517,9 +516,12 @@ H5_VERSION = @H5_VERSION@
HADDR_T = @HADDR_T@
HAVE_DMALLOC = @HAVE_DMALLOC@
HAVE_Fortran_INTEGER_SIZEOF_16 = @HAVE_Fortran_INTEGER_SIZEOF_16@
+HAVE_LIBHDFS = @HAVE_LIBHDFS@
HAVE_PTHREAD = @HAVE_PTHREAD@
HDF5_HL = @HDF5_HL@
HDF5_INTERFACES = @HDF5_INTERFACES@
+HDF5_TESTS = @HDF5_TESTS@
+HDF5_TOOLS = @HDF5_TOOLS@
HDF_CXX = @HDF_CXX@
HDF_FORTRAN = @HDF_FORTRAN@
HDF_JAVA = @HDF_JAVA@
@@ -546,6 +548,7 @@ JAVA_JUNIT = @JAVA_JUNIT@
JAVA_PATH_NAME = @JAVA_PATH_NAME@
JAVA_VERSION = @JAVA_VERSION@
JNIFLAGS = @JNIFLAGS@
+JNI_LDFLAGS = @JNI_LDFLAGS@
JUNIT = @JUNIT@
LARGE_PARALLEL_IO = @LARGE_PARALLEL_IO@
LD = @LD@
@@ -600,6 +603,7 @@ PREADWRITE = @PREADWRITE@
PROFILING = @PROFILING@
RANLIB = @RANLIB@
ROOT = @ROOT@
+ROS3_VFD = @ROS3_VFD@
RUNPARALLEL = @RUNPARALLEL@
RUNSERIAL = @RUNSERIAL@
R_INTEGER = @R_INTEGER@
@@ -624,7 +628,6 @@ UNAME_INFO = @UNAME_INFO@
USE_FILTER_DEFLATE = @USE_FILTER_DEFLATE@
USE_FILTER_SZIP = @USE_FILTER_SZIP@
USINGMEMCHECKER = @USINGMEMCHECKER@
-UUDECODE = @UUDECODE@
VERSION = @VERSION@
WORDS_BIGENDIAN = @WORDS_BIGENDIAN@
_ACJNI_JAVAC = @_ACJNI_JAVAC@
@@ -749,7 +752,7 @@ libh5repack_la_SOURCES = h5repack.c h5repack_copy.c h5repack_filters.c \
h5repack_verify.c
libh5repack_la_LDFLAGS = $(AM_LDFLAGS)
-libh5repack_la_LIBADD = $(LIBH5TOOLS) $(LIBH5TEST) $(LIBHDF5)
+libh5repack_la_LIBADD = $(LIBH5TOOLS) $(LIBHDF5)
h5repack_SOURCES = h5repack_main.c
# Add h5repack specific linker flags here
@@ -1331,7 +1334,7 @@ all-local: $(EXTRA_LIB) $(EXTRA_PROG) $(chk_TESTS)
# make install-doc doesn't do anything outside of doc directory, but
# Makefiles should recognize it.
# UPDATE: docs no longer reside in this build tree, so this target
-# is depreciated.
+# is deprecated.
install-doc uninstall-doc:
@echo "Nothing to be done."
diff --git a/tools/src/h5repack/h5repack.c b/tools/src/h5repack/h5repack.c
index a63e56f..0183cbf 100644
--- a/tools/src/h5repack/h5repack.c
+++ b/tools/src/h5repack/h5repack.c
@@ -41,7 +41,9 @@ static int have_request(pack_opt_t *options);
* Return: 0, ok, -1, fail
*-------------------------------------------------------------------------
*/
-int h5repack(const char* infile, const char* outfile, pack_opt_t *options) {
+int
+h5repack(const char* infile, const char* outfile, pack_opt_t *options)
+{
/* check input */
if (check_options(options) < 0)
return -1;
@@ -55,7 +57,7 @@ int h5repack(const char* infile, const char* outfile, pack_opt_t *options) {
return -1;
return 0;
-}
+} /* end h5repack() */
/*-------------------------------------------------------------------------
* Function: h5repack_init
@@ -86,7 +88,7 @@ h5repack_init(pack_opt_t *options, int verbose, hbool_t latest)
}
return (options_table_init(&(options->op_tbl)));
-}
+} /* end h5repack_init() */
/*-------------------------------------------------------------------------
* Function: h5repack_end
@@ -95,9 +97,11 @@ h5repack_init(pack_opt_t *options, int verbose, hbool_t latest)
*-------------------------------------------------------------------------
*/
-int h5repack_end(pack_opt_t *options) {
+int
+h5repack_end(pack_opt_t *options)
+{
return options_table_free(options->op_tbl);
-}
+} /* end h5repack_end() */
/*-------------------------------------------------------------------------
* Function: h5repack_addfilter
@@ -138,7 +142,7 @@ h5repack_addfilter(const char *str, pack_opt_t *options)
HDfree(obj_list);
return 0;
-}
+} /* end h5repack_addfilter() */
/*-------------------------------------------------------------------------
* Function: h5repack_addlayout
@@ -175,7 +179,7 @@ h5repack_addlayout(const char *str, pack_opt_t *options)
if (pack.layout == H5D_CHUNKED) {
/* -2 means the NONE option, remove chunking
and set the global layout to contiguous */
- if (pack.chunk.rank == -2)
+ if (pack.chunk.rank == -2) /* TODO: fix 'magic number' */
options->layout_g = H5D_CONTIGUOUS;
/* otherwise set the global chunking type */
else {
@@ -192,10 +196,10 @@ h5repack_addlayout(const char *str, pack_opt_t *options)
HDfree(obj_list);
ret_value = 0;
- }
+ } /* end if obj_list exists */
return ret_value;
-}
+} /* end h5repack_addlayout() */
/* Note: The below copy_named_datatype(), named_datatype_free(), copy_attr()
* were located in h5repack_copy.c as static prior to bugfix1726.
@@ -215,8 +219,9 @@ h5repack_addlayout(const char *str, pack_opt_t *options)
* to free the stack.
*-------------------------------------------------------------------------
*/
-hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
- named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options) {
+hid_t
+copy_named_datatype(hid_t type_in, hid_t fidout, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options)
+{
named_dt_t *dt = *named_dt_head_p; /* Stack pointer */
named_dt_t *dt_ret = NULL; /* Datatype to return */
H5O_info_t oinfo; /* Object info of input dtype */
@@ -250,13 +255,14 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
/* Check if this type is the one requested */
if (oinfo.addr == dt->addr_in) {
dt_ret = dt;
- } /* end if */
- } /* end if */
- } /* end for */
- } /* end else */
+ }
+ } /* end if named datatype */
+ } /* end for each object in traversal table */
+ } /* end else (create the stack) */
/* Handle the case that the requested datatype was not found. This is
- * possible if the datatype was committed anonymously in the input file. */
+ * possible if the datatype was committed anonymously in the input file.
+ */
if (!dt_ret) {
/* Push the new datatype onto the stack */
if (NULL == (dt_ret = (named_dt_t *)HDmalloc(sizeof(named_dt_t))))
@@ -267,10 +273,11 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
/* Update the address and id */
dt_ret->addr_in = oinfo.addr;
dt_ret->id_out = -1;
- } /* end if */
+ } /* end if requested datatype not found */
/* If the requested datatype does not yet exist in the output file, copy it
- * anonymously */
+ * anonymously
+ */
if (dt_ret->id_out < 0) {
if (options->use_native == 1)
dt_ret->id_out = H5Tget_native_type(type_in, H5T_DIR_DEFAULT);
@@ -280,18 +287,20 @@ hid_t copy_named_datatype(hid_t type_in, hid_t fidout,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_native_type-H5Tcopy failed");
if (H5Tcommit_anon(fidout, dt_ret->id_out, H5P_DEFAULT, H5P_DEFAULT) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tcommit_anon failed");
- } /* end if */
+ } /* end if named datatype not yet in output file */
/* Set return value */
ret_value = dt_ret->id_out;
- /* Increment the ref count on id_out, because the calling function will try to close it */
- if(H5Iinc_ref(ret_value) < 0)
+ /* Increment the ref count on id_out, because the calling function will try
+ * to close it. (TODO: fix scope envy)
+ */
+ if (H5Iinc_ref(ret_value) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Iinc_ref failed");
done:
return ret_value;
-} /* end copy_named_datatype */
+} /* end copy_named_datatype() */
/*-------------------------------------------------------------------------
* Function: named_datatype_free
@@ -299,7 +308,9 @@ done:
* Purpose: Frees the stack of named datatypes.
*-------------------------------------------------------------------------
*/
-int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) {
+int
+named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err)
+{
named_dt_t *dt = *named_dt_head_p;
int ret_value = -1;
@@ -310,13 +321,13 @@ int named_datatype_free(named_dt_t **named_dt_head_p, int ignore_err) {
dt = dt->next;
HDfree(*named_dt_head_p);
*named_dt_head_p = dt;
- } /* end while */
+ }
ret_value = 0;
done:
return (ret_value);
-} /* end named_datatype_free */
+} /* end named_datatype_free() */
/*-------------------------------------------------------------------------
* Function: copy_attr
@@ -330,8 +341,7 @@ done:
*-------------------------------------------------------------------------
*/
int
-copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
- trav_table_t *travt, pack_opt_t *options)
+copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p, trav_table_t *travt, pack_opt_t *options)
{
int ret_value = 0;
hid_t attr_id = -1; /* attr ID */
@@ -364,7 +374,6 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
if ((attr_id = H5Aopen_by_idx(loc_in, ".", H5_INDEX_CRT_ORDER, H5_ITER_INC, (hsize_t) u, H5P_DEFAULT, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aopen_by_idx failed");
- /* get name */
if (H5Aget_name(attr_id, (size_t) 255, name) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
@@ -386,17 +395,17 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
if ((wtype_id = copy_named_datatype(ftype_id, fidout, named_dt_head_p, travt, options)) < 0) {
H5Fclose(fidout);
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_named_datatype failed");
- } /* end if */
+ }
if (H5Fclose(fidout) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fclose failed");
- } /* end if */
+ } /* end if datatype is committed and we have a traversal table */
else {
if (options->use_native == 1)
wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT);
else
wtype_id = H5Tcopy(ftype_id);
- } /* end else */
+ } /* end else: uncommitted datatype and/or no traversal table */
/* get the dataspace handle */
if ((space_id = H5Aget_space(attr_id)) < 0)
@@ -413,12 +422,12 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
if ((msize = H5Tget_size(wtype_id)) == 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
- /*-------------------------------------------------------------------------
- * object references are a special case. We cannot just copy the buffers,
- * but instead we recreate the reference.
- * This is done on a second sweep of the file that just copies the referenced
- * objects at copy_refs_attr()
- *-------------------------------------------------------------------------
+ /*---------------------------------------------------------------------
+ * object references are a special case. We cannot just copy the
+ * buffers, but instead we recreate the reference.
+ * This is done on a second sweep of the file that just copies the
+ * referenced objects at copy_refs_attr().
+ *---------------------------------------------------------------------
*/
type_class = H5Tget_class(wtype_id);
is_ref = (type_class == H5T_REFERENCE);
@@ -429,7 +438,7 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
is_ref = (is_ref || (H5Tget_class(base_type) == H5T_REFERENCE));
if (H5Tclose(base_type) < 0)
H5TOOLS_INFO(H5E_tools_min_id_g, "H5Tclose base_type failed");
- }
+ } /* end if type_class is variable length or array */
if (type_class == H5T_COMPOUND) {
int nmembers = H5Tget_nmembers(wtype_id);
@@ -444,13 +453,13 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
is_ref = 1;
break;
}
- } /* for (j=0; i<nmembers; j++) */
- } /* if (type_class == H5T_COMPOUND) */
+ } /* end for each member */
+ } /* end if type_class is H5T_COMPOUND */
if (!is_ref) {
- /*-------------------------------------------------------------------------
+ /*-----------------------------------------------------------------
* read to memory
- *-------------------------------------------------------------------------
+ *-----------------------------------------------------------------
*/
buf = (void *)HDmalloc((size_t)(nelmts * msize));
@@ -460,9 +469,9 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
if (H5Aread(attr_id, wtype_id, buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aread failed");
- /*-------------------------------------------------------------------------
+ /*-----------------------------------------------------------------
* copy
- *-------------------------------------------------------------------------
+ *-----------------------------------------------------------------
*/
if ((attr_out = H5Acreate2(loc_out, name, wtype_id, space_id, H5P_DEFAULT, H5P_DEFAULT)) < 0)
@@ -483,11 +492,11 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
} /*H5T_REFERENCE*/
if (options->verbose)
- printf(FORMAT_OBJ_ATTR, "attr", name);
+ HDprintf(FORMAT_OBJ_ATTR, "attr", name);
- /*-------------------------------------------------------------------------
+ /*---------------------------------------------------------------------
* close
- *-------------------------------------------------------------------------
+ *---------------------------------------------------------------------
*/
if (H5Sclose(space_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
@@ -501,19 +510,18 @@ copy_attr(hid_t loc_in, hid_t loc_out, named_dt_t **named_dt_head_p,
if (H5Aclose(attr_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Aclose failed");
attr_id = -1;
- } /* for u */
+ } /* for u (each attribute) */
done:
H5E_BEGIN_TRY {
if (buf) {
- /* Check if we have VL data and string in the attribute's datatype that must
- * be reclaimed */
+ /* Check if we have VL data and string in the attribute's
+ * datatype that must be reclaimed
+ */
if (TRUE == h5tools_detect_vlen(wtype_id))
H5Dvlen_reclaim(wtype_id, space_id, H5P_DEFAULT, buf);
-
- /* Free buf */
HDfree(buf);
- } /* end if */
+ }
H5Aclose(attr_out);
H5Sclose(space_id);
@@ -525,27 +533,29 @@ done:
return ret_value;
} /* end copy_attr() */
-/*-------------------------------------------------------------------------
+/*-----------------------------------------------------------------------------
* Function: check_options
*
* Purpose: print options, checks for invalid options
*
* Return: void, return -1 on error
- *-------------------------------------------------------------------------
+ *-----------------------------------------------------------------------------
*/
-static int check_options(pack_opt_t *options) {
+static int
+check_options(pack_opt_t *options)
+{
int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
unsigned int i;
int k, j, has_cp = 0, has_ck = 0;
char slayout[30];
/*-------------------------------------------------------------------------
- * objects to layout
- *-------------------------------------------------------------------------
- */
- if (options->verbose && have_request(options) /* only print if requested */) {
+ * Objects to layout
+ *-------------------------------------------------------------------------
+ */
+ if (options->verbose && have_request(options)) {
if (options->all_layout == 1) {
- printf("All objects to modify layout are...\n");
+ HDprintf("All objects to modify layout are...\n");
switch (options->layout_g) {
case H5D_COMPACT:
strcpy(slayout, "compact");
@@ -566,76 +576,76 @@ static int check_options(pack_opt_t *options) {
strcpy(slayout, "invalid layout\n");
HGOTO_DONE(FAIL);
}
- printf(" Apply %s layout to all", slayout);
+ HDprintf(" Apply %s layout to all", slayout);
if (H5D_CHUNKED == options->layout_g) {
- printf("with dimension [ ");
+ HDprintf("with dimension [ ");
for (j = 0; j < options->chunk_g.rank; j++)
- printf("%d ", (int) options->chunk_g.chunk_lengths[j]);
- printf("]");
+ HDprintf("%d ", (int) options->chunk_g.chunk_lengths[j]);
+ HDprintf("]");
}
- printf("\n");
+ HDprintf("\n");
}
else
- printf("No all objects to modify layout\n");
- }/* verbose */
+ HDprintf("No all objects to modify layout\n");
+ } /* end if verbose */
for (i = 0; i < options->op_tbl->nelems; i++) {
char* name = options->op_tbl->objs[i].path;
if (options->op_tbl->objs[i].chunk.rank > 0) {
if (options->verbose) {
- printf(" <%s> with chunk size ", name);
+ HDprintf(" <%s> with chunk size ", name);
for (k = 0; k < options->op_tbl->objs[i].chunk.rank; k++)
- printf("%d ", (int) options->op_tbl->objs[i].chunk.chunk_lengths[k]);
- printf("\n");
+ HDprintf("%d ", (int) options->op_tbl->objs[i].chunk.chunk_lengths[k]);
+ HDprintf("\n");
}
has_ck = 1;
}
- else if (options->op_tbl->objs[i].chunk.rank == -2) {
+ else if (options->op_tbl->objs[i].chunk.rank == -2) { /* TODO: replace 'magic number' */
if (options->verbose)
- printf(" <%s> %s\n", name, "NONE (contiguous)");
+ HDprintf(" <%s> %s\n", name, "NONE (contiguous)");
has_ck = 1;
}
- }
+ } /* end for each object in options */
if (options->all_layout == 1 && has_ck)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid chunking input: 'all' option is present with other objects");
/*-------------------------------------------------------------------------
- * objects to filter
- *-------------------------------------------------------------------------
- */
+ * Objects to filter
+ *-------------------------------------------------------------------------
+ */
- if (options->verbose && have_request(options) /* only print if requested */) {
+ if (options->verbose && have_request(options)) {
if (options->all_filter == 1) {
- printf("All objects to apply filter are...\n");
+ HDprintf("All objects to apply filter are...\n");
for (k = 0; k < options->n_filter_g; k++) {
H5Z_filter_t filtn = options->filter_g[k].filtn;
if (filtn < 0) {
- printf(" Unknown\n");
+ HDprintf(" Unknown\n");
continue;
}
switch (filtn) {
case H5Z_FILTER_NONE:
- printf(" Uncompress all\n");
+ HDprintf(" Uncompress all\n");
break;
case H5Z_FILTER_SHUFFLE:
case H5Z_FILTER_FLETCHER32:
- printf(" All with %s\n", get_sfilter(filtn));
+ HDprintf(" All with %s\n", get_sfilter(filtn));
break;
case H5Z_FILTER_SZIP:
case H5Z_FILTER_DEFLATE:
- printf(" All with %s, parameter %d\n", get_sfilter(filtn), options->filter_g[k].cd_values[0]);
+ HDprintf(" All with %s, parameter %d\n", get_sfilter(filtn), options->filter_g[k].cd_values[0]);
break;
default:
- printf(" User Defined %d\n", filtn);
+ HDprintf(" User Defined %d\n", filtn);
break;
- } /* k */
- };
- }
+ } /* end switch */
+ } /* end for each filter */
+ } /* end if options->all_filter == 1 (TODO: meaning) */
else
- printf("No all objects to apply filter\n");
- } /* verbose */
+ HDprintf("No all objects to apply filter\n");
+ } /* end if verbose */
for (i = 0; i < options->op_tbl->nelems; i++) {
pack_info_t pack = options->op_tbl->objs[i];
@@ -643,24 +653,26 @@ static int check_options(pack_opt_t *options) {
for (j = 0; j < pack.nfilters; j++) {
if (options->verbose) {
- if(pack.filter[j].filtn >= 0) {
- if(pack.filter[j].filtn > H5Z_FILTER_SCALEOFFSET)
- printf(" <%s> with %s filter %d\n", name, get_sfilter(pack.filter[j].filtn), pack.filter[j].filtn);
- else
- printf(" <%s> with %s filter\n", name, get_sfilter(pack.filter[j].filtn));
+ if (pack.filter[j].filtn >= 0) {
+ if (pack.filter[j].filtn > H5Z_FILTER_SCALEOFFSET) {
+ HDprintf(" <%s> with %s filter %d\n", name, get_sfilter(pack.filter[j].filtn), pack.filter[j].filtn);
+ }
+ else {
+ HDprintf(" <%s> with %s filter\n", name, get_sfilter(pack.filter[j].filtn));
+ }
}
}
has_cp = 1;
- } /* j */
- } /* i */
+ } /* end for each filter */
+ } /* end for each object in options table */
if (options->all_filter == 1 && has_cp)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid compression input: 'all' option is present with other objects");
/*-------------------------------------------------------------------------
- * check options for the latest format
- *-------------------------------------------------------------------------
- */
+ * Check options for the latest format
+ *-------------------------------------------------------------------------
+ */
if (options->grp_compact < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid maximum number of links to store as header messages");
@@ -672,13 +684,13 @@ static int check_options(pack_opt_t *options) {
if (options->msg_size[i] < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid shared message size");
- /*--------------------------------------------------------------------------------
- * verify new user userblock options; file name must be present
- *---------------------------------------------------------------------------------
- */
+ /*------------------------------------------------------------------------
+ * Verify new user userblock options; file name must be present
+ *------------------------------------------------------------------------
+ */
if (options->ublock_filename != NULL && options->ublock_size == 0) {
if (options->verbose) {
- printf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n", options->ublock_filename);
+ HDprintf("Warning: user block size missing for file %s. Assigning a default size of 1024...\n", options->ublock_filename);
options->ublock_size = 1024;
}
}
@@ -686,35 +698,37 @@ static int check_options(pack_opt_t *options) {
if (options->ublock_filename == NULL && options->ublock_size != 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "file name missing for user block", options->ublock_filename);
- /*--------------------------------------------------------------------------------
- * verify alignment options; threshold is zero default but alignment not
- *---------------------------------------------------------------------------------
- */
+ /*------------------------------------------------------------------------
+ * Verify alignment options; threshold is zero default but alignment not
+ *------------------------------------------------------------------------
+ */
if (options->alignment == 0 && options->threshold != 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "alignment for H5Pset_alignment missing");
done:
return ret_value;
-}
+} /* end check_options() */
/*-------------------------------------------------------------------------
* Function: check_objects
*
- * Purpose: locate all HDF5 objects in the file and compare with user
- * supplied list
+ * Purpose: Locate all HDF5 objects in the file and compare with user-supplied
+ * list.
*
* Return: 0, ok, -1 no
*-------------------------------------------------------------------------
*/
-static int check_objects(const char* fname, pack_opt_t *options) {
- int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
+static int
+check_objects(const char* fname, pack_opt_t *options)
+{
hid_t fid = -1;
hid_t did = -1;
hid_t sid = -1;
unsigned int i;
- unsigned int uf;
+ int ifil;
trav_table_t *travt = NULL;
+ int ret_value = 0; /*no need to LEAVE() on ERROR: HERR_INIT(int, SUCCEED) */
/* nothing to do */
if (options->op_tbl->nelems == 0)
@@ -747,38 +761,40 @@ static int check_objects(const char* fname, pack_opt_t *options) {
*/
if (options->verbose)
- printf("Opening file. Searching %d objects to modify ...\n", travt->nobjs);
+ HDprintf("Opening file. Searching %zu objects to modify ...\n", travt->nobjs);
for (i = 0; i < options->op_tbl->nelems; i++) {
- char* name = options->op_tbl->objs[i].path;
+ pack_info_t obj = options->op_tbl->objs[i];
+ char* name = obj.path;
+
if (options->verbose)
- printf(" <%s>", name);
+ HDprintf(" <%s>", name);
/* the input object names are present in the file and are valid */
if (h5trav_getindext(name, travt) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "%s Could not find <%s> in file <%s>. Exiting...\n",
(options->verbose ? "\n" : ""), name, fname);
if (options->verbose)
- printf("...Found\n");
+ HDprintf("...Found\n");
- for (uf = 0; uf < options->op_tbl->objs[i].nfilters; uf++) {
- if (options->op_tbl->objs[i].filter[uf].filtn < 0)
+ for (ifil = 0; ifil < obj.nfilters; ifil++) {
+ if (obj.filter[ifil].filtn < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "invalid filter");
/* check for extra filter conditions */
- switch (options->op_tbl->objs[i].filter[uf].filtn) {
+ switch (obj.filter[ifil].filtn) {
/* chunk size must be smaller than pixels per block */
case H5Z_FILTER_SZIP:
{
int j;
hsize_t csize = 1;
- unsigned ppb = options->op_tbl->objs[i].filter[uf].cd_values[0];
+ unsigned ppb = obj.filter[ifil].cd_values[0];
hsize_t dims[H5S_MAX_RANK];
int rank;
- if (options->op_tbl->objs[i].chunk.rank > 0) {
- rank = options->op_tbl->objs[i].chunk.rank;
+ if (obj.chunk.rank > 0) {
+ rank = obj.chunk.rank;
for (j = 0; j < rank; j++)
- csize *= options->op_tbl->objs[i].chunk.chunk_lengths[j];
+ csize *= obj.chunk.chunk_lengths[j];
}
else {
if ((did = H5Dopen2(fid, name, H5P_DEFAULT)) < 0)
@@ -799,16 +815,16 @@ static int check_objects(const char* fname, pack_opt_t *options) {
}
if (csize < ppb) {
- printf(" <warning: SZIP settings, chunk size is smaller than pixels per block>\n");
+ HDprintf(" <warning: SZIP settings, chunk size is smaller than pixels per block>\n");
HGOTO_DONE(0);
}
- }
+ } /* end case SZIP */
break;
default:
break;
- }
- } /* for uf */
- } /* for i */
+ } /* end switch */
+ } /* for ifil (each user-defined filter) */
+ } /* for i (each object in options traversal table) */
done:
H5E_BEGIN_TRY {
@@ -819,7 +835,7 @@ done:
if (travt)
trav_table_free(travt);
return ret_value;
-}
+} /* end check_objects() */
/*-------------------------------------------------------------------------
* Function: have_request
@@ -829,14 +845,15 @@ done:
* Return: 1 yes, 0 no
*-------------------------------------------------------------------------
*/
-static int have_request(pack_opt_t *options) {
+static int
+have_request(pack_opt_t *options)
+{
if (options->all_filter || options->all_layout || options->op_tbl->nelems)
return 1;
return 0;
-
-}
+} /* end have_request() */
/*-------------------------------------------------------------------------
* Function: get_sfilter
@@ -846,8 +863,9 @@ static int have_request(pack_opt_t *options) {
* Return: name of filter, exit on error
*-------------------------------------------------------------------------
*/
-
-static const char* get_sfilter(H5Z_filter_t filtn) {
+static const char *
+get_sfilter(H5Z_filter_t filtn)
+{
if (filtn < 0)
return NULL;
else if (filtn == H5Z_FILTER_NONE)
@@ -866,5 +884,5 @@ static const char* get_sfilter(H5Z_filter_t filtn) {
return "SOFF";
else
return "UD";
-}
+} /* end get_sfilter() */
diff --git a/tools/src/h5repack/h5repack_copy.c b/tools/src/h5repack/h5repack_copy.c
index 0567269..f6409e3 100644
--- a/tools/src/h5repack/h5repack_copy.c
+++ b/tools/src/h5repack/h5repack_copy.c
@@ -33,25 +33,11 @@
/* size of buffer/# of bytes to xfer at a time when copying userblock */
#define USERBLOCK_XFER_SIZE 512
-/* check H5Dread()/H5Dwrite() error, e.g. memory allocation error inside the library. */
-#define CHECK_H5DRW_ERROR(_fun, _fail, _did, _mtid, _msid, _fsid, _pid, _buf) { \
- H5E_BEGIN_TRY { \
- if(_fun(_did, _mtid, _msid, _fsid, _pid, _buf) < 0) { \
- hid_t _err_num = 0; \
- char _msg[80]; \
- H5Ewalk2(H5E_DEFAULT, H5E_WALK_DOWNWARD, walk_error_callback, &_err_num); \
- H5Eget_msg(_err_num, NULL, _msg, (size_t)80); \
- error_msg("%s %s -- %s\n", #_fun, "failed", _msg); \
- HGOTO_DONE(_fail) \
- } \
- } H5E_END_TRY; \
-}
-
/*-------------------------------------------------------------------------
* local functions
*-------------------------------------------------------------------------
*/
-static int Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
+static int get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p);
static void print_dataset_info(hid_t dcpl_id, char *objname, double per, int pr);
static int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
@@ -61,15 +47,7 @@ static int copy_user_block(const char *infile, const char *outfile,
#if defined (H5REPACK_DEBUG_USER_BLOCK)
static void print_user_block(const char *filename, hid_t fid);
#endif
-static herr_t walk_error_callback(unsigned n, const H5E_error2_t *err_desc, void *udata);
-
-/* get the major number from the error stack. */
-static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t *err_desc, void *udata) {
- if (err_desc)
- *((hid_t *) udata) = err_desc->maj_num;
- return 0;
-}
/*-------------------------------------------------------------------------
* Function: copy_objects
@@ -80,8 +58,8 @@ static herr_t walk_error_callback(H5_ATTR_UNUSED unsigned n, const H5E_error2_t
* -1 no
*-------------------------------------------------------------------------
*/
-
-int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
+int
+copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
{
int ret_value = 0;
hid_t fidin = -1;
@@ -167,8 +145,7 @@ int copy_objects(const char* fnamein, const char* fnameout, pack_opt_t *options)
/* Adjust group creation parameters for root group */
/* (So that it is created in "dense storage" form) */
- if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact,
- (unsigned) options->grp_indexed) < 0)
+ if (H5Pset_link_phase_change(fcpl, (unsigned) options->grp_compact, (unsigned) options->grp_indexed) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_link_phase_change failed to adjust group creation parameters for root group");
for (i = 0; i < 5; i++) {
@@ -318,7 +295,7 @@ print_user_block(fnamein, fidin);
*-------------------------------------------------------------------------
*/
if (options->verbose)
- printf("Making new file ...\n");
+ HDprintf("Making new file ...\n");
if ((fidout = H5Fcreate(fnameout, H5F_ACC_TRUNC, fcpl, fapl)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Fcreate could not create file <%s>:", fnameout);
@@ -387,10 +364,10 @@ done:
trav_table_free(travt);
return ret_value;
-}
+} /* end copy_objects() */
/*-------------------------------------------------------------------------
- * Function: Get_hyperslab
+ * Function: get_hyperslab
*
* Purpose: Calulate a hyperslab from a dataset for higher performance.
* The size of hyperslab is limitted by H5TOOLS_BUFSIZE.
@@ -422,7 +399,7 @@ done:
*-----------------------------------------*/
int
-Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
+get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
size_t size_datum, hsize_t dims_hslab[], hsize_t * hslab_nbytes_p)
{
int ret_value = 0;
@@ -543,7 +520,7 @@ Get_hyperslab(hid_t dcpl_id, int rank_dset, hsize_t dims_dset[],
done:
return ret_value;
-}
+} /* end get_hyperslab() */
/*-------------------------------------------------------------------------
* Function: do_copy_objects
@@ -591,7 +568,7 @@ done:
* in (2) is that, when using the strip mine size, it assures that the "remaining" part
* of the dataset that does not fill an entire strip mine is processed.
*
- * 1. figure out a hyperslab (dimentions) and size (refer to Get_hyperslab()).
+ * 1. figure out a hyperslab (dimentions) and size (refer to get_hyperslab()).
* 2. Calculate the hyperslab selections as the selection is moving forward.
* Selection would be same as the hyperslab except for the remaining edge portion
* of the dataset. The code take care of the remaining portion if exist.
@@ -599,7 +576,8 @@ done:
*-------------------------------------------------------------------------
*/
-int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
+int
+do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
pack_opt_t *options) /* repack options */
{
int ret_value = 0;
@@ -634,7 +612,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
unsigned crt_order_flags; /* group creation order flag */
unsigned i;
unsigned u;
- unsigned uf;
+ int ifil;
int is_ref = 0;
htri_t is_named;
hbool_t limit_maxdims;
@@ -646,9 +624,9 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
*/
if (options->verbose) {
- printf("-----------------------------------------\n");
- printf(" Type Filter (Compression) Name\n");
- printf("-----------------------------------------\n");
+ HDprintf("-----------------------------------------\n");
+ HDprintf(" Type Filter (Compression) Name\n");
+ HDprintf("-----------------------------------------\n");
}
if (travt->objs) {
@@ -667,7 +645,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
*/
case H5TRAV_TYPE_GROUP:
if (options->verbose)
- printf(FORMAT_OBJ, "group", travt->objs[i].name);
+ HDprintf(FORMAT_OBJ, "group", travt->objs[i].name);
/* open input group */
if ((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
@@ -740,8 +718,8 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (options->op_tbl->objs) {
for (u = 0; u < options->op_tbl->nelems; u++) {
if (HDstrcmp(travt->objs[i].name, options->op_tbl->objs[u].path) == 0)
- for (uf = 0; uf < options->op_tbl->objs[uf].nfilters; uf++) {
- if (options->op_tbl->objs[u].filter[uf].filtn > 0)
+ for (ifil = 0; ifil < options->op_tbl->objs[ifil].nfilters; ifil++) {
+ if (options->op_tbl->objs[u].filter[ifil].filtn > 0)
req_filter = 1;
}
}
@@ -799,8 +777,6 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_type failed");
if ((dcpl_in = H5Dget_create_plist(dset_in)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_create_plist failed");
- if ((dcpl_out = H5Pcopy(dcpl_in)) < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed");
if ((rank = H5Sget_simple_extent_ndims(f_space_id)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sget_simple_extent_ndims failed");
HDmemset(dims, 0, sizeof dims);
@@ -809,6 +785,19 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (H5Dget_space_status(dset_in, &space_status) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dget_space_status failed");
+ /* If the input dataset has external storage, it must be contiguous.
+ * Accordingly, there would be no filter or chunk properties to preserve,
+ * so create a new DCPL.
+ * Otherwise, copy dcpl_in.
+ */
+ if (H5Pget_external_count(dcpl_in)) {
+ if ((dcpl_out = H5Pcreate(H5P_DATASET_CREATE)) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcreate failed");
+ }
+ else if ((dcpl_out = H5Pcopy(dcpl_in)) < 0) {
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pcopy failed");
+ }
+
nelmts = 1;
for (j = 0; j < rank; j++)
nelmts *= dims[j];
@@ -819,7 +808,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
wtype_id = H5Tget_native_type(ftype_id, H5T_DIR_DEFAULT);
else
wtype_id = H5Tcopy(ftype_id);
- } /* end if */
+ }
if ((msize = H5Tget_size(wtype_id)) == 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Tget_size failed");
@@ -863,7 +852,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
/* only if layout change requested for entire file or
* individual obj */
- if (options->all_layout > 0 || req_obj_layout == 1)
+ if (options->all_layout > 0 || req_obj_layout == 1) {
/*-------------------------------------------------
* Unset the unlimited max dims if convert to other
* than chunk layouts, because unlimited max dims
@@ -883,14 +872,14 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
/* if convert to COMPACT */
if (options->layout_g == H5D_COMPACT)
- /* should be smaller than 64K */
if (size_dset > MAX_COMPACT_DSIZE)
limit_maxdims = FALSE;
/* unset unlimited max dims */
if (limit_maxdims)
H5Sset_extent_simple(f_space_id, rank, dims, NULL);
- }
+ } /* end if not chunked */
+ } /* end if layout change requested for entire file or individual object */
/*-------------------------------------------------------------------------
* create the output dataset;
@@ -902,12 +891,12 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (dset_out == FAIL) {
H5Epush2(H5tools_ERR_STACK_g, __FILE__, FUNC, __LINE__, H5tools_ERR_CLS_g, H5E_tools_g, H5E_tools_min_id_g, "H5Dcreate2 failed");
if (options->verbose)
- printf(" warning: could not create dataset <%s>. Applying original settings\n", travt->objs[i].name);
+ HDprintf(" warning: could not create dataset <%s>. Applying original settings\n", travt->objs[i].name);
if ((dset_out = H5Dcreate2(fidout, travt->objs[i].name, wtype_id, f_space_id, H5P_DEFAULT, dcpl_in, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dcreate2 failed");
apply_f = 0;
- }
+ } /* end if retry dataset create */
/*-------------------------------------------------------------------------
* read/write
@@ -931,8 +920,8 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (TRUE == H5Tdetect_class(wtype_id, H5T_VLEN))
if (H5Dvlen_reclaim(wtype_id, f_space_id, H5P_DEFAULT, buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dvlen_reclaim failed");
- /* free */
- if (buf != NULL) {
+
+ if (buf != NULL) { /* TODO: is buf potentially released by H5Dvlen_reclaim()? */
HDfree(buf);
buf = NULL;
}
@@ -968,17 +957,19 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
dset_layout = H5Pget_layout(dcpl_out);
if (dset_layout == H5D_CHUNKED)
dcpl_tmp = dcpl_out; /* writing dataset */
- else { /* if reading dataset is chunked */
+ else {
dset_layout = H5Pget_layout(dcpl_in);
if (dset_layout == H5D_CHUNKED)
dcpl_tmp = dcpl_in; /* reading dataset */
}
/* get hyperslab dims and size in byte */
- if (Get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0)
- HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Get_hyperslab failed");
+ if (get_hyperslab(dcpl_tmp, rank, dims, p_type_nbytes, hslab_dims, &hslab_nbytes) < 0)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "get_hyperslab failed");
hslab_buf = HDmalloc((size_t)hslab_nbytes);
+ if (hslab_buf == NULL)
+ HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "can't allocate space for hyperslab");
hslab_nelmts = hslab_nbytes / p_type_nbytes;
hslab_space = H5Screate_simple(1, &hslab_nelmts, NULL);
@@ -1005,12 +996,12 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
if (H5Sselect_hyperslab(hslab_space, H5S_SELECT_SET, zero, NULL, &hs_select_nelmts, NULL) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sselect_hyperslab failed");
- }
+ } /* end if rank > 0 */
else {
H5Sselect_all(f_space_id);
H5Sselect_all(hslab_space);
hs_select_nelmts = 1;
- } /* rank */
+ } /* end (else) rank == 0 */
if(H5Dread(dset_in, wtype_id, hslab_space, f_space_id, H5P_DEFAULT, hslab_buf) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dread failed");
@@ -1029,20 +1020,19 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
hs_sel_offset[k - 1] = 0;
else
carry = 0;
- } /* k */
- } /* elmtno */
+ }
+ } /* end for (hyperslab selection loop) */
H5Sclose(hslab_space);
- /* free */
if (hslab_buf != NULL) {
HDfree(hslab_buf);
hslab_buf = NULL;
}
- } /* hyperslab read */
- } /* if (nelmts>0 && space_status==H5D_SPACE_STATUS_NOT_ALLOCATED) */
+ } /* end if reading/writing by hyperslab */
+ } /* end if (nelmts > 0 && space_status != H5D_SPACE_STATUS_NOT_ALLOCATED) */
/*-------------------------------------------------------------------------
- * amount of compression used
+ * print amount of compression used
*-------------------------------------------------------------------------
*/
if (options->verbose) {
@@ -1062,14 +1052,14 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
print_dataset_info(dcpl_in, travt->objs[i].name, ratio, 0);
/* print a message that the filter was not applied
- (in case there was a filter)
+ * (in case there was a filter)
*/
if (has_filter && apply_s == 0)
- printf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n", travt->objs[i].name, (int) options->min_comp);
+ HDprintf(" <warning: filter not applied to %s. dataset smaller than %d bytes>\n", travt->objs[i].name, (int) options->min_comp);
if (has_filter && apply_f == 0)
- printf(" <warning: could not apply the filter to %s>\n", travt->objs[i].name);
- } /* verbose */
+ HDprintf(" <warning: could not apply the filter to %s>\n", travt->objs[i].name);
+ } /* end if verbose (print compression) */
/*-------------------------------------------------------------------------
* copy attrs
@@ -1078,14 +1068,13 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (copy_attr(dset_in, dset_out, &named_dt_head, travt, options) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_attr failed");
- /*close */
if (H5Dclose(dset_out) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
- }/*!H5T_REFERENCE*/
- }/*h5tools_canreadf*/
+ } /* end if not a reference */
+ } /* end if h5tools_canreadf (filter availability check) */
/*-------------------------------------------------------------------------
- * close
+ * Close
*-------------------------------------------------------------------------
*/
if (H5Tclose(ftype_id) < 0)
@@ -1102,7 +1091,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
}
/*-------------------------------------------------------------------------
- * we do not have request for filter/chunking use H5Ocopy instead
+ * We do not have request for filter/chunking; use H5Ocopy instead
*-------------------------------------------------------------------------
*/
else {
@@ -1116,11 +1105,6 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
if (H5Pset_copy_object(pid, H5O_COPY_WITHOUT_ATTR_FLAG) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pset_copy_object failed");
- /*-------------------------------------------------------------------------
- * do the copy
- *-------------------------------------------------------------------------
- */
-
if (H5Ocopy(fidin, /* Source file or group identifier */
travt->objs[i].name, /* Name of the source object to be copied */
fidout, /* Destination file or group identifier */
@@ -1129,12 +1113,11 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
H5P_DEFAULT) < 0) /* Properties which apply to the new hard link */
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Ocopy failed");
- /* close property */
if (H5Pclose(pid) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pclose failed");
/*-------------------------------------------------------------------------
- * copy attrs manually
+ * Copy attrs manually
*-------------------------------------------------------------------------
*/
if ((dset_in = H5Dopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
@@ -1149,9 +1132,9 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Dclose failed");
if (options->verbose)
- printf(FORMAT_OBJ, "dset", travt->objs[i].name);
+ HDprintf(FORMAT_OBJ, "dset", travt->objs[i].name);
- } /* end do we have request for filter/chunking */
+ } /* end whether we have request for filter/chunking */
break;
/*-------------------------------------------------------------------------
@@ -1160,7 +1143,7 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
*/
case H5TRAV_TYPE_NAMED_DATATYPE:
if (options->verbose)
- printf(FORMAT_OBJ, "type", travt->objs[i].name);
+ HDprintf(FORMAT_OBJ, "type", travt->objs[i].name);
if ((type_in = H5Topen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Topen2 failed");
@@ -1199,20 +1182,20 @@ int do_copy_objects(hid_t fidin, hid_t fidout, trav_table_t *travt,
case H5TRAV_TYPE_LINK:
case H5TRAV_TYPE_UDLINK:
if (options->verbose)
- printf(FORMAT_OBJ, "link", travt->objs[i].name);
+ HDprintf(FORMAT_OBJ, "link", travt->objs[i].name);
if (H5Lcopy(fidin, travt->objs[i].name, fidout, travt->objs[i].name, H5P_DEFAULT, H5P_DEFAULT) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Lcopy failed");
if (options->verbose)
- printf(FORMAT_OBJ, "link", travt->objs[i].name);
+ HDprintf(FORMAT_OBJ, "link", travt->objs[i].name);
break;
default:
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "Object type not found");
} /* switch */
- } /* end for */
- } /* end if */
+ } /* end for each object to traverse */
+ } /* end if there are objects */
done:
@@ -1250,7 +1233,7 @@ done:
HDfree(hslab_buf);
return ret_value;
-}
+} /* end do_copy_objects() */
/*-------------------------------------------------------------------------
* Function: print_dataset_info
@@ -1300,7 +1283,7 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr)
{
unsigned level = cd_values[0];
- sprintf(temp,"(%d)", level);
+ HDsprintf(temp,"(%d)", level);
HDstrcat(strfilter, temp);
}
#endif
@@ -1314,7 +1297,7 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr)
unsigned options_mask = cd_values[0]; /* from dcpl, not filt*/
unsigned ppb = cd_values[1];
- sprintf(temp,"(%d,", ppb);
+ HDsprintf(temp,"(%d,", ppb);
HDstrcat(strfilter, temp);
if (options_mask & H5_SZIP_EC_OPTION_MASK)
HDstrcpy(temp, "EC) ");
@@ -1344,21 +1327,21 @@ print_dataset_info(hid_t dcpl_id, char *objname, double ratio, int pr)
default:
HDstrcat(strfilter, "UD ");
break;
- } /* switch */
- }/*i*/
+ } /* end switch */
+ } /* end for each filter */
if (!pr)
- printf(FORMAT_OBJ, "dset", objname);
+ HDprintf(FORMAT_OBJ, "dset", objname);
else {
- char str[255], temp[28];
+ char str[512], temp[512];
HDstrcpy(str, "dset ");
HDstrcat(str, strfilter);
- sprintf(temp, " (%.3f:1)", ratio);
+ HDsprintf(temp, " (%.3f:1)", ratio);
HDstrcat(str, temp);
- printf(FORMAT_OBJ, str, objname);
+ HDprintf(FORMAT_OBJ, str, objname);
}
-}
+} /* end print_dataset_info() */
/*-------------------------------------------------------------------------
* Function: copy_user_block
@@ -1428,7 +1411,7 @@ done:
HDclose(outfid);
return ret_value;
-}
+} /* end copy_user_block() */
/*-------------------------------------------------------------------------
* Function: print_user_block
@@ -1483,10 +1466,10 @@ print_user_block(const char *filename, hid_t fid)
for (i = 0; i < nread; i++) {
- printf("%c ", rbuf[i]);
+ HDprintf("%c ", rbuf[i]);
}
- printf("\n");
+ HDprintf("\n");
if (nread < 0) {
HGOTO_ERROR(H5E_tools_g, H5E_tools_min_id_g, "nread < 0");
@@ -1501,6 +1484,6 @@ done:
HDclose(fh);
return;
-}
+} /* end print_user_block() */
#endif
diff --git a/tools/src/h5repack/h5repack_filters.c b/tools/src/h5repack/h5repack_filters.c
index 3d9472a..7e32def 100644
--- a/tools/src/h5repack/h5repack_filters.c
+++ b/tools/src/h5repack/h5repack_filters.c
@@ -42,7 +42,8 @@ static int aux_copy_obj(hid_t dcpl_id, /* dataset creation property list */
H5D_layout_t layout;
int rank; /* rank of dataset */
hsize_t chsize[64]; /* chunk size in elements */
- unsigned int i;
+ int i;
+ unsigned u;
/* get information about input filters */
if ((nfilters = H5Pget_nfilters(dcpl_id)) < 0)
@@ -65,8 +66,8 @@ static int aux_copy_obj(hid_t dcpl_id, /* dataset creation property list */
if ((rank = H5Pget_chunk(dcpl_id, NELMTS(chsize), chsize/*out*/)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Pget_chunk failed");
objout->chunk.rank = rank;
- for (i = 0; i < rank; i++)
- objout->chunk.chunk_lengths[i] = chsize[i];
+ for (u = 0; u < (unsigned)rank; u++)
+ objout->chunk.chunk_lengths[u] = chsize[u];
}
done:
@@ -85,8 +86,7 @@ static int aux_find_obj(const char* name, /* object name from traverse list */
pack_info_t *obj /*OUT*/) /* info about object to filter */
{
char *pdest = NULL;
- char *pname = NULL;
- int result;
+ const char *pname = NULL;
unsigned int i;
for (i = 0; i < options->op_tbl->nelems; i++) {
diff --git a/tools/src/h5repack/h5repack_main.c b/tools/src/h5repack/h5repack_main.c
index dec25f9..b4e1985 100644
--- a/tools/src/h5repack/h5repack_main.c
+++ b/tools/src/h5repack/h5repack_main.c
@@ -23,7 +23,8 @@ static void leave(int ret) H5_ATTR_NORETURN;
/* module-scoped variables */
-static int has_i_o = 0;
+static int has_i = 0;
+static int has_o = 0;
const char *infile = NULL;
const char *outfile = NULL;
@@ -33,34 +34,34 @@ const char *outfile = NULL;
*/
static const char *s_opts = "hVvf:l:m:e:nLj:k:c:d:s:u:b:M:t:a:i:o:S:P:T:G:q:z:E";
static struct long_options l_opts[] = {
- { "help", no_arg, 'h' },
- { "version", no_arg, 'V' },
- { "verbose", no_arg, 'v' },
- { "filter", require_arg, 'f' },
- { "layout", require_arg, 'l' },
- { "minimum", require_arg, 'm' },
- { "file", require_arg, 'e' },
- { "native", no_arg, 'n' },
- { "latest", no_arg, 'L' },
- { "low", require_arg, 'j' },
- { "high", require_arg, 'k' },
- { "compact", require_arg, 'c' },
- { "indexed", require_arg, 'd' },
- { "ssize", require_arg, 's' },
- { "ublock", require_arg, 'u' },
- { "block", require_arg, 'b' },
+ { "help", no_arg, 'h' },
+ { "version", no_arg, 'V' },
+ { "verbose", no_arg, 'v' },
+ { "filter", require_arg, 'f' },
+ { "layout", require_arg, 'l' },
+ { "minimum", require_arg, 'm' },
+ { "file", require_arg, 'e' },
+ { "native", no_arg, 'n' },
+ { "latest", no_arg, 'L' },
+ { "low", require_arg, 'j' },
+ { "high", require_arg, 'k' },
+ { "compact", require_arg, 'c' },
+ { "indexed", require_arg, 'd' },
+ { "ssize", require_arg, 's' },
+ { "ublock", require_arg, 'u' },
+ { "block", require_arg, 'b' },
{ "metadata_block_size", require_arg, 'M' },
- { "threshold", require_arg, 't' },
- { "alignment", require_arg, 'a' },
- { "infile", require_arg, 'i' }, /* -i for backward compability */
- { "outfile", require_arg, 'o' }, /* -o for backward compability */
- { "fs_strategy", require_arg, 'S' },
- { "fs_persist", require_arg, 'P' },
- { "fs_threshold", require_arg, 'T' },
- { "fs_pagesize", require_arg, 'G' },
- { "sort_by", require_arg, 'q' },
- { "sort_order", require_arg, 'z' },
- { "enable-error-stack", no_arg, 'E' },
+ { "threshold", require_arg, 't' },
+ { "alignment", require_arg, 'a' },
+ { "infile", require_arg, 'i' }, /* for backward compability */
+ { "outfile", require_arg, 'o' }, /* for backward compability */
+ { "fs_strategy", require_arg, 'S' },
+ { "fs_persist", require_arg, 'P' },
+ { "fs_threshold", require_arg, 'T' },
+ { "fs_pagesize", require_arg, 'G' },
+ { "sort_by", require_arg, 'q' },
+ { "sort_order", require_arg, 'z' },
+ { "enable-error-stack", no_arg, 'E' },
{ NULL, 0, '\0' }
};
@@ -83,13 +84,17 @@ static void usage(const char *prog) {
PRINTVALSTREAM(rawoutstream, " -v, --verbose Verbose mode, print object information\n");
PRINTVALSTREAM(rawoutstream, " -V, --version Print version number and exit\n");
PRINTVALSTREAM(rawoutstream, " -n, --native Use a native HDF5 type when repacking\n");
- PRINTVALSTREAM(rawoutstream, " --enable-error-stack Prints messages from the HDF5 error stack as they occur\n");
+ PRINTVALSTREAM(rawoutstream, " --enable-error-stack Prints messages from the HDF5 error stack as they\n");
+ PRINTVALSTREAM(rawoutstream, " occur\n");
PRINTVALSTREAM(rawoutstream, " -L, --latest Use latest version of file format\n");
- PRINTVALSTREAM(rawoutstream, " This option will take precedence over the -j and -k options\n");
- PRINTVALSTREAM(rawoutstream, " --low=BOUND The low bound for library release versions to use when creating\n");
- PRINTVALSTREAM(rawoutstream, " objects in the file (default is H5F_LIBVER_EARLIEST)\n");
- PRINTVALSTREAM(rawoutstream, " --high=BOUND The high bound for library release versions to use when creating\n");
- PRINTVALSTREAM(rawoutstream, " objects in the file (default is H5F_LIBVER_LATEST)\n");
+ PRINTVALSTREAM(rawoutstream, " This option will take precedence over the options\n");
+ PRINTVALSTREAM(rawoutstream, " --low and --high\n");
+ PRINTVALSTREAM(rawoutstream, " --low=BOUND The low bound for library release versions to use\n");
+ PRINTVALSTREAM(rawoutstream, " when creating objects in the file\n");
+ PRINTVALSTREAM(rawoutstream, " (default is H5F_LIBVER_EARLIEST)\n");
+ PRINTVALSTREAM(rawoutstream, " --high=BOUND The high bound for library release versions to use\n");
+ PRINTVALSTREAM(rawoutstream, " when creating objects in the file\n");
+ PRINTVALSTREAM(rawoutstream, " (default is H5F_LIBVER_LATEST)\n");
PRINTVALSTREAM(rawoutstream, " -c L1, --compact=L1 Maximum number of links in header messages\n");
PRINTVALSTREAM(rawoutstream, " -d L2, --indexed=L2 Minimum number of links in the indexed format\n");
PRINTVALSTREAM(rawoutstream, " -s S[:F], --ssize=S[:F] Shared object header message minimum size\n");
@@ -104,10 +109,14 @@ static void usage(const char *prog) {
PRINTVALSTREAM(rawoutstream, " -z Z, --sort_order=Z Sort groups and attributes by order Z\n");
PRINTVALSTREAM(rawoutstream, " -f FILT, --filter=FILT Filter type\n");
PRINTVALSTREAM(rawoutstream, " -l LAYT, --layout=LAYT Layout type\n");
- PRINTVALSTREAM(rawoutstream, " -S FS_STRATEGY, --fs_strategy=FS_STRATEGY File space management strategy for H5Pset_file_space_strategy\n");
- PRINTVALSTREAM(rawoutstream, " -P FS_PERSIST, --fs_persist=FS_PERSIST Persisting or not persisting free-space for H5Pset_file_space_strategy\n");
- PRINTVALSTREAM(rawoutstream, " -T FS_THRESHOLD, --fs_threshold=FS_THRESHOLD Free-space section threshold for H5Pset_file_space_strategy\n");
- PRINTVALSTREAM(rawoutstream, " -G FS_PAGESIZE, --fs_pagesize=FS_PAGESIZE File space page size for H5Pset_file_space_page_size\n");
+ PRINTVALSTREAM(rawoutstream, " -S FS_STRATEGY, --fs_strategy=FS_STRATEGY File space management strategy for\n");
+ PRINTVALSTREAM(rawoutstream, " H5Pset_file_space_strategy\n");
+ PRINTVALSTREAM(rawoutstream, " -P FS_PERSIST, --fs_persist=FS_PERSIST Persisting or not persisting free-\n");
+ PRINTVALSTREAM(rawoutstream, " space for H5Pset_file_space_strategy\n");
+ PRINTVALSTREAM(rawoutstream, " -T FS_THRESHOLD, --fs_threshold=FS_THRESHOLD Free-space section threshold\n");
+ PRINTVALSTREAM(rawoutstream, " for H5Pset_file_space_strategy\n");
+ PRINTVALSTREAM(rawoutstream, " -G FS_PAGESIZE, --fs_pagesize=FS_PAGESIZE File space page size for\n");
+ PRINTVALSTREAM(rawoutstream, " H5Pset_file_space_page_size\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " M - is an integer greater than 1, size of dataset in bytes (default is 0)\n");
PRINTVALSTREAM(rawoutstream, " E - is a filename.\n");
@@ -115,15 +124,17 @@ static void usage(const char *prog) {
PRINTVALSTREAM(rawoutstream, " U - is a filename.\n");
PRINTVALSTREAM(rawoutstream, " T - is an integer\n");
PRINTVALSTREAM(rawoutstream, " A - is an integer greater than zero\n");
- PRINTVALSTREAM(rawoutstream, " Q - is the sort index type for the input file. It can be \"name\" or \"creation_order\" (default)\n");
- PRINTVALSTREAM(rawoutstream, " Z - is the sort order type for the input file. It can be \"descending\" or \"ascending\" (default)\n");
+ PRINTVALSTREAM(rawoutstream, " Q - is the sort index type for the input file. It can be \"name\" or\n");
+ PRINTVALSTREAM(rawoutstream, " \"creation_order\" (default)\n");
+ PRINTVALSTREAM(rawoutstream, " Z - is the sort order type for the input file. It can be \"descending\" or\n");
+ PRINTVALSTREAM(rawoutstream, " \"ascending\" (default)\n");
PRINTVALSTREAM(rawoutstream, " B - is the user block size, any value that is 512 or greater and is\n");
PRINTVALSTREAM(rawoutstream, " a power of 2 (1024 default)\n");
PRINTVALSTREAM(rawoutstream, " F - is the shared object header message type, any of <dspace|dtype|fill|\n");
PRINTVALSTREAM(rawoutstream, " pline|attr>. If F is not specified, S applies to all messages\n");
PRINTVALSTREAM(rawoutstream, "\n");
- PRINTVALSTREAM(rawoutstream, " BOUND is an integer indicating the library release versions to use when creating\n");
- PRINTVALSTREAM(rawoutstream, " objects in the file (see H5Pset_libver_bounds()):\n");
+ PRINTVALSTREAM(rawoutstream, " BOUND is an integer indicating the library release versions to use when\n");
+ PRINTVALSTREAM(rawoutstream, " creating objects in the file (see H5Pset_libver_bounds()):\n");
PRINTVALSTREAM(rawoutstream, " 0: This is H5F_LIBVER_EARLIEST in H5F_libver_t struct\n");
PRINTVALSTREAM(rawoutstream, " 1: This is H5F_LIBVER_V18 in H5F_libver_t struct\n");
PRINTVALSTREAM(rawoutstream, " 2: This is H5F_LIBVER_V110 in H5F_libver_t struct\n");
@@ -131,24 +142,31 @@ static void usage(const char *prog) {
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " FS_STRATEGY is a string indicating the file space strategy used:\n");
PRINTVALSTREAM(rawoutstream, " FSM_AGGR:\n");
- PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are free-space managers, aggregators and virtual file driver.\n");
+ PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are free-space\n");
+ PRINTVALSTREAM(rawoutstream, " managers, aggregators and virtual file driver.\n");
PRINTVALSTREAM(rawoutstream, " PAGE:\n");
- PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are free-space managers with embedded paged aggregation and virtual file driver.\n");
+ PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are free-space\n");
+ PRINTVALSTREAM(rawoutstream, " managers with embedded paged aggregation and virtual file driver.\n");
PRINTVALSTREAM(rawoutstream, " AGGR:\n");
- PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are aggregators and virtual file driver.\n");
+ PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are aggregators and\n");
+ PRINTVALSTREAM(rawoutstream, " virtual file driver.\n");
PRINTVALSTREAM(rawoutstream, " NONE:\n");
- PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are virtual file driver.\n");
- PRINTVALSTREAM(rawoutstream, " The default strategy when not set is FSM_AGGR without persisting free-space.\n");
+ PRINTVALSTREAM(rawoutstream, " The mechanisms used in managing file space are virtual file\n");
+ PRINTVALSTREAM(rawoutstream, " driver.\n");
+ PRINTVALSTREAM(rawoutstream, " The default strategy when not set is FSM_AGGR without persisting free-\n");
+ PRINTVALSTREAM(rawoutstream, " space.\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " FS_PERSIST is 1 to persisting free-space or 0 to not persisting free-space.\n");
PRINTVALSTREAM(rawoutstream, " The default when not set is not persisting free-space.\n");
PRINTVALSTREAM(rawoutstream, " The value is ignored for AGGR and NONE strategies.\n");
PRINTVALSTREAM(rawoutstream, "\n");
- PRINTVALSTREAM(rawoutstream, " FS_THRESHOLD is the minimum size (in bytes) of free-space sections to be tracked by the library.\n");
+ PRINTVALSTREAM(rawoutstream, " FS_THRESHOLD is the minimum size (in bytes) of free-space sections to be\n");
+ PRINTVALSTREAM(rawoutstream, " tracked by the library.\n");
PRINTVALSTREAM(rawoutstream, " The default when not set is 1.\n");
PRINTVALSTREAM(rawoutstream, " The value is ignored for AGGR and NONE strategies.\n");
PRINTVALSTREAM(rawoutstream, "\n");
- PRINTVALSTREAM(rawoutstream, " FS_PAGESIZE is the size (in bytes) >=512 that is used by the library when the file space strategy PAGE is used.\n");
+ PRINTVALSTREAM(rawoutstream, " FS_PAGESIZE is the size (in bytes) >=512 that is used by the library when\n");
+ PRINTVALSTREAM(rawoutstream, " the file space strategy PAGE is used.\n");
PRINTVALSTREAM(rawoutstream, " The default when not set is 4096.\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " FILT - is a string with the format:\n");
@@ -176,9 +194,9 @@ static void usage(const char *prog) {
PRINTVALSTREAM(rawoutstream, " NBIT (no parameter)\n");
PRINTVALSTREAM(rawoutstream, " SOFF=<scale_factor,scale_type> scale_factor is an integer and scale_type\n");
PRINTVALSTREAM(rawoutstream, " is either IN or DS\n");
- PRINTVALSTREAM(rawoutstream, " UD=<filter_number,filter_flag,cd_value_count,value_1[,value_2,...,value_N]>\n");
- PRINTVALSTREAM(rawoutstream, " required values for filter_number,filter_flag,cd_value_count,value_1\n");
- PRINTVALSTREAM(rawoutstream, " optional values for value_2 to value_N\n");
+ PRINTVALSTREAM(rawoutstream, " UD=<filter_number,filter_flag,cd_value_count,value1[,value2,...,valueN]>\n");
+ PRINTVALSTREAM(rawoutstream, " Required values: filter_number, filter_flag, cd_value_count, value1\n");
+ PRINTVALSTREAM(rawoutstream, " Optional values: value2 to valueN\n");
PRINTVALSTREAM(rawoutstream, " NONE (no parameter)\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " LAYT - is a string with the format:\n");
@@ -215,12 +233,7 @@ static void usage(const char *prog) {
PRINTVALSTREAM(rawoutstream, "4) h5repack -L -c 10 -s 20:dtype file1 file2\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " Using latest file format with maximum compact group size of 10 and\n");
- PRINTVALSTREAM(rawoutstream, " and minimum shared datatype size of 20\n");
- PRINTVALSTREAM(rawoutstream, "\n");
- PRINTVALSTREAM(rawoutstream, "5) h5repack --low=0 --high=1 file1 file2\n");
- PRINTVALSTREAM(rawoutstream, "\n");
- PRINTVALSTREAM(rawoutstream, " Set low=H5F_LIBVER_EARLIEST and high=H5F_LIBVER_V18 via H5Pset_libver_bounds() when\n");
- PRINTVALSTREAM(rawoutstream, " creating the repacked file: file2\n");
+ PRINTVALSTREAM(rawoutstream, " minimum shared datatype size of 20\n");
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, "5) h5repack -f SHUF -f GZIP=1 file1 file2\n");
PRINTVALSTREAM(rawoutstream, "\n");
@@ -230,6 +243,11 @@ static void usage(const char *prog) {
PRINTVALSTREAM(rawoutstream, "\n");
PRINTVALSTREAM(rawoutstream, " Add bzip2 filter to all datasets\n");
PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, "7) h5repack --low=0 --high=1 file1 file2\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
+ PRINTVALSTREAM(rawoutstream, " Set low=H5F_LIBVER_EARLIEST and high=H5F_LIBVER_V18 via\n");
+ PRINTVALSTREAM(rawoutstream, " H5Pset_libver_bounds() when creating the repacked file, file2\n");
+ PRINTVALSTREAM(rawoutstream, "\n");
}
/*-------------------------------------------------------------------------
@@ -264,7 +282,7 @@ int read_info(const char *filename, pack_opt_t *options)
int i, rc = 1;
int ret_value = EXIT_SUCCESS;
- if ((fp = HDfopen(filename, "r")) == (FILE *) NULL) {
+ if (NULL == (fp = HDfopen(filename, "r"))) {
error_msg("cannot open options file %s\n", filename);
h5tools_setstatus(EXIT_FAILURE);
ret_value = EXIT_FAILURE;
@@ -273,90 +291,46 @@ int read_info(const char *filename, pack_opt_t *options)
/* cycle until end of file reached */
while (1) {
- rc = fscanf(fp, "%s", stype);
- if (rc == -1)
- break;
-
- /*-------------------------------------------------------------------------
- * filter
- *-------------------------------------------------------------------------
- */
- if (HDstrcmp(stype,"-f") == 0) {
- /* find begining of info */
- i = 0;
- c = '0';
- while (c != ' ') {
- if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
- error_msg("fscanf error\n");
- h5tools_setstatus(EXIT_FAILURE);
- ret_value = EXIT_FAILURE;
- goto done;
- } /* end if */
- if (HDfeof(fp))
- break;
- }
- c = '0';
- /* go until end */
- while (c != ' ') {
- if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
- error_msg("fscanf error\n");
- h5tools_setstatus(EXIT_FAILURE);
- ret_value = EXIT_FAILURE;
- goto done;
- } /* end if */
- comp_info[i] = c;
- i++;
- if (HDfeof(fp))
- break;
- if (c == 10 /*eol*/)
- break;
- }
- comp_info[i - 1] = '\0'; /*cut the last " */
- if (h5repack_addfilter(comp_info, options) == -1) {
- error_msg("could not add compression option\n");
+ /* Info indicator must be for layout or filter */
+ if (HDstrcmp(stype,"-l") && HDstrcmp(stype, "-f")) {
+ error_msg("bad file format for %s", filename);
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
+ }
+
+ /* find begining of info */
+ i = 0;
+ c = '0';
+ while (c != ' ') {
+ if (fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
+ error_msg("fscanf error\n");
h5tools_setstatus(EXIT_FAILURE);
ret_value = EXIT_FAILURE;
goto done;
}
+ if (HDfeof(fp))
+ break;
}
- /*-------------------------------------------------------------------------
- * layout
- *-------------------------------------------------------------------------
- */
- else if (HDstrcmp(stype,"-l") == 0) {
-
- /* find begining of info */
- i = 0;
- c = '0';
- while (c != ' ') {
- if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
- error_msg("fscanf error\n");
- h5tools_setstatus(EXIT_FAILURE);
- ret_value = EXIT_FAILURE;
- goto done;
- } /* end if */
- if (HDfeof(fp))
- break;
- }
- c = '0';
- /* go until end */
- while (c != ' ') {
- if(fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
- error_msg("fscanf error\n");
- h5tools_setstatus(EXIT_FAILURE);
- ret_value = EXIT_FAILURE;
- goto done;
- } /* end if */
- comp_info[i] = c;
- i++;
- if (HDfeof(fp))
- break;
- if (c == 10 /*eol*/)
- break;
+ c = '0';
+ /* go until end */
+ while (c != ' ') {
+ if (fscanf(fp, "%c", &c) < 0 && HDferror(fp)) {
+ error_msg("fscanf error\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
}
- comp_info[i - 1] = '\0'; /*cut the last " */
+ comp_info[i++] = c;
+ if (HDfeof(fp))
+ break;
+ if (c == 10 /*eol*/)
+ break;
+ }
+ comp_info[i - 1] = '\0'; /*cut the last " */
+ if (!HDstrcmp(stype, "-l")) {
if (h5repack_addlayout(comp_info, options) == -1) {
error_msg("could not add chunck option\n");
h5tools_setstatus(EXIT_FAILURE);
@@ -364,17 +338,15 @@ int read_info(const char *filename, pack_opt_t *options)
goto done;
}
}
- /*-------------------------------------------------------------------------
- * not valid
- *-------------------------------------------------------------------------
- */
else {
- error_msg("bad file format for %s", filename);
- h5tools_setstatus(EXIT_FAILURE);
- ret_value = EXIT_FAILURE;
- goto done;
+ if (h5repack_addfilter(comp_info, options) == -1) {
+ error_msg("could not add compression option\n");
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = EXIT_FAILURE;
+ goto done;
+ }
}
- }
+ } /* end while info-read cycling */
done:
if (fp)
@@ -398,9 +370,9 @@ set_sort_by(const char *form)
{
H5_index_t idx_type = H5_INDEX_UNKNOWN;
- if (HDstrcmp(form,"name")==0) /* H5_INDEX_NAME */
+ if (!HDstrcmp(form, "name"))
idx_type = H5_INDEX_NAME;
- else if (HDstrcmp(form,"creation_order")==0) /* H5_INDEX_CRT_ORDER */
+ else if (!HDstrcmp(form, "creation_order"))
idx_type = H5_INDEX_CRT_ORDER;
return idx_type;
@@ -421,9 +393,9 @@ set_sort_order(const char *form)
{
H5_iter_order_t iter_order = H5_ITER_UNKNOWN;
- if (HDstrcmp(form,"ascending")==0) /* H5_ITER_INC */
+ if (!HDstrcmp(form, "ascending"))
iter_order = H5_ITER_INC;
- else if (HDstrcmp(form,"descending")==0) /* H5_ITER_DEC */
+ else if (!HDstrcmp(form, "descending"))
iter_order = H5_ITER_DEC;
return iter_order;
@@ -442,19 +414,19 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
int ret_value = 0;
/* parse command line options */
- while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
+ while (EOF != (opt = get_option(argc, argv, s_opts, l_opts))) {
switch ((char) opt) {
/* -i for backward compatibility */
case 'i':
infile = opt_arg;
- has_i_o = 1;
+ has_i++;
break;
/* -o for backward compatibility */
case 'o':
outfile = opt_arg;
- has_i_o = 1;
+ has_o++;
break;
case 'h':
@@ -519,7 +491,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
case 'j':
options->low_bound = (H5F_libver_t)HDatoi(opt_arg);
- if(options->low_bound < H5F_LIBVER_EARLIEST || options->low_bound > H5F_LIBVER_LATEST) {
+ if (options->low_bound < H5F_LIBVER_EARLIEST || options->low_bound > H5F_LIBVER_LATEST) {
error_msg("in parsing low bound\n");
goto done;
}
@@ -527,7 +499,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
case 'k':
options->high_bound = (H5F_libver_t)HDatoi(opt_arg);
- if(options->high_bound < H5F_LIBVER_EARLIEST || options->high_bound > H5F_LIBVER_LATEST) {
+ if (options->high_bound < H5F_LIBVER_EARLIEST || options->high_bound > H5F_LIBVER_LATEST) {
error_msg("in parsing high bound\n");
goto done;
}
@@ -549,10 +521,10 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
{
int idx = 0;
int ssize = 0;
- char *msgPtr = HDstrchr( opt_arg, ':');
+ char *msgPtr = HDstrchr(opt_arg, ':');
options->latest = TRUE; /* must use latest format */
if (msgPtr == NULL) {
- ssize = HDatoi( opt_arg );
+ ssize = HDatoi(opt_arg);
for (idx = 0; idx < 5; idx++)
options->msg_size[idx] = ssize;
}
@@ -562,15 +534,15 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
HDstrcpy(msgType, msgPtr + 1);
msgPtr[0] = '\0';
ssize = HDatoi( opt_arg );
- if (HDstrncmp(msgType, "dspace",6) == 0)
+ if (!HDstrncmp(msgType, "dspace", 6))
options->msg_size[0] = ssize;
- else if (HDstrncmp(msgType, "dtype", 5) == 0)
+ else if (!HDstrncmp(msgType, "dtype", 5))
options->msg_size[1] = ssize;
- else if (HDstrncmp(msgType, "fill", 4) == 0)
+ else if (!HDstrncmp(msgType, "fill", 4))
options->msg_size[2] = ssize;
- else if (HDstrncmp(msgType, "pline", 5) == 0)
+ else if (!HDstrncmp(msgType, "pline", 5))
options->msg_size[3] = ssize;
- else if (HDstrncmp(msgType, "attr", 4) == 0)
+ else if (!HDstrncmp(msgType, "attr", 4))
options->msg_size[4] = ssize;
}
}
@@ -607,13 +579,13 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
char strategy[MAX_NC_NAME];
HDstrcpy(strategy, opt_arg);
- if(!HDstrcmp(strategy, "FSM_AGGR"))
+ if (!HDstrcmp(strategy, "FSM_AGGR"))
options->fs_strategy = H5F_FSPACE_STRATEGY_FSM_AGGR;
- else if(!HDstrcmp(strategy, "PAGE"))
+ else if (!HDstrcmp(strategy, "PAGE"))
options->fs_strategy = H5F_FSPACE_STRATEGY_PAGE;
- else if(!HDstrcmp(strategy, "AGGR"))
+ else if (!HDstrcmp(strategy, "AGGR"))
options->fs_strategy = H5F_FSPACE_STRATEGY_AGGR;
- else if(!HDstrcmp(strategy, "NONE"))
+ else if (!HDstrcmp(strategy, "NONE"))
options->fs_strategy = H5F_FSPACE_STRATEGY_NONE;
else {
error_msg("invalid file space management strategy\n", opt_arg);
@@ -621,7 +593,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
ret_value = -1;
goto done;
}
- if(options->fs_strategy == (H5F_fspace_strategy_t)0)
+ if (options->fs_strategy == (H5F_fspace_strategy_t)0)
/* To distinguish the "specified" zero value */
options->fs_strategy = (H5F_fspace_strategy_t)-1;
}
@@ -629,27 +601,27 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
case 'P':
options->fs_persist = HDatoi(opt_arg);
- if(options->fs_persist == 0)
+ if (options->fs_persist == 0)
/* To distinguish the "specified" zero value */
options->fs_persist = -1;
break;
case 'T':
options->fs_threshold = HDatol(opt_arg);
- if(options->fs_threshold == 0)
+ 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);
- if(options->fs_pagesize == 0)
+ if (options->fs_pagesize == 0)
/* To distinguish the "specified" zero value */
options->fs_pagesize = -1;
break;
case 'q':
- if((sort_by = set_sort_by(opt_arg)) < 0) {
+ if (H5_INDEX_UNKNOWN == set_sort_by(opt_arg)) {
error_msg(" failed to set sort by form <%s>\n", opt_arg);
h5tools_setstatus(EXIT_FAILURE);
ret_value = -1;
@@ -658,7 +630,7 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
break;
case 'z':
- if((sort_order = set_sort_order(opt_arg)) < 0) {
+ if (set_sort_order(opt_arg) == H5_ITER_UNKNOWN) {
error_msg(" failed to set sort order form <%s>\n", opt_arg);
h5tools_setstatus(EXIT_FAILURE);
ret_value = -1;
@@ -672,18 +644,35 @@ int parse_command_line(int argc, const char **argv, pack_opt_t* options)
default:
break;
- } /* switch */
- } /* while */
-
- if (has_i_o == 0) {
- /* check for file names to be processed */
- if (argc <= opt_ind || argv[opt_ind + 1] == NULL) {
- error_msg("missing file names\n");
- usage(h5tools_getprogname());
- h5tools_setstatus(EXIT_FAILURE);
- ret_value = -1;
- }
- }
+ } /* end switch */
+ } /* end while there are more options to parse */
+
+ /* 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 (!HDstrcmp(infile, outfile)) {
+ error_msg("file names cannot be the same\n");
+ usage(h5tools_getprogname());
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ }
+ }
+ else {
+ error_msg("file names missing\n");
+ usage(h5tools_getprogname());
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ }
+ }
+ else if (has_i != 1 || has_o != 1) {
+ error_msg("filenames must be either both -i -o or both positional\n");
+ usage(h5tools_getprogname());
+ h5tools_setstatus(EXIT_FAILURE);
+ ret_value = -1;
+ }
done:
return ret_value;
@@ -740,28 +729,6 @@ int main(int argc, const char **argv)
if (parse_command_line(argc, argv, &options) < 0)
goto done;
- /* get file names if they were not yet got */
- if (has_i_o == 0) {
-
- if (argv[opt_ind] != NULL && argv[opt_ind + 1] != NULL) {
- infile = argv[opt_ind];
- outfile = argv[opt_ind + 1];
-
- if ( HDstrcmp( infile, outfile ) == 0) {
- error_msg("file names cannot be the same\n");
- usage(h5tools_getprogname());
- h5tools_setstatus(EXIT_FAILURE);
- goto done;
- }
- }
- else {
- error_msg("file names missing\n");
- usage(h5tools_getprogname());
- h5tools_setstatus(EXIT_FAILURE);
- goto done;
- }
- }
-
if (enable_error_stack > 0) {
H5Eset_auto2(H5E_DEFAULT, func, edata);
H5Eset_auto2(H5tools_ERR_STACK_g, tools_func, tools_edata);
diff --git a/tools/src/h5repack/h5repack_refs.c b/tools/src/h5repack/h5repack_refs.c
index a275443..7e8951f 100644
--- a/tools/src/h5repack/h5repack_refs.c
+++ b/tools/src/h5repack/h5repack_refs.c
@@ -22,7 +22,7 @@
*/
static const char* MapIdToName(hid_t refobj_id,trav_table_t *travt);
-static int copy_refs_attr(hid_t loc_in, hid_t loc_out, pack_opt_t *options,
+static int copy_refs_attr(hid_t loc_in, hid_t loc_out,
trav_table_t *travt, hid_t fidout);
static herr_t update_ref_value(hid_t obj_id, H5R_type_t ref_type, void *ref_in,
hid_t fid_out, void *ref_out, trav_table_t *travt);
@@ -81,7 +81,7 @@ int do_copy_refobjs(hid_t fidin,
if((grp_in = H5Gopen2(fidin, travt->objs[i].name, H5P_DEFAULT)) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Gopen2 failed");
- if(copy_refs_attr(grp_in, grp_out, options, travt, fidout) < 0)
+ if(copy_refs_attr(grp_in, grp_out, travt, fidout) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed");
if(H5Gclose(grp_out) < 0)
@@ -158,7 +158,7 @@ int do_copy_refobjs(hid_t fidin,
if(nelmts) {
buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf==NULL) {
- printf("cannot read into memory\n" );
+ HDprintf("cannot read into memory\n" );
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
} /* end if */
if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
@@ -166,7 +166,7 @@ int do_copy_refobjs(hid_t fidin,
refbuf = (hobj_ref_t*) HDcalloc((unsigned)nelmts, msize);
if(refbuf == NULL){
- printf("cannot allocate memory\n" );
+ HDprintf("cannot allocate memory\n" );
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed");
} /* end if */
for(u = 0; u < nelmts; u++) {
@@ -183,8 +183,8 @@ int do_copy_refobjs(hid_t fidin,
if(H5Rcreate(&refbuf[u], fidout, refname, H5R_OBJECT, (hid_t)-1) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Rcreate failed");
if(options->verbose) {
- printf(FORMAT_OBJ,"dset",travt->objs[i].name );
- printf("object <%s> object reference created to <%s>\n",
+ HDprintf(FORMAT_OBJ,"dset",travt->objs[i].name );
+ HDprintf("object <%s> object reference created to <%s>\n",
travt->objs[i].name,
refname);
}
@@ -234,7 +234,7 @@ int do_copy_refobjs(hid_t fidin,
if(nelmts) {
buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf == NULL) {
- printf("cannot read into memory\n");
+ HDprintf("cannot read into memory\n");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
} /* end if */
if(H5Dread(dset_in, mtype_id, H5S_ALL, H5S_ALL, H5P_DEFAULT, buf) < 0)
@@ -246,7 +246,7 @@ int do_copy_refobjs(hid_t fidin,
*/
refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
if(refbuf == NULL) {
- printf("cannot allocate memory\n");
+ HDprintf("cannot allocate memory\n");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed");
} /* end if */
@@ -271,8 +271,8 @@ int do_copy_refobjs(hid_t fidin,
if(H5Sclose(region_id) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "H5Sclose failed");
if(options->verbose) {
- printf(FORMAT_OBJ,"dset",travt->objs[i].name );
- printf("object <%s> region reference created to <%s>\n",
+ HDprintf(FORMAT_OBJ,"dset",travt->objs[i].name );
+ HDprintf("object <%s> region reference created to <%s>\n",
travt->objs[i].name,
refname);
}
@@ -316,7 +316,7 @@ int do_copy_refobjs(hid_t fidin,
* copy referenced objects in attributes
*-------------------------------------------------------------------------
*/
- if(copy_refs_attr(dset_in, dset_out, options, travt, fidout) < 0)
+ if(copy_refs_attr(dset_in, dset_out, travt, fidout) < 0)
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "copy_refs_attr failed");
/*-------------------------------------------------------------------------
@@ -426,7 +426,6 @@ done:
static int copy_refs_attr(hid_t loc_in,
hid_t loc_out,
- pack_opt_t *options,
trav_table_t *travt,
hid_t fidout) /* for saving references */
{
@@ -450,7 +449,6 @@ static int copy_refs_attr(hid_t loc_in,
is_ref_comp = 0;
void *refbuf = NULL;
void *buf = NULL;
- const char *refname = NULL;
unsigned *ref_comp_index = NULL;
size_t *ref_comp_size = NULL;
int ref_comp_field_n = 0;
@@ -592,7 +590,7 @@ static int copy_refs_attr(hid_t loc_in,
if((is_ref || is_ref_array) && (H5R_OBJ_REF_BUF_SIZE==msize)) {
buf = (hobj_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf == NULL) {
- printf("cannot read into memory\n");
+ HDprintf("cannot read into memory\n");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
} /* end if */
if(H5Aread(attr_id, mtype_id, buf) < 0)
@@ -600,23 +598,20 @@ static int copy_refs_attr(hid_t loc_in,
refbuf = (hobj_ref_t *)HDcalloc((unsigned)nelmts, msize);
if(refbuf == NULL) {
- printf("cannot allocate memory\n");
+ HDprintf("cannot allocate memory\n");
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed");
} /* end if */
- for(i = 0; i < (unsigned)nelmts; i++) {
- if (update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, &((hobj_ref_t *)refbuf)[i], travt)<0)
+ for(i = 0; i < (unsigned)nelmts; i++)
+ if(update_ref_value(attr_id, H5R_OBJECT, &((hobj_ref_t *)buf)[i], fidout, &((hobj_ref_t *)refbuf)[i], travt) < 0)
continue;
- if(options->verbose)
- printf("object <%s> reference created to <%s>\n", name, refname);
- } /* i */
} /* H5T_STD_REF_OBJ */
/* handle region references */
else if((is_ref || is_ref_array) && (H5R_DSET_REG_REF_BUF_SIZE == msize)) {
buf = (hdset_reg_ref_t *)HDmalloc((unsigned)(nelmts * msize));
if(buf == NULL) {
- printf( "cannot read into memory\n" );
+ HDprintf( "cannot read into memory\n" );
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
} /* end if */
if(H5Aread(attr_id, mtype_id, buf) < 0)
@@ -628,16 +623,13 @@ static int copy_refs_attr(hid_t loc_in,
*/
refbuf = (hdset_reg_ref_t *)HDcalloc(sizeof(hdset_reg_ref_t), (size_t)nelmts); /*init to zero */
if(refbuf == NULL) {
- printf( "cannot allocate memory\n" );
+ HDprintf( "cannot allocate memory\n" );
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDcalloc failed");
} /* end if */
- for(i = 0; i < (unsigned)nelmts; i++) {
- if (update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, &((hdset_reg_ref_t *)refbuf)[i], travt)<0)
+ for(i = 0; i < (unsigned)nelmts; i++)
+ if(update_ref_value(attr_id, H5R_DATASET_REGION, &((hdset_reg_ref_t *)buf)[i], fidout, &((hdset_reg_ref_t *)refbuf)[i], travt) < 0)
continue;
- if(options->verbose)
- printf("object <%s> region reference created to <%s>\n", name, refname);
- }
} /* H5T_STD_REF_DSETREG */
else if (is_ref_vlen) {
/* handle VLEN of references */
@@ -646,7 +638,7 @@ static int copy_refs_attr(hid_t loc_in,
refbuf = buf; /* reuse the read buffer for write */
if(buf == NULL) {
- printf( "cannot read into memory\n" );
+ HDprintf( "cannot read into memory\n" );
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
} /* end if */
@@ -687,7 +679,7 @@ static int copy_refs_attr(hid_t loc_in,
refbuf = buf; /* reuse the read buffer for write */
if(buf == NULL) {
- printf( "cannot read into memory\n" );
+ HDprintf( "cannot read into memory\n" );
HGOTO_ERROR(FAIL, H5E_tools_min_id_g, "HDmalloc failed");
} /* end if */
@@ -700,7 +692,7 @@ static int copy_refs_attr(hid_t loc_in,
size_t idx = (i * msize) + H5Tget_member_offset(mtype_id, ref_comp_index[j]);
hobj_ref_t ref_out;
- if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)(((char *)buf)+idx), fidout, &ref_out, travt)<0)
+ if (update_ref_value(attr_id, H5R_OBJECT, (hobj_ref_t *)((void *)(((char *)buf)+idx)), fidout, &ref_out, travt) < 0) /* Extra (void *) cast to quiet "cast to create alignment" warning - 2019/07/05, QAK */
continue;
HDmemcpy(((char *)buf)+idx, &ref_out, ref_comp_size[j]);
} /* if */
generated by cgit v0.12 at 2024-10-28 07:07:46 (GMT)