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Merge3 839 hdf5 1 12 #907

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merged 14 commits into from
Aug 13, 2021
Merged

Merge3 839 hdf5 1 12 #907

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1c422dc
Reorganization of C and POSIX headers in H5public.h & H5private.h (#793)
derobins Jun 24, 2021
9f2019b
Brings the tools getopt(3) replacement into the main library (#803)
derobins Jun 29, 2021
dd62956
Remove version-check for relnum in H5check. (#812)
byrnHDF Jul 27, 2021
9485d00
Remove checks for winsock2.h (#813)
derobins Jul 6, 2021
9306a4b
Removes develop header cruft (#828)
derobins Jul 9, 2021
0f2075d
OESS-168:Remove implicit conversion warnings. (#829)
hyoklee Jul 12, 2021
fe0f64a
Add support for parallel filters to h5repack (#832)
jhendersonHDF Jul 14, 2021
79a276b
Perform option arg variables (#834)
byrnHDF Jul 15, 2021
1cc3991
OESS-168:Remove clang warnings. (#835)
hyoklee Jul 26, 2021
2521b1c
Removes unused commented-out code from h5jamgentest.c (#851)
derobins Jul 22, 2021
0f5c371
Updates a comment in H5mpi.c (#863)
derobins Jul 28, 2021
09046a6
Unsigned comparison to 0 warning avoidance (#869)
lrknox Aug 2, 2021
7a13f22
Updates the RELEASE.txt file with a note about the variable-length fi…
derobins Aug 3, 2021
527f364
Add parallel version of h5pfc script (#881)
byrnHDF Aug 7, 2021
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3 changes: 0 additions & 3 deletions config/cmake/H5pubconf.h.in
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Expand Up @@ -457,9 +457,6 @@
/* Define if your system has window style path name. */
#cmakedefine H5_HAVE_WINDOW_PATH @H5_HAVE_WINDOW_PATH@

/* Define to 1 if you have the <winsock2.h> header file. */
#cmakedefine H5_HAVE_WINSOCK2_H @H5_HAVE_WINSOCK2_H@

/* Define to 1 if you have the <zlib.h> header file. */
#cmakedefine H5_HAVE_ZLIB_H @H5_HAVE_ZLIB_H@

Expand Down
6 changes: 0 additions & 6 deletions config/cmake_ext_mod/ConfigureChecks.cmake
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Expand Up @@ -53,7 +53,6 @@ if (MINGW)
set (${HDF_PREFIX}_HAVE_MINGW 1)
set (WINDOWS 1) # MinGW tries to imitate Windows
set (CMAKE_REQUIRED_FLAGS "-DWIN32_LEAN_AND_MEAN=1 -DNOGDI=1")
set (${HDF_PREFIX}_HAVE_WINSOCK2_H 1)
set (__USE_MINGW_ANSI_STDIO 1)
endif ()

Expand Down Expand Up @@ -122,11 +121,6 @@ CHECK_INCLUDE_FILE_CONCAT ("setjmp.h" ${HDF_PREFIX}_HAVE_SETJMP_H)
CHECK_INCLUDE_FILE_CONCAT ("stddef.h" ${HDF_PREFIX}_HAVE_STDDEF_H)
CHECK_INCLUDE_FILE_CONCAT ("unistd.h" ${HDF_PREFIX}_HAVE_UNISTD_H)

# Windows
if (NOT CYGWIN)
CHECK_INCLUDE_FILE_CONCAT ("winsock2.h" ${HDF_PREFIX}_HAVE_WINSOCK2_H)
endif ()

CHECK_INCLUDE_FILE_CONCAT ("globus/common.h" ${HDF_PREFIX}_HAVE_GLOBUS_COMMON_H)
CHECK_INCLUDE_FILE_CONCAT ("pdb.h" ${HDF_PREFIX}_HAVE_PDB_H)
CHECK_INCLUDE_FILE_CONCAT ("pthread.h" ${HDF_PREFIX}_HAVE_PTHREAD_H)
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13 changes: 13 additions & 0 deletions fortran/src/CMakeLists.txt
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Expand Up @@ -582,4 +582,17 @@ if (NOT WIN32 AND NOT MINGW)
PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
COMPONENT fortlibraries
)
if (HDF5_ENABLE_PARALLEL AND MPI_Fortran_FOUND)
configure_file (
${HDF_RESOURCES_DIR}/libh5cc.in
${HDF5_BINARY_DIR}/CMakeFiles/h5pfc
@ONLY
)
install (
FILES ${HDF5_BINARY_DIR}/CMakeFiles/h5pfc
DESTINATION ${HDF5_INSTALL_BIN_DIR}
PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
COMPONENT fortlibraries
)
endif ()
endif ()
2 changes: 2 additions & 0 deletions hl/test/test_ds.c
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Expand Up @@ -5205,6 +5205,8 @@ test_attach_detach(void)

HL_TESTING2("permutations of attaching and detaching");

gid = var1_id = var2_id = var3_id = H5I_INVALID_HID;

if ((fid = H5Fcreate(FILE8, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT)) < 0)
goto out;

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8 changes: 4 additions & 4 deletions hl/test/test_packet.c
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Expand Up @@ -45,10 +45,10 @@ typedef struct particle_t {
* a static array of particles for writing and checking reads
*-------------------------------------------------------------------------
*/
static particle_t testPart[NRECORDS] = {{"zero", 0, 0, 0.0f, 0.0f}, {"one", 10, 10, 1.0f, 10.0f},
{"two", 20, 20, 2.0f, 20.0f}, {"three", 30, 30, 3.0f, 30.0f},
{"four", 40, 40, 4.0f, 40.0f}, {"five", 50, 50, 5.0f, 50.0f},
{"six", 60, 60, 6.0f, 60.0f}, {"seven", 70, 70, 7.0f, 70.0f}};
static particle_t testPart[NRECORDS] = {{"zero", 0, 0, 0.0f, 0.0}, {"one", 10, 10, 1.0f, 10.0},
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Just noticed another "f" in the 4th value, I think it should be removed like the 5th value?

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No, the fourth element in the structure is a float, the fifth is a double, and the numbers with .0f for the fifth were single precision values implicitly converted to double precision. Removing the f from the fifth value eliminated that warning; removing it from the fourth would probably add the opposite warning (for clang).

{"two", 20, 20, 2.0f, 20.0}, {"three", 30, 30, 3.0f, 30.0},
{"four", 40, 40, 4.0f, 40.0}, {"five", 50, 50, 5.0f, 50.0},
{"six", 60, 60, 6.0f, 60.0}, {"seven", 70, 70, 7.0f, 70.0}};

/*-------------------------------------------------------------------------
* function that compares one particle
Expand Down
40 changes: 20 additions & 20 deletions hl/test/test_table.c
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Expand Up @@ -199,7 +199,7 @@ test_table(hid_t fid, int do_write)
hsize_t chunk_size = 10;
int compress = 0;
int * fill = NULL;
particle_t fill1[1] = {{"no data", -1, -99.0f, -99.0f, -1}};
particle_t fill1[1] = {{"no data", -1, -99.0, -99.0, -1}};
int fill1_new[1] = {-100};
hsize_t position;
char tname[20];
Expand Down Expand Up @@ -227,23 +227,23 @@ test_table(hid_t fid, int do_write)
particle2_t rbuf2[NRECORDS];
particle3_t rbuf3[NRECORDS];
particle_t rbufc[NRECORDS * 2];
particle_t abuf[2] = {{"eight", 80, 8.0f, 80.0f, 80}, {"nine", 90, 9.0f, 90.0f, 90}};
particle_t ibuf[2] = {{"zero", 0, 0.0f, 0.0f, 0}, {"zero", 0, 0.0f, 0.0f, 0}};
particle_t abuf[2] = {{"eight", 80, 8.0, 80.0, 80}, {"nine", 90, 9.0, 90.0, 90}};
particle_t ibuf[2] = {{"zero", 0, 0.0, 0.0, 0}, {"zero", 0, 0.0, 0.0, 0}};
particle_t wbufd[NRECORDS];
particle_t wbuf[NRECORDS] = {{
"zero",
0,
0.0f,
0.0f,
0.0,
0.0,
0,
},
{"one", 10, 1.0f, 10.0f, 10},
{"two", 20, 2.0f, 20.0f, 20},
{"three", 30, 3.0f, 30.0f, 30},
{"four", 40, 4.0f, 40.0f, 40},
{"five", 50, 5.0f, 50.0f, 50},
{"six", 60, 6.0f, 60.0f, 60},
{"seven", 70, 7.0f, 70.0f, 70}};
{"one", 10, 1.0, 10.0, 10},
{"two", 20, 2.0, 20.0, 20},
{"three", 30, 3.0, 30.0, 30},
{"four", 40, 4.0, 40.0, 40},
{"five", 50, 5.0, 50.0, 50},
{"six", 60, 6.0, 60.0, 60},
{"seven", 70, 7.0, 70.0, 70}};
/* buffers for the field "Pressure" and "New_field" */
float pressure_in[NRECORDS] = {0.0f, 1.0f, 2.0f, 3.0f, 4.0f, 5.0f, 6.0f, 7.0f};
float pressure_out[NRECORDS];
Expand Down Expand Up @@ -332,14 +332,14 @@ test_table(hid_t fid, int do_write)
HOFFSET(particle4_t, aty), HOFFSET(particle4_t, rro)};

/* Define an array of Particles */
particle4_t p_data[NRECORDS] = {{12112, 1.4f, 2.5f, {1, 2, 3}, {4, 5, 6}, {99, 100}},
{12113, 1.4f, 2.5f, {1, 2, 3}, {4, 5, 6}, {99, 100}},
{12114, 1.4f, 2.5f, {1, 2, 3}, {4, 5, 6}, {99, 100}},
{12115, 1.4f, 2.5f, {1, 2, 3}, {4, 5, 6}, {99, 100}},
{12116, 1.4f, 2.5f, {1, 2, 3}, {4, 5, 6}, {99, 100}},
{12117, 1.4f, 2.5f, {1, 2, 3}, {4, 5, 6}, {99, 100}},
{12118, 1.4f, 2.5f, {1, 2, 3}, {4, 5, 6}, {99, 100}},
{12119, 1.4f, 2.5f, {1, 2, 3}, {4, 5, 6}, {99, 100}}};
particle4_t p_data[NRECORDS] = {{12112, 1.4, 2.5, {1, 2, 3}, {4, 5, 6}, {99, 100}},
{12113, 1.4, 2.5, {1, 2, 3}, {4, 5, 6}, {99, 100}},
{12114, 1.4, 2.5, {1, 2, 3}, {4, 5, 6}, {99, 100}},
{12115, 1.4, 2.5, {1, 2, 3}, {4, 5, 6}, {99, 100}},
{12116, 1.4, 2.5, {1, 2, 3}, {4, 5, 6}, {99, 100}},
{12117, 1.4, 2.5, {1, 2, 3}, {4, 5, 6}, {99, 100}},
{12118, 1.4, 2.5, {1, 2, 3}, {4, 5, 6}, {99, 100}},
{12119, 1.4, 2.5, {1, 2, 3}, {4, 5, 6}, {99, 100}}};

/*-------------------------------------------------------------------------
* initialize table parameters
Expand Down
60 changes: 30 additions & 30 deletions hl/tools/h5watch/h5watch.c
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Expand Up @@ -58,27 +58,27 @@ static void parse_command_line(int argc, const char *argv[]);
* The long-named ones can be partially spelled. When
* adding more, make sure that they don't clash with each other.
*/
static const char * s_opts = "?";
static struct long_options l_opts[] = {{"help", no_arg, 'h'}, {"hel", no_arg, 'h'},
{"dim", no_arg, 'd'}, {"di", no_arg, 'd'},
{"label", no_arg, 'l'}, {"labe", no_arg, 'l'},
{"lab", no_arg, 'l'}, {"la", no_arg, 'l'},
{"simple", no_arg, 'S'}, {"simpl", no_arg, 'S'},
{"simp", no_arg, 'S'}, {"sim", no_arg, 'S'},
{"si", no_arg, 'S'}, {"hexdump", no_arg, 'x'},
{"hexdum", no_arg, 'x'}, {"hexdu", no_arg, 'x'},
{"hexd", no_arg, 'x'}, {"hex", no_arg, 'x'},
{"width", require_arg, 'w'}, {"widt", require_arg, 'w'},
{"wid", require_arg, 'w'}, {"wi", require_arg, 'w'},
{"polling", require_arg, 'p'}, {"pollin", require_arg, 'p'},
{"polli", require_arg, 'p'}, {"poll", require_arg, 'p'},
{"pol", require_arg, 'p'}, {"po", require_arg, 'p'},
{"fields", require_arg, 'f'}, {"field", require_arg, 'f'},
{"fiel", require_arg, 'f'}, {"fie", require_arg, 'f'},
{"fi", require_arg, 'f'}, {"version", no_arg, 'V'},
{"versio", no_arg, 'V'}, {"versi", no_arg, 'V'},
{"vers", no_arg, 'V'}, {"ver", no_arg, 'V'},
{"ve", no_arg, 'V'}, {NULL, 0, '\0'}};
static const char * s_opts = "?";
static struct h5_long_options l_opts[] = {{"help", no_arg, 'h'}, {"hel", no_arg, 'h'},
{"dim", no_arg, 'd'}, {"di", no_arg, 'd'},
{"label", no_arg, 'l'}, {"labe", no_arg, 'l'},
{"lab", no_arg, 'l'}, {"la", no_arg, 'l'},
{"simple", no_arg, 'S'}, {"simpl", no_arg, 'S'},
{"simp", no_arg, 'S'}, {"sim", no_arg, 'S'},
{"si", no_arg, 'S'}, {"hexdump", no_arg, 'x'},
{"hexdum", no_arg, 'x'}, {"hexdu", no_arg, 'x'},
{"hexd", no_arg, 'x'}, {"hex", no_arg, 'x'},
{"width", require_arg, 'w'}, {"widt", require_arg, 'w'},
{"wid", require_arg, 'w'}, {"wi", require_arg, 'w'},
{"polling", require_arg, 'p'}, {"pollin", require_arg, 'p'},
{"polli", require_arg, 'p'}, {"poll", require_arg, 'p'},
{"pol", require_arg, 'p'}, {"po", require_arg, 'p'},
{"fields", require_arg, 'f'}, {"field", require_arg, 'f'},
{"fiel", require_arg, 'f'}, {"fie", require_arg, 'f'},
{"fi", require_arg, 'f'}, {"version", no_arg, 'V'},
{"versio", no_arg, 'V'}, {"versi", no_arg, 'V'},
{"vers", no_arg, 'V'}, {"ver", no_arg, 'V'},
{"ve", no_arg, 'V'}, {NULL, 0, '\0'}};

/*-------------------------------------------------------------------------
* Function: doprint()
Expand Down Expand Up @@ -677,7 +677,7 @@ parse_command_line(int argc, const char *argv[])
}

/* parse command line options */
while ((opt = get_option(argc, argv, s_opts, l_opts)) != EOF) {
while ((opt = H5_get_option(argc, argv, s_opts, l_opts)) != EOF) {
switch ((char)opt) {
case '?':
case 'h': /* --help */
Expand All @@ -691,7 +691,7 @@ parse_command_line(int argc, const char *argv[])
break;

case 'w': /* --width=N */
g_display_width = (int)HDstrtol(opt_arg, NULL, 0);
g_display_width = (int)HDstrtol(H5_optarg, NULL, 0);
if (g_display_width < 0) {
usage(h5tools_getprogname());
leave(EXIT_FAILURE);
Expand All @@ -711,8 +711,8 @@ parse_command_line(int argc, const char *argv[])
break;

case 'p': /* --polling=N */
/* g_polling_interval = HDstrtod(opt_arg, NULL); */
if ((tmp = (int)HDstrtol(opt_arg, NULL, 10)) <= 0) {
/* g_polling_interval = HDstrtod(H5_optarg, NULL); */
if ((tmp = (int)HDstrtol(H5_optarg, NULL, 10)) <= 0) {
usage(h5tools_getprogname());
leave(EXIT_FAILURE);
}
Expand All @@ -721,15 +721,15 @@ parse_command_line(int argc, const char *argv[])

case 'f': /* --fields=<list_of_fields> */
if (g_list_of_fields == NULL) {
if ((g_list_of_fields = HDstrdup(opt_arg)) == NULL) {
if ((g_list_of_fields = HDstrdup(H5_optarg)) == NULL) {
error_msg("memory allocation failed (file %s:line %d)\n", __FILE__, __LINE__);
leave(EXIT_FAILURE);
}
}
else {
char *str;

if ((str = HDstrdup(opt_arg)) == NULL) {
if ((str = HDstrdup(H5_optarg)) == NULL) {
error_msg("memory allocation failed (file %s:line %d)\n", __FILE__, __LINE__);
leave(EXIT_FAILURE);
}
Expand All @@ -751,7 +751,7 @@ parse_command_line(int argc, const char *argv[])
}

/* check for object to be processed */
if (argc <= opt_ind) {
if (argc <= H5_optind) {
error_msg("missing dataset name\n");
usage(h5tools_getprogname());
leave(EXIT_FAILURE);
Expand Down Expand Up @@ -821,7 +821,7 @@ main(int argc, const char *argv[])
/* parse command line options */
parse_command_line(argc, argv);

if (argc <= opt_ind) {
if (argc <= H5_optind) {
error_msg("missing dataset name\n");
usage(h5tools_getprogname());
leave(EXIT_FAILURE);
Expand All @@ -845,7 +845,7 @@ main(int argc, const char *argv[])
* then there must have been something wrong with the file (perhaps it
* doesn't exist).
*/
if ((fname = HDstrdup(argv[opt_ind])) == NULL) {
if ((fname = HDstrdup(argv[H5_optind])) == NULL) {
error_msg("memory allocation failed (file %s:line %d)\n", __FILE__, __LINE__);
h5tools_setstatus(EXIT_FAILURE);
goto done;
Expand Down
4 changes: 2 additions & 2 deletions hl/tools/h5watch/h5watchgentest.c
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Expand Up @@ -224,7 +224,7 @@ main(void)
one_cbuf[i].field2.b.a = 20;
one_cbuf[i].field2.b.b = 40;
one_cbuf[i].field2.b.c = 80;
one_cbuf[i].field3 = 3.0F;
one_cbuf[i].field3 = 3.0;
one_cbuf[i].field4.a = 4;
one_cbuf[i].field4.b = 8;
} /* end for */
Expand Down Expand Up @@ -313,7 +313,7 @@ main(void)
two_cbuf[i].field2.b.a = 20;
two_cbuf[i].field2.b.b = 40;
two_cbuf[i].field2.b.c = 80;
two_cbuf[i].field3 = 3.0F;
two_cbuf[i].field3 = 3.0;
two_cbuf[i].field4.a = 4;
two_cbuf[i].field4.b = 8;
} /* end for */
Expand Down
23 changes: 23 additions & 0 deletions release_docs/RELEASE.txt
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Expand Up @@ -75,6 +75,25 @@ New Features

Library:
--------
- Change how the release part of version, in major.minor.release is checked
for compatibility

The HDF5 library uses a function, H5check_version, to check that
the version defined in the header files, which is used to compile an
application is compatible with the version codified in the library, which
the application loads at runtime. This previously required an exact match
or the library would print a warning, dump the build settings and then
abort or continue. An environment variable controlled the logic.

Now the function first checks that the library release version, in
major.minor.release, is not older than the version in the headers.
Secondly, if the release version is different, it checks if either
the library version or the header version is in the exception list, in
which case the release part of version, in major.minor.release, must
be exact. An environment variable still controls the logic.

(ADB - 2021/07/27)

- H5Gcreate1() now rejects size_hint parameters larger than UINT32_MAX

The size_hint value is ultimately stored in a uint32_t struct field,
Expand Down Expand Up @@ -399,6 +418,10 @@ The following platforms are not supported but have been tested for this release.
Known Problems
==============

Setting a variable-length dataset fill value will leak the memory allocated
for the p field of the hvl_t struct. A fix is in progress for this.
HDFFV-10840

testflushrefresh.sh will fail when run with "make check-passthrough-vol"
on centos7, with 3 Errors/Segmentation faults. These will not occur when
run with "make check". See https://github.com/HDFGroup/hdf5/issues/673
Expand Down
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