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Merge2 839 issue PRs to hdf5 1 12 #906

Merged
merged 19 commits into from
Aug 13, 2021
Merged

Merge2 839 issue PRs to hdf5 1 12 #906

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26e771c
Use internal version of H5Eprint2 to avoid possible stack overflow (#…
jhendersonHDF May 26, 2021
3e8965b
Reduces overly-pedantic casting in the public headers (#644)
derobins May 15, 2021
09c6265
Fix H5FD_mpio_Debug="rw" can report MPI_count instead of bytes (#699)
brtnfld May 28, 2021
b7b4d94
Removes pre-C99 build and header cruft (#700)
derobins May 28, 2021
9bf4c9c
Clean up type size checks in configure.ac (#702)
derobins May 29, 2021
06e9a8f
Removes some DEC Alpha cruft from H5detect and H5private.h (#708)
derobins Jun 2, 2021
dece16e
Updates bin/trace script to correctly wrap H5TRACE macros near clang-…
derobins Jun 3, 2021
928c41a
Adds __STDC_FORMAT_MACROS before including inttypes.h w/ C++ (#726)
derobins Jun 4, 2021
c417a42
Moves H5PacketTable default ctor inside source file (#731)
derobins Jun 6, 2021
5b2528a
Remove private H5_GCC_DIAG_OFF/ON from standalone program (#734)
byrnHDF Jun 7, 2021
3fa974f
Organize and align compiler flags (#741)
byrnHDF Jun 11, 2021
6f0a976
Fixes C++ warnings when passing hsize_t values to printf in test code…
derobins Jun 11, 2021
fa027c7
Normalization of H5_nanosleep() with VFD SWMR branch (#746)
derobins Jun 11, 2021
3254fd3
Correct missing variable declaration.
lrknox Aug 13, 2021
c0f1516
Fixes some H5SL include statements (#758)
derobins Jun 16, 2021
4476617
Fixes non-C99 format strings in tarray test code (#766)
derobins Jun 18, 2021
ee6172a
Cleans up some POSIX header bits in H5private.h (#783)
derobins Jun 23, 2021
f202772
Further simplifies Autotools type size checks (#789)
derobins Jun 23, 2021
23c4ac3
Normalization of CMake H5pubconf.h with Autotools (#791)
derobins Jun 23, 2021
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38 changes: 32 additions & 6 deletions bin/trace
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Original file line number Diff line number Diff line change
Expand Up @@ -343,10 +343,33 @@ sub rewrite_func ($$$$$) {
# Compose the trace macro
$trace = "H5TRACE" . scalar(@arg_str) . "(\"$rettype\", \"";
$trace .= join("", @arg_str) . "\"";
my $len = 4 + length $trace; # Add 4, for indenting the line
for (@arg_name) {
# Wrap lines that will be longer than the limit, after ');' is added
if ($len + length >= ($max_trace_macro_line_len - 2)) {
$argtrace .= join("", @arg_str) . "\"";

# Add 4 for indenting the line
my $len = 4 + length($trace);

for my $i (0 .. $#arg_name) {
# Handle wrapping

# Be VERY careful here! clang-format and this script MUST agree
# on which lines get wrapped or there will be churn as each tries
# to undo the other's output.
#
# TWO cases must be handled:
# 1) The argument is that last one and ');' will be appended
# 2) The argument is NOT the last one and ',' will be appended
#
# NB: clang-format does NOT consider terminal newlines when
# counting columns for the ColumnLimit
#
# The extra '2' added after $len includes the ', ' that would be
# added BEFORE the argument.
#
my $adjust = ($i + 1 == scalar(@arg_str)) ? 2 : 1;
my $len_if_added = $len + 2 + length($arg_name[$i]) + $adjust;

# Wrap lines that will be longer than the limit
if ($len_if_added > $max_trace_macro_line_len) {
# Wrap line, with indention
$trace .= ",\n ";
$len = 13; # Set to 13, for indention
Expand All @@ -362,8 +385,11 @@ sub rewrite_func ($$$$$) {
}

# Append argument
$trace .= "$_";
$len += length; # Add length of appended argument name
$trace .= "$arg_name[$i]";
$argtrace .= ", $arg_name[$i]";

# Add length of appended argument name
$len += length($arg_name[$i]);
}

# Append final ');' for macro
Expand Down
31 changes: 16 additions & 15 deletions c++/test/tarray.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -178,9 +178,9 @@ test_array_compound_array()
// Check the array dimensions
for (ii = 0; ii < ndims; ii++)
if (rdims1[ii] != tdims1[ii]) {
TestErrPrintf(
"Array dimension information doesn't match!, rdims1[%d]=%lld, tdims1[%d]=%lld\n", ii,
rdims1[ii], ii, tdims1[ii]);
TestErrPrintf("Array dimension information doesn't match!, rdims1[%d]=%" PRIuHSIZE
", tdims1[%d]=%" PRIuHSIZE "\n",
ii, rdims1[ii], ii, tdims1[ii]);
continue;
} // end if

Expand All @@ -197,9 +197,9 @@ test_array_compound_array()
// Check the array dimensions
for (ii = 0; ii < ndims; ii++)
if (rdims1[ii] != tdims1[ii]) {
TestErrPrintf(
"Array dimension information doesn't match!, rdims1[%d]=%lld, tdims1[%d]=%lld\n", ii,
rdims1[ii], ii, tdims1[ii]);
TestErrPrintf("Array dimension information doesn't match!, rdims1[%d]=%" PRIuHSIZE
", tdims1[%d]=%" PRIuHSIZE "\n",
ii, rdims1[ii], ii, tdims1[ii]);
continue;
} // end if

Expand Down Expand Up @@ -248,9 +248,9 @@ test_array_compound_array()
// Check the array dimensions
for (ii = 0; ii < ndims; ii++)
if (rdims1[ii] != tdims1[ii]) {
TestErrPrintf(
"Array dimension information doesn't match!, rdims1[%d]=%lld, tdims1[%d]=%lld\n", ii,
rdims1[ii], ii, tdims1[ii]);
TestErrPrintf("Array dimension information doesn't match!, rdims1[%d]=%" PRIuHSIZE
", tdims1[%d]=%" PRIuHSIZE "\n",
ii, rdims1[ii], ii, tdims1[ii]);
continue;
} // end if

Expand All @@ -265,8 +265,9 @@ test_array_compound_array()
for (idxi = 0; idxi < SPACE1_DIM1; idxi++) {
for (idxj = 0; idxj < ARRAY1_DIM1; idxj++) {
if (wdata[idxi][idxj].i != rdata[idxi][idxj].i) {
TestErrPrintf("Array data information doesn't match!, wdata[%lld][%lld].i=%d, "
"rdata[%lld][%lld].i=%d\n",
TestErrPrintf("Array data information doesn't match!, wdata[%" PRIuHSIZE "][%" PRIuHSIZE
"].i=%d, "
"rdata[%" PRIuHSIZE "][%" PRIuHSIZE "].i=%d\n",
idxi, idxj, wdata[idxi][idxj].i, idxi, idxj, rdata[idxi][idxj].i);
continue;
} // end if
Expand Down Expand Up @@ -457,11 +458,11 @@ test_array_info()
// Check the array dimensions
for (ii = 0; ii < ndims; ii++)
if (rdims1[ii] != tdims1[ii]) {
TestErrPrintf(
"Array dimension information doesn't match!, rdims1[%d]=%llu, tdims1[%d]=z%llu\n", ii,
rdims1[ii], ii, tdims1[ii]);
TestErrPrintf("Array dimension information doesn't match!, rdims1[%d]=%" PRIuHSIZE
", tdims1[%d]=%" PRIuHSIZE "\n",
ii, rdims1[ii], ii, tdims1[ii]);
continue;
} // end if
}
}

// Close all
Expand Down
60 changes: 36 additions & 24 deletions c++/test/tattr.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -169,7 +169,8 @@ test_attr_basic_write()
// Verify values read in
for (i = 0; i < ATTR1_DIM1; i++)
if (attr_data1[i] != read_data1[i])
TestErrPrintf("%d: attribute data different: attr_data1[%llu]=%d,read_data1[%llu]=%d\n",
TestErrPrintf("%d: attribute data different: attr_data1[%" PRIuHSIZE
"]=%d,read_data1[%" PRIuHSIZE "]=%d\n",
__LINE__, i, attr_data1[i], i, read_data1[i]);

// Create two more attributes for this dataset, but only write to one.
Expand All @@ -185,7 +186,8 @@ test_attr_basic_write()
// Verify values read in
for (i = 0; i < ATTR1_DIM1; i++)
if (attr_data1a[i] != read_data1[i])
TestErrPrintf("%d: attribute data different: attr_data1a[%llu]=%d,read_data1[%llu]=%d\n",
TestErrPrintf("%d: attribute data different: attr_data1a[%" PRIuHSIZE
"]=%d,read_data1[%" PRIuHSIZE "]=%d\n",
__LINE__, i, attr_data1a[i], i, read_data1[i]);

// Close both attributes
Expand Down Expand Up @@ -448,7 +450,8 @@ test_attr_rename()
// Verify values read in
for (i = 0; i < ATTR1_DIM1; i++)
if (attr_data1[i] != read_data1[i])
TestErrPrintf("%d: attribute data different: attr_data1[%llu]=%d,read_data1[%llu%d\n",
TestErrPrintf("%d: attribute data different: attr_data1[%" PRIuHSIZE
"]=%d,read_data1[%" PRIuHSIZE "]=%d\n",
__LINE__, i, attr_data1[i], i, read_data1[i]);

// Close attribute
Expand All @@ -472,7 +475,8 @@ test_attr_rename()
// Verify values read in
for (i = 0; i < ATTR1_DIM1; i++)
if (attr_data1a[i] != read_data1[i])
TestErrPrintf("%d: attribute data different: attr_data1a[%llu]=%d,read_data1[%llu]=%d\n",
TestErrPrintf("%d: attribute data different: attr_data1a[%" PRIuHSIZE
"]=%d,read_data1[%" PRIuHSIZE "]=%d\n",
__LINE__, i, attr_data1a[i], i, read_data1[i]);

// Close attribute
Expand Down Expand Up @@ -537,7 +541,8 @@ test_attr_basic_read()
// Verify values read in
for (i = 0; i < ATTR1_DIM1; i++)
if (attr_data1[i] != read_data1[i])
TestErrPrintf("%d: attribute data different: attr_data1[%llu]=%d, read_data1[%llu]=%d\n",
TestErrPrintf("%d: attribute data different: attr_data1[%" PRIuHSIZE
"]=%d, read_data1[%" PRIuHSIZE "]=%d\n",
__LINE__, i, attr_data1[i], i, read_data1[i]);

/*
Expand Down Expand Up @@ -568,8 +573,9 @@ test_attr_basic_read()
for (i = 0; i < ATTR2_DIM1; i++)
for (j = 0; j < ATTR2_DIM2; j++)
if (attr_data2[i][j] != read_data2[i][j]) {
TestErrPrintf("%d: attribute data different: attr_data2[%llu][%llu]=%d, "
"read_data2[%llu][%llu]=%d\n",
TestErrPrintf("%d: attribute data different: attr_data2[%" PRIuHSIZE "][%" PRIuHSIZE
"]=%d, "
"read_data2[%" PRIuHSIZE "][%" PRIuHSIZE "]=%d\n",
__LINE__, i, j, attr_data2[i][j], i, j, read_data2[i][j]);
}
PASSED();
Expand Down Expand Up @@ -772,14 +778,17 @@ test_attr_compound_read()
for (ii = 0; ii < ATTR4_DIM1; ii++)
for (jj = 0; jj < ATTR4_DIM2; jj++)
if (HDmemcmp(&attr_data4[ii][jj], &read_data4[ii][jj], sizeof(struct attr4_struct)) != 0) {
TestErrPrintf("%d:attribute data different: attr_data4[%llu][%llu].i=%d, "
"read_data4[%llu][%llu].i=%d\n",
TestErrPrintf("%d:attribute data different: attr_data4[%" PRIuHSIZE "][%" PRIuHSIZE
"].i=%d, "
"read_data4[%" PRIuHSIZE "][%" PRIuHSIZE "].i=%d\n",
__LINE__, ii, jj, attr_data4[ii][jj].i, ii, jj, read_data4[ii][jj].i);
TestErrPrintf("%d:attribute data different: attr_data4[%llu][%llu].d=%f, "
"read_data4[%llu][%llu].d=%f\n",
TestErrPrintf("%d:attribute data different: attr_data4[%" PRIuHSIZE "][%" PRIuHSIZE
"].d=%f, "
"read_data4[%" PRIuHSIZE "][%" PRIuHSIZE "].d=%f\n",
__LINE__, ii, jj, attr_data4[ii][jj].d, ii, jj, read_data4[ii][jj].d);
TestErrPrintf("%d:attribute data different: attr_data4[%llu][%llu].c=%c, "
"read_data4[%llu][%llu].c=%c\n",
TestErrPrintf("%d:attribute data different: attr_data4[%" PRIuHSIZE "][%" PRIuHSIZE
"].c=%c, "
"read_data4[%" PRIuHSIZE "][%" PRIuHSIZE "].c=%c\n",
__LINE__, ii, jj, attr_data4[ii][jj].c, ii, jj, read_data4[ii][jj].c);
} /* end if */

Expand Down Expand Up @@ -1042,10 +1051,10 @@ test_attr_mult_read()

// Get the dims of the dataspace and verify them
hsize_t dims[ATTR_MAX_DIMS]; // Attribute dimensions
int ndims = space.getSimpleExtentDims(dims);
if ((long)dims[0] != (long)ATTR1_DIM1)
TestErrPrintf("%d:attribute dimensions different: dims[0]=%d, should be %llu\n", __LINE__,
(int)dims[0], ATTR1_DIM1);
(void)space.getSimpleExtentDims(dims);
if (dims[0] != ATTR1_DIM1)
TestErrPrintf("%d:attribute dimensions different: dims[0]=%d, should be %" PRIuHSIZE "\n",
__LINE__, static_cast<int>(dims[0]), ATTR1_DIM1);

/* Verify Datatype */

Expand All @@ -1072,7 +1081,8 @@ test_attr_mult_read()
// Verify values read in
for (i = 0; i < ATTR1_DIM1; i++)
if (attr_data1[i] != read_data1[i])
TestErrPrintf("%d: attribute data different: attr_data1[%llu]=%d,read_data1[%llu]=%d\n",
TestErrPrintf("%d: attribute data different: attr_data1[%" PRIuHSIZE
"]=%d,read_data1[%" PRIuHSIZE "]=%d\n",
__LINE__, i, attr_data1[i], i, read_data1[i]);

// Verify Name
Expand All @@ -1095,7 +1105,7 @@ test_attr_mult_read()
verify_val(rank, ATTR2_RANK, "DataSpace::getSimpleExtentNdims", __LINE__, __FILE__);

// Get the dims of the dataspace and verify them
ndims = space.getSimpleExtentDims(dims);
int ndims = space.getSimpleExtentDims(dims);

verify_val((long)dims[0], (long)ATTR2_DIM1, "DataSpace::getSimpleExtentDims", __LINE__, __FILE__);
verify_val((long)dims[1], (long)ATTR2_DIM2, "DataSpace::getSimpleExtentDims", __LINE__, __FILE__);
Expand Down Expand Up @@ -1127,8 +1137,9 @@ test_attr_mult_read()
for (i = 0; i < ATTR2_DIM1; i++)
for (j = 0; j < ATTR2_DIM2; j++)
if (attr_data2[i][j] != read_data2[i][j])
TestErrPrintf("%d: attribute data different: attr_data2[%llu][%llu]=%d, "
"read_data2[%llu][%llu]=%d\n",
TestErrPrintf("%d: attribute data different: attr_data2[%" PRIuHSIZE "][%" PRIuHSIZE
"]=%d, "
"read_data2[%" PRIuHSIZE "][%" PRIuHSIZE "]=%d\n",
__LINE__, i, j, attr_data2[i][j], i, j, read_data2[i][j]);

// Verify Name
Expand Down Expand Up @@ -1181,9 +1192,10 @@ test_attr_mult_read()
for (i = 0; i < ATTR3_DIM1; i++)
for (j = 0; j < ATTR3_DIM2; j++)
for (k = 0; k < ATTR3_DIM3; k++)
if (attr_data3[i][j][k] != read_data3[i][j][k])
TestErrPrintf("%d: attribute data different: attr_data3[%llu][%llu][%llu]=%f, "
"read_data3[%llu][%llu][%llu]=%f\n",
if (abs(attr_data3[i][j][k] - read_data3[i][j][k]) > DBL_EPSILON)
TestErrPrintf("%d: attribute data different: attr_data3[%" PRIuHSIZE "][%" PRIuHSIZE
"][%" PRIuHSIZE "]=%f, "
"read_data3[%" PRIuHSIZE "][%" PRIuHSIZE "][%" PRIuHSIZE "]=%f\n",
__LINE__, i, j, k, attr_data3[i][j][k], i, j, k, read_data3[i][j][k]);

// Verify Name
Expand Down
44 changes: 15 additions & 29 deletions config/cmake/H5pubconf.h.in
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Expand Up @@ -35,6 +35,10 @@
/* Define if dev_t is a scalar */
#cmakedefine H5_DEV_T_IS_SCALAR @H5_DEV_T_IS_SCALAR@

/* Define if your system is IBM ppc64le and cannot convert some long double
values correctly. */
#cmakedefine H5_DISABLE_SOME_LDOUBLE_CONV @H5_DISABLE_SOME_LDOUBLE_CONV@

/* Define to dummy `main' function (if any) required to link to the Fortran
libraries. */
#cmakedefine H5_FC_DUMMY_MAIN @H5_FC_DUMMY_MAIN@
Expand Down Expand Up @@ -111,7 +115,7 @@
#cmakedefine H5_HAVE_CODESTACK @H5_HAVE_CODESTACK@

/* Define to 1 if you have the <curl/curl.h> header file. */
#cmakedefine H5_HAVE_CURL_H @H5_HAVE_CURL_H@
#cmakedefine H5_HAVE_CURL_CURL_H @H5_HAVE_CURL_H@

/* Define if Darwin or Mac OS X */
#cmakedefine H5_HAVE_DARWIN @H5_HAVE_DARWIN@
Expand Down Expand Up @@ -198,15 +202,9 @@
optimization operation */
#cmakedefine H5_HAVE_INSTRUMENTED_LIBRARY @H5_HAVE_INSTRUMENTED_LIBRARY@

/* Define to 1 if you have the <inttypes.h> header file. */
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These removals are okay as far as binary compatibility?

#cmakedefine H5_HAVE_INTTYPES_H @H5_HAVE_INTTYPES_H@

/* Define to 1 if you have the `ioctl' function. */
#cmakedefine H5_HAVE_IOCTL @H5_HAVE_IOCTL@

/* Define to 1 if you have the <io.h> header file. */
#cmakedefine H5_HAVE_IO_H @H5_HAVE_IO_H@

/* Define to 1 if you have the `crypto' library (-lcrypto). */
#cmakedefine H5_HAVE_LIBCRYPTO @H5_HAVE_LIBCRYPTO@

Expand Down Expand Up @@ -358,21 +356,12 @@
/* Define to 1 if you have the `stat64' function. */
#cmakedefine H5_HAVE_STAT64 @H5_HAVE_STAT64@

/* Define if `struct stat' has the `st_blocks' field */
/* Define if struct stat has the st_blocks field */
#cmakedefine H5_HAVE_STAT_ST_BLOCKS @H5_HAVE_STAT_ST_BLOCKS@

/* Define to 1 if you have the <stdbool.h> header file. */
#cmakedefine H5_HAVE_STDBOOL_H @H5_HAVE_STDBOOL_H@

/* Define to 1 if you have the <stddef.h> header file. */
#cmakedefine H5_HAVE_STDDEF_H @H5_HAVE_STDDEF_H@

/* Define to 1 if you have the <stdint.h> header file. */
#cmakedefine H5_HAVE_STDINT_H @H5_HAVE_STDINT_H@

/* Define to 1 if you have the <stdint.h> header file for Cplusplus. */
#cmakedefine H5_HAVE_STDINT_H_CXX @H5_HAVE_STDINT_H_CXX@

/* Define to 1 if you have the <stdlib.h> header file. */
#cmakedefine H5_HAVE_STDLIB_H @H5_HAVE_STDLIB_H@

Expand Down Expand Up @@ -508,9 +497,6 @@
with special algorithm. */
#cmakedefine H5_LONG_TO_LDOUBLE_SPECIAL @H5_LONG_TO_LDOUBLE_SPECIAL@

/* Define if your system is power6 and cannot convert some long double values. */
#cmakedefine H5_DISABLE_SOME_LDOUBLE_CONV @H5_DISABLE_SOME_LDOUBLE_CONV@

/* Define to the sub-directory where libtool stores uninstalled libraries. */
#cmakedefine H5_LT_OBJDIR @H5_LT_OBJDIR@

Expand Down Expand Up @@ -716,9 +702,6 @@
/* The size of `__int64', as computed by sizeof. */
#define H5_SIZEOF___INT64 @H5_SIZEOF___INT64@

/* Define to 1 if you have the ANSI C header files. */
#cmakedefine H5_STDC_HEADERS @H5_STDC_HEADERS@

/* Define if strict file format checks are enabled */
#cmakedefine H5_STRICT_FORMAT_CHECKS @H5_STRICT_FORMAT_CHECKS@

Expand All @@ -729,18 +712,21 @@
/* Define to 1 if you can safely include both <sys/time.h> and <time.h>. */
#cmakedefine H5_TIME_WITH_SYS_TIME @H5_TIME_WITH_SYS_TIME@

/* Define using v1.6 public API symbols by default */
#cmakedefine H5_USE_16_API_DEFAULT @H5_USE_16_API_DEFAULT@

/* Define using v1.8 public API symbols by default */
#cmakedefine H5_USE_18_API_DEFAULT @H5_USE_18_API_DEFAULT@

/* Define using v1.10 public API symbols by default */
#cmakedefine H5_USE_110_API_DEFAULT @H5_USE_110_API_DEFAULT@

/* Define using v1.12 public API symbols by default */
#cmakedefine H5_USE_112_API_DEFAULT @H5_USE_112_API_DEFAULT@

/* Define using v1.14 public API symbols by default */
#cmakedefine H5_USE_114_API_DEFAULT @H5_USE_114_API_DEFAULT@

/* Define using v1.6 public API symbols by default */
#cmakedefine H5_USE_16_API_DEFAULT @H5_USE_16_API_DEFAULT@

/* Define using v1.8 public API symbols by default */
#cmakedefine H5_USE_18_API_DEFAULT @H5_USE_18_API_DEFAULT@

/* Define if the library will use file locking */
#cmakedefine H5_USE_FILE_LOCKING @H5_USE_FILE_LOCKING@

Expand Down
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