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adding patch: HDF5-1.14.3_suppress_fp_exceptions.patch
HDF5 v1.14.3 was broken, this patch is the hotfix that was published soon after the release. See: HDFGroup/hdf5#3831
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easybuild/easyconfigs/h/HDF5/HDF5-1.14.3_suppress_fp_exceptions.patch
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,223 @@ | ||
| See: https://github.com/HDFGroup/hdf5/commit/e0d095ebf020706ec7d7c82e6674b18f1a0a2d5b | ||
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| Created using | ||
| git checkout hdf5-1_14_3 | ||
| git cherry-pick e0d095ebf020706ec7d7c82e6674b18f1a0a2d5b | ||
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| commit 7c58dd64db0a6c04dea46dee1c7effbe8103ae82 | ||
| Author: Dana Robinson <43805+derobins@users.noreply.github.com> | ||
| Date: Tue Nov 7 08:13:30 2023 -0800 | ||
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| Disable FP exceptions in H5T init code (#3837) | ||
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| The H5T floating-point datatype initialization code can raise exceptions when handling signaling NaNs. This change disables FE_INVALID exceptions during initialization. | ||
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| Also removes the -ieee=full change for NAG Fortran as that shouldn't be necessary anymore. | ||
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| Fixes #3831 | ||
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| diff --git a/config/linux-gnulibc1 b/config/linux-gnulibc1 | ||
| index 328f8d3cec..079f08d96c 100644 | ||
| --- a/config/linux-gnulibc1 | ||
| +++ b/config/linux-gnulibc1 | ||
| @@ -173,10 +173,7 @@ case $FC_BASENAME in | ||
| nagfor) | ||
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| F9XSUFFIXFLAG="" | ||
| - # NOTE: The default is -ieee=stop, which will cause problems | ||
| - # when the H5T module performs floating-point type | ||
| - # introspection | ||
| - AM_FCFLAGS="$AM_FCFLAGS -ieee=full" | ||
| + AM_FCFLAGS="$AM_FCFLAGS" | ||
| FSEARCH_DIRS="" | ||
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| # Production | ||
| diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt | ||
| index 200576332b..7de2a56974 100644 | ||
| --- a/release_docs/RELEASE.txt | ||
| +++ b/release_docs/RELEASE.txt | ||
| @@ -250,6 +250,29 @@ Bug Fixes since HDF5-1.14.2 release | ||
| =================================== | ||
| Library | ||
| ------- | ||
| + - Suppressed floating-point exceptions in H5T init code | ||
| + | ||
| + The floating-point datatype initialization code in H5Tinit_float.c | ||
| + could raise FE_INVALID exceptions while munging bits and performing | ||
| + comparisons that might involve NaN. This was not a problem when the | ||
| + initialization code was executed in H5detect at compile time (prior | ||
| + to 1.14.3), but now that the code is executed at library startup | ||
| + (1.14.3+), these exceptions can be caught by user code, as is the | ||
| + default in the NAG Fortran compiler. | ||
| + | ||
| + Starting in 1.14.4, we now suppress floating-point exceptions while | ||
| + initializing the floating-point types and clear FE_INVALID before | ||
| + restoring the original environment. | ||
| + | ||
| + Fixes GitHub #3831 | ||
| + | ||
| + - Fixed a file handle leak in the core VFD | ||
| + | ||
| + When opening a file with the core VFD and a file image, if the file | ||
| + already exists, the file check would leak the POSIX file handle. | ||
| + | ||
| + Fixes GitHub issue #635 | ||
| + | ||
| - Fixed some issues with chunk index metadata not getting read | ||
| collectively when collective metadata reads are enabled | ||
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| @@ -619,12 +642,6 @@ Known Problems | ||
| this release with link errors. As a result, Windows binaries for this release | ||
| will not include Fortran. The problem will be addressed in HDF5 1.14.4. | ||
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| - IEEE standard arithmetic enables software to raise exceptions such as overflow, | ||
| - division by zero, and other illegal operations without interrupting or halting | ||
| - the program flow. The HDF5 C library intentionally performs these exceptions. | ||
| - Therefore, the "-ieee=full" nagfor switch is necessary when compiling a program | ||
| - to avoid stopping on an exception. | ||
| - | ||
| CMake files do not behave correctly with paths containing spaces. | ||
| Do not use spaces in paths because the required escaping for handling spaces | ||
| results in very complex and fragile build files. | ||
| diff --git a/src/H5Tinit_float.c b/src/H5Tinit_float.c | ||
| index 3b9e127fe4..3213f00fec 100644 | ||
| --- a/src/H5Tinit_float.c | ||
| +++ b/src/H5Tinit_float.c | ||
| @@ -51,19 +51,23 @@ | ||
| * Function: DETECT_F | ||
| * | ||
| * Purpose: This macro takes a floating point type like `double' and | ||
| - * a base name like `natd' and detects byte order, mantissa | ||
| - * location, exponent location, sign bit location, presence or | ||
| - * absence of implicit mantissa bit, and exponent bias and | ||
| - * initializes a detected_t structure with those properties. | ||
| + * and detects byte order, mantissa location, exponent location, | ||
| + * sign bit location, presence or absence of implicit mantissa | ||
| + * bit, and exponent bias and initializes a detected_t structure | ||
| + * with those properties. | ||
| + * | ||
| + * Note that these operations can raise floating-point | ||
| + * exceptions and building with some compiler options | ||
| + * (especially Fortran) can cause problems. | ||
| *------------------------------------------------------------------------- | ||
| */ | ||
| -#define DETECT_F(TYPE, VAR, INFO) \ | ||
| +#define DETECT_F(TYPE, INFO) \ | ||
| do { \ | ||
| - TYPE _v1, _v2, _v3; \ | ||
| - unsigned char _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)]; \ | ||
| - unsigned char _pad_mask[sizeof(TYPE)]; \ | ||
| - unsigned char _byte_mask; \ | ||
| - int _i, _j, _last = (-1); \ | ||
| + TYPE _v1, _v2, _v3; \ | ||
| + uint8_t _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)]; \ | ||
| + uint8_t _pad_mask[sizeof(TYPE)]; \ | ||
| + uint8_t _byte_mask; \ | ||
| + int _i, _j, _last = -1; \ | ||
| \ | ||
| memset(&INFO, 0, sizeof(INFO)); \ | ||
| INFO.size = sizeof(TYPE); \ | ||
| @@ -81,7 +85,7 @@ | ||
| _v1 = (TYPE)4.0L; \ | ||
| H5MM_memcpy(_buf1, (const void *)&_v1, sizeof(TYPE)); \ | ||
| for (_i = 0; _i < (int)sizeof(TYPE); _i++) \ | ||
| - for (_byte_mask = (unsigned char)1; _byte_mask; _byte_mask = (unsigned char)(_byte_mask << 1)) { \ | ||
| + for (_byte_mask = (uint8_t)1; _byte_mask; _byte_mask = (uint8_t)(_byte_mask << 1)) { \ | ||
| _buf1[_i] ^= _byte_mask; \ | ||
| H5MM_memcpy((void *)&_v2, (const void *)_buf1, sizeof(TYPE)); \ | ||
| H5_GCC_CLANG_DIAG_OFF("float-equal") \ | ||
| @@ -118,7 +122,7 @@ | ||
| _v1 = (TYPE)1.0L; \ | ||
| _v2 = (TYPE)-1.0L; \ | ||
| if (H5T__bit_cmp(sizeof(TYPE), INFO.perm, &_v1, &_v2, _pad_mask, &(INFO.sign)) < 0) \ | ||
| - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to detect byte order"); \ | ||
| + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to determine sign bit"); \ | ||
| \ | ||
| /* Mantissa */ \ | ||
| INFO.mpos = 0; \ | ||
| @@ -126,12 +130,11 @@ | ||
| _v1 = (TYPE)1.0L; \ | ||
| _v2 = (TYPE)1.5L; \ | ||
| if (H5T__bit_cmp(sizeof(TYPE), INFO.perm, &_v1, &_v2, _pad_mask, &(INFO.msize)) < 0) \ | ||
| - HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to detect byte order"); \ | ||
| + HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to determine mantissa"); \ | ||
| INFO.msize += 1 + (unsigned)(INFO.imp ? 0 : 1) - INFO.mpos; \ | ||
| \ | ||
| /* Exponent */ \ | ||
| - INFO.epos = INFO.mpos + INFO.msize; \ | ||
| - \ | ||
| + INFO.epos = INFO.mpos + INFO.msize; \ | ||
| INFO.esize = INFO.sign - INFO.epos; \ | ||
| \ | ||
| _v1 = (TYPE)1.0L; \ | ||
| @@ -456,17 +459,24 @@ H5T__set_precision(H5T_fpoint_det_t *d) | ||
| herr_t H5_NO_UBSAN | ||
| H5T__init_native_float_types(void) | ||
| { | ||
| + fenv_t saved_fenv; | ||
| H5T_fpoint_det_t det; | ||
| H5T_t *dt = NULL; | ||
| herr_t ret_value = SUCCEED; | ||
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| FUNC_ENTER_PACKAGE | ||
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| + /* Turn off floating-point exceptions while initializing to avoid | ||
| + * tripping over signaling NaNs while looking at "don't care" bits. | ||
| + */ | ||
| + if (feholdexcept(&saved_fenv) != 0) | ||
| + HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't save floating-point environment"); | ||
| + | ||
| /* H5T_NATIVE_FLOAT */ | ||
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| /* Get the type's characteristics */ | ||
| memset(&det, 0, sizeof(H5T_fpoint_det_t)); | ||
| - DETECT_F(float, FLOAT, det); | ||
| + DETECT_F(float, det); | ||
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| /* Allocate and fill type structure */ | ||
| if (NULL == (dt = H5T__alloc())) | ||
| @@ -497,7 +507,7 @@ H5T__init_native_float_types(void) | ||
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| /* Get the type's characteristics */ | ||
| memset(&det, 0, sizeof(H5T_fpoint_det_t)); | ||
| - DETECT_F(double, DOUBLE, det); | ||
| + DETECT_F(double, det); | ||
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| /* Allocate and fill type structure */ | ||
| if (NULL == (dt = H5T__alloc())) | ||
| @@ -528,7 +538,7 @@ H5T__init_native_float_types(void) | ||
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| /* Get the type's characteristics */ | ||
| memset(&det, 0, sizeof(H5T_fpoint_det_t)); | ||
| - DETECT_F(long double, LDOUBLE, det); | ||
| + DETECT_F(long double, det); | ||
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| /* Allocate and fill type structure */ | ||
| if (NULL == (dt = H5T__alloc())) | ||
| @@ -561,6 +571,14 @@ H5T__init_native_float_types(void) | ||
| H5T_native_order_g = det.order; | ||
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| done: | ||
| + /* Clear any FE_INVALID exceptions from NaN handling */ | ||
| + if (feclearexcept(FE_INVALID) != 0) | ||
| + HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't clear floating-point exceptions"); | ||
| + | ||
| + /* Restore the original environment */ | ||
| + if (feupdateenv(&saved_fenv) != 0) | ||
| + HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't restore floating-point environment"); | ||
| + | ||
| if (ret_value < 0) { | ||
| if (dt != NULL) { | ||
| dt->shared = H5FL_FREE(H5T_shared_t, dt->shared); | ||
| diff --git a/src/H5private.h b/src/H5private.h | ||
| index 14a0ac3225..3aaa0d5245 100644 | ||
| --- a/src/H5private.h | ||
| +++ b/src/H5private.h | ||
| @@ -26,6 +26,7 @@ | ||
| #include <ctype.h> | ||
| #include <errno.h> | ||
| #include <fcntl.h> | ||
| +#include <fenv.h> | ||
| #include <float.h> | ||
| #include <math.h> | ||
| #include <setjmp.h> |