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-rw-r--r--var/spack/repos/builtin/packages/hdf5/hdf5_1_14_3_fpe.patch203
-rw-r--r--var/spack/repos/builtin/packages/hdf5/package.py9
2 files changed, 212 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/hdf5/hdf5_1_14_3_fpe.patch b/var/spack/repos/builtin/packages/hdf5/hdf5_1_14_3_fpe.patch
new file mode 100644
index 0000000000..90ab32a0f4
--- /dev/null
+++ b/var/spack/repos/builtin/packages/hdf5/hdf5_1_14_3_fpe.patch
@@ -0,0 +1,203 @@
+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 $FC_BASENAME in
+ nagfor)
+
+ F9XSUFFIXFLAG=""
+- # NOTE: The default is -ieee=stop, which will cause problems
+- # when the H5T module performs floating-point type
+- # introspection
+- AM_FCFLAGS="$AM_FCFLAGS -ieee=full"
++ AM_FCFLAGS="$AM_FCFLAGS"
+ FSEARCH_DIRS=""
+
+ # Production
+diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
+index 200576332b..0aa139761d 100644
+--- a/release_docs/RELEASE.txt
++++ b/release_docs/RELEASE.txt
+@@ -246,6 +246,27 @@ Support for new platforms, languages and compilers
+ -
+
+
++Patches applied since the HDF5-1.14.3 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
++
++
+ Bug Fixes since HDF5-1.14.2 release
+ ===================================
+ Library
+@@ -619,12 +640,6 @@ 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.
+
+- 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..02bb3bad77 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.
++ * 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;
+
+ FUNC_ENTER_PACKAGE
+
++ /* 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 */
+
+ /* Get the type's characteristics */
+ memset(&det, 0, sizeof(H5T_fpoint_det_t));
+- DETECT_F(float, FLOAT, det);
++ DETECT_F(float, det);
+
+ /* Allocate and fill type structure */
+ if (NULL == (dt = H5T__alloc()))
+@@ -497,7 +507,7 @@ H5T__init_native_float_types(void)
+
+ /* Get the type's characteristics */
+ memset(&det, 0, sizeof(H5T_fpoint_det_t));
+- DETECT_F(double, DOUBLE, det);
++ DETECT_F(double, det);
+
+ /* Allocate and fill type structure */
+ if (NULL == (dt = H5T__alloc()))
+@@ -528,7 +538,7 @@ H5T__init_native_float_types(void)
+
+ /* Get the type's characteristics */
+ memset(&det, 0, sizeof(H5T_fpoint_det_t));
+- DETECT_F(long double, LDOUBLE, det);
++ DETECT_F(long double, det);
+
+ /* 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;
+
+ 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>
diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py
index 87a53995e4..a150a2f35b 100644
--- a/var/spack/repos/builtin/packages/hdf5/package.py
+++ b/var/spack/repos/builtin/packages/hdf5/package.py
@@ -173,6 +173,15 @@ class Hdf5(CMakePackage):
# described in #2 we allow for such combination.
# conflicts('+mpi+cxx')
+ # Patch needed for HDF5 1.14.3 to fix signaling FPE checks from triggering
+ # at dynamic type system initialization. The type system's builtin types
+ # were refactored in 1.14.3 and switched from compile-time to run-time
+ # initialization. This patch suppresses floating point exception checks
+ # that would otherwise be triggered by this code. Later HDF5 versions
+ # will include the patch code changes.
+ # See https://github.com/HDFGroup/hdf5/pull/3837
+ patch("hdf5_1_14_3_fpe.patch", when="@1.14.3")
+
# There are known build failures with intel@18.0.1. This issue is
# discussed and patch is provided at
# https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/747951.
generated by cgit v1.2.3-70-g09d2 (git 2.46.0) at 2025-01-23 18:17:31 +0000