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HDF5 FPE fixes. #408

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Feb 28, 2024
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HDF5 FPE fixes. #408

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203 changes: 203 additions & 0 deletions var/spack/repos/builtin/packages/hdf5/hdf5_1_14_3_fpe.patch
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Original file line number Diff line number Diff line change
@@ -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>
9 changes: 9 additions & 0 deletions var/spack/repos/builtin/packages/hdf5/package.py
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Original file line number Diff line number Diff line change
Expand Up @@ -171,6 +171,15 @@ 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.
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