hdf5: fixes floating point exceptions generated when fpe trapping is enabled (#42880)
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Ryan Honeyager
GitHub
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ebaeea7820
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var/spack/repos/builtin/packages/hdf5/hdf5_1_14_3_fpe.patch
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203
var/spack/repos/builtin/packages/hdf5/hdf5_1_14_3_fpe.patch
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@ -0,0 +1,203 @@
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diff --git a/config/linux-gnulibc1 b/config/linux-gnulibc1
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index 328f8d3cec..079f08d96c 100644
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--- a/config/linux-gnulibc1
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+++ b/config/linux-gnulibc1
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@@ -173,10 +173,7 @@ case $FC_BASENAME in
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nagfor)
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F9XSUFFIXFLAG=""
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- # NOTE: The default is -ieee=stop, which will cause problems
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- # when the H5T module performs floating-point type
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- # introspection
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- AM_FCFLAGS="$AM_FCFLAGS -ieee=full"
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+ AM_FCFLAGS="$AM_FCFLAGS"
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FSEARCH_DIRS=""
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# Production
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diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
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index 200576332b..0aa139761d 100644
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--- a/release_docs/RELEASE.txt
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+++ b/release_docs/RELEASE.txt
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@@ -246,6 +246,27 @@ Support for new platforms, languages and compilers
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-
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+Patches applied since the HDF5-1.14.3 release
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+=============================================
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+ Library
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+ -------
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+ - Suppressed floating-point exceptions in H5T init code
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+
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+ The floating-point datatype initialization code in H5Tinit_float.c
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+ could raise FE_INVALID exceptions while munging bits and performing
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+ comparisons that might involve NaN. This was not a problem when the
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+ initialization code was executed in H5detect at compile time (prior
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+ to 1.14.3), but now that the code is executed at library startup
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+ (1.14.3+), these exceptions can be caught by user code, as is the
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+ default in the NAG Fortran compiler.
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+
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+ Starting in 1.14.4, we now suppress floating-point exceptions while
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+ initializing the floating-point types and clear FE_INVALID before
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+ restoring the original environment.
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+
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+ Fixes GitHub #3831
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+
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+
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Bug Fixes since HDF5-1.14.2 release
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===================================
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Library
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@@ -619,12 +640,6 @@ Known Problems
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this release with link errors. As a result, Windows binaries for this release
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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,
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- division by zero, and other illegal operations without interrupting or halting
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- the program flow. The HDF5 C library intentionally performs these exceptions.
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- Therefore, the "-ieee=full" nagfor switch is necessary when compiling a program
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- to avoid stopping on an exception.
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-
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CMake files do not behave correctly with paths containing spaces.
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Do not use spaces in paths because the required escaping for handling spaces
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results in very complex and fragile build files.
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diff --git a/src/H5Tinit_float.c b/src/H5Tinit_float.c
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index 3b9e127fe4..02bb3bad77 100644
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--- a/src/H5Tinit_float.c
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+++ b/src/H5Tinit_float.c
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@@ -51,19 +51,23 @@
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* Function: DETECT_F
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*
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* Purpose: This macro takes a floating point type like `double' and
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- * a base name like `natd' and detects byte order, mantissa
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- * location, exponent location, sign bit location, presence or
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- * absence of implicit mantissa bit, and exponent bias and
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- * initializes a detected_t structure with those properties.
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+ * detects byte order, mantissa location, exponent location,
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+ * sign bit location, presence or absence of implicit mantissa
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+ * bit, and exponent bias and initializes a detected_t structure
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+ * with those properties.
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+ *
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+ * Note that these operations can raise floating-point
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+ * exceptions and building with some compiler options
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+ * (especially Fortran) can cause problems.
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*-------------------------------------------------------------------------
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*/
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-#define DETECT_F(TYPE, VAR, INFO) \
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+#define DETECT_F(TYPE, INFO) \
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do { \
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- TYPE _v1, _v2, _v3; \
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- unsigned char _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)]; \
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- unsigned char _pad_mask[sizeof(TYPE)]; \
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- unsigned char _byte_mask; \
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- int _i, _j, _last = (-1); \
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+ TYPE _v1, _v2, _v3; \
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+ uint8_t _buf1[sizeof(TYPE)], _buf3[sizeof(TYPE)]; \
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+ uint8_t _pad_mask[sizeof(TYPE)]; \
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+ uint8_t _byte_mask; \
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+ int _i, _j, _last = -1; \
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\
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memset(&INFO, 0, sizeof(INFO)); \
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INFO.size = sizeof(TYPE); \
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@@ -81,7 +85,7 @@
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_v1 = (TYPE)4.0L; \
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H5MM_memcpy(_buf1, (const void *)&_v1, sizeof(TYPE)); \
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for (_i = 0; _i < (int)sizeof(TYPE); _i++) \
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- for (_byte_mask = (unsigned char)1; _byte_mask; _byte_mask = (unsigned char)(_byte_mask << 1)) { \
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+ for (_byte_mask = (uint8_t)1; _byte_mask; _byte_mask = (uint8_t)(_byte_mask << 1)) { \
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_buf1[_i] ^= _byte_mask; \
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H5MM_memcpy((void *)&_v2, (const void *)_buf1, sizeof(TYPE)); \
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H5_GCC_CLANG_DIAG_OFF("float-equal") \
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@@ -118,7 +122,7 @@
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_v1 = (TYPE)1.0L; \
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_v2 = (TYPE)-1.0L; \
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if (H5T__bit_cmp(sizeof(TYPE), INFO.perm, &_v1, &_v2, _pad_mask, &(INFO.sign)) < 0) \
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- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to detect byte order"); \
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+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to determine sign bit"); \
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\
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/* Mantissa */ \
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INFO.mpos = 0; \
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@@ -126,12 +130,11 @@
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_v1 = (TYPE)1.0L; \
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_v2 = (TYPE)1.5L; \
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if (H5T__bit_cmp(sizeof(TYPE), INFO.perm, &_v1, &_v2, _pad_mask, &(INFO.msize)) < 0) \
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- HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to detect byte order"); \
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+ HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, FAIL, "failed to determine mantissa"); \
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INFO.msize += 1 + (unsigned)(INFO.imp ? 0 : 1) - INFO.mpos; \
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\
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/* Exponent */ \
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- INFO.epos = INFO.mpos + INFO.msize; \
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- \
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+ INFO.epos = INFO.mpos + INFO.msize; \
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INFO.esize = INFO.sign - INFO.epos; \
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\
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_v1 = (TYPE)1.0L; \
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@@ -456,17 +459,24 @@ H5T__set_precision(H5T_fpoint_det_t *d)
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herr_t H5_NO_UBSAN
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H5T__init_native_float_types(void)
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{
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+ fenv_t saved_fenv;
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H5T_fpoint_det_t det;
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H5T_t *dt = NULL;
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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
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+ * tripping over signaling NaNs while looking at "don't care" bits.
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+ */
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+ if (feholdexcept(&saved_fenv) != 0)
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+ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't save floating-point environment");
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+
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/* H5T_NATIVE_FLOAT */
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/* Get the type's characteristics */
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memset(&det, 0, sizeof(H5T_fpoint_det_t));
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- DETECT_F(float, FLOAT, det);
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+ DETECT_F(float, det);
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/* Allocate and fill type structure */
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if (NULL == (dt = H5T__alloc()))
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@@ -497,7 +507,7 @@ H5T__init_native_float_types(void)
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/* Get the type's characteristics */
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memset(&det, 0, sizeof(H5T_fpoint_det_t));
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- DETECT_F(double, DOUBLE, det);
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+ DETECT_F(double, det);
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/* Allocate and fill type structure */
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if (NULL == (dt = H5T__alloc()))
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@@ -528,7 +538,7 @@ H5T__init_native_float_types(void)
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/* Get the type's characteristics */
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memset(&det, 0, sizeof(H5T_fpoint_det_t));
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- DETECT_F(long double, LDOUBLE, det);
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+ DETECT_F(long double, det);
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/* Allocate and fill type structure */
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if (NULL == (dt = H5T__alloc()))
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@@ -561,6 +571,14 @@ H5T__init_native_float_types(void)
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H5T_native_order_g = det.order;
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done:
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+ /* Clear any FE_INVALID exceptions from NaN handling */
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+ if (feclearexcept(FE_INVALID) != 0)
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+ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't clear floating-point exceptions");
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+
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+ /* Restore the original environment */
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+ if (feupdateenv(&saved_fenv) != 0)
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+ HSYS_GOTO_ERROR(H5E_DATATYPE, H5E_CANTSET, FAIL, "can't restore floating-point environment");
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+
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if (ret_value < 0) {
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if (dt != NULL) {
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dt->shared = H5FL_FREE(H5T_shared_t, dt->shared);
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diff --git a/src/H5private.h b/src/H5private.h
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index 14a0ac3225..3aaa0d5245 100644
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--- a/src/H5private.h
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+++ b/src/H5private.h
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@@ -26,6 +26,7 @@
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#include <ctype.h>
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#include <errno.h>
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#include <fcntl.h>
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+#include <fenv.h>
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#include <float.h>
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#include <math.h>
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#include <setjmp.h>
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@ -173,6 +173,15 @@ class Hdf5(CMakePackage):
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# described in #2 we allow for such combination.
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# conflicts('+mpi+cxx')
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# Patch needed for HDF5 1.14.3 to fix signaling FPE checks from triggering
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# at dynamic type system initialization. The type system's builtin types
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# were refactored in 1.14.3 and switched from compile-time to run-time
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# initialization. This patch suppresses floating point exception checks
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# that would otherwise be triggered by this code. Later HDF5 versions
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# will include the patch code changes.
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# See https://github.com/HDFGroup/hdf5/pull/3837
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patch("hdf5_1_14_3_fpe.patch", when="@1.14.3")
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# There are known build failures with intel@18.0.1. This issue is
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# discussed and patch is provided at
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# https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/747951.
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