Set NVHPC maximum optimization level to -O1 for now #3800

jhendersonHDF · 2023-10-30T20:52:43Z

Compiling HDF5 with NVHPC 23.5 - 23.9 results in test failures in 4 different test files that need to be resolved. Since those tests pass with an optimization level of -O1 (and -O0) and it is currently unclear whether the test failures are due to issues in HDF5 or issues in the 'nvc' compiler, set the maximum optimization level for NVHPC to -O1 until the test failures are resolved.

jhendersonHDF · 2023-10-30T20:56:09Z

The MPI I/O FAPL preserve PR test failure still exists on some systems until I can figure out what's going on there, but these changes pass locally with NVHPC 23.5 - 23.9 and on at least one system that isn't having the FAPL preserve test failure

jhendersonHDF · 2023-10-30T20:57:07Z

config/nvidia-flags

@@ -106,7 +107,8 @@ if test "X-nvc" = "X-$cc_vendor" -o "X-nvcc" = "X-$cc_vendor"; then
    ################

    HIGH_OPT_CFLAGS="-O1"         # -O2+ currently has test failures.


Looks like we already did this previously for Autotools builds, which is why the NVHPC action passes tests for Autotools builds, but the tests were disabled for CMake builds

jhendersonHDF · 2023-10-30T21:21:20Z

Looks like this is hitting a separate failure in testphdf5 and also a new one on JUnit-TestH5D. More investigation needed..

brtnfld · 2023-10-30T21:23:07Z

config/cmake/HDFCompilerFlags.cmake

+  # asserts and other library debug code. Compiling with -O1 also does not appear
+  # to have these issues, so set maximum optimization level to -O1 for now until
+  # it can be determined whether these issues are compiler-specific or issues
+  # in the library.


Do we have a keyword that we can add to this to indicate we should revisit the issue at a later date?

I thought about creating an issue to track this, but open to other suggestions as well.

@derobins , we probably need to develop a procedure indicating workarounds that should be revisited at a future date. Otherwise, they will be forgotten about.

brtnfld

lgtm

jhendersonHDF · 2023-10-30T21:54:19Z

Actually, the Autotools NVHPC workflow doesn't seem to be getting any flags from nvidia-flags at all:

Languages:
----------
                              C: yes
                     C Compiler: /opt/nvidia/hpc_sdk/Linux_x86_64/23.7/comm_libs/openmpi4/bin/mpicc
                       CPPFLAGS: 
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API -I/home/runner/work/hdf5/hdf5/src/H5FDsubfiling
                    AM_CPPFLAGS: 
                        C Flags: 
                     H5 C Flags:       
                     AM C Flags: 
               Shared C Library: yes
               Static C Library: yes
                        Fortran: yes
               Fortran Compiler: /opt/nvidia/hpc_sdk/Linux_x86_64/23.7/comm_libs/openmpi4/bin/mpifort
                  Fortran Flags: -fPIC -fortranlibs
               H5 Fortran Flags:      
               AM Fortran Flags: 
         Shared Fortran Library: yes
         Static Fortran Library: yes
               Module Directory: ${includedir}
                            C++: no
                           Java: no

jhendersonHDF · 2023-10-31T19:13:09Z

The testphdf5 failure has been fixed now, but there's still a segfault in JUnit-TestH5D that I haven't seen anywhere else

lrknox · 2023-11-01T13:14:20Z

The testphdf5 failure has been fixed now, but there's still a segfault in JUnit-TestH5D that I haven't seen anywhere else

Java fails in nvhpc-cmake.yml test. The nvhpc-auto.yml test doesn't enable java. We suggest disabling java for the cmake test also and creating an issue for java with nvhpc. The failing test is the java test of H5Pset_fapl_multi (muti).

Compiling HDF5 with NVHPC 23.5 - 23.9 results in test failures in 4 different test files that need to be resolved. Since those tests pass with an optimization level of -O1 (and -O0) and it is currently unclear whether the test failures are due to issues in HDF5 or issues in the 'nvc' compiler, set the maximum optimization level for NVHPC to -O1 until the test failures are resolved.

* Set NVHPC maximum optimization level to -O1 for now Compiling HDF5 with NVHPC 23.5 - 23.9 results in test failures in 4 different test files that need to be resolved. Since those tests pass with an optimization level of -O1 (and -O0) and it is currently unclear whether the test failures are due to issues in HDF5 or issues in the 'nvc' compiler, set the maximum optimization level for NVHPC to -O1 until the test failures are resolved. * Disable nvhpc Java testing in CMake and amend known issues * Re-enable testing of Autotools nvhpc

* Preserve MPI-I/O file hints when fapl is closed (#3755) * Fix for issue #3025: Save the MPI info in the file struct so H5Fget_access_plist() can retrieve it from there. * Add compression tests for subfiling (#3769) * Fix typo in comment (#3775) * Fixed a file handle leak in the core VFD (#3779) 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 * Fix a format string warning in the C++ examples (#3776) * Cancel running GitHub workflows on push to same PR (#3772) * Cancel running GitHub workflows on push to same PR * Remove github.sha from workflow concurrency groups * Print some messages in parallel tests on MPI rank 0 only (#3785) Avoids overly verbose output from all processes emitting progress, etc. info. * Avoid attempted use of NULL pointer in parallel compression code (#3786) The parallel compression test code tests for the case where all MPI ranks have no selection in a dataset when writing to it. Add an early exit to the code to avoid attempting to use a NULL pointer due to there being no work to do. * Don't install h5tools_test_utils test program on system (#3793) * Add Doxygen to H5FDsplitter.h (#3794) * H5FD_CURR_SPLITTER_VFD_CONFIG_VERSION * H5FD_SPLITTER_PATH_MAX * H5FD_SPLITTER_MAGIC * H5FD_splitter_vfd_config_t * H5Pset_fapl_splitter() * H5Pget_fapl_splitter() * Update Doxygen initializers & identifiers in VFDs (#3795) * Add Doxygen for all H5FD_<VFD> initializers * Add Doxygen for all H5FD_<VFD>_VALUE values * Mark H5FD_<vfd>_init() calls private in Doxygen * Fix memory corruption in 'MPI I/O FAPL preserve' test (#3806) * Fix usage of h5_clean_files in t_pflush2.c (#3807) * Fix parallel driver check in h5_fixname_real (#3808) * Fix a couple usages of MPI_Info_get (#3809) * Remove H5system.c warning on Windows oneAPI. (#3812) * Add processing of NVHPC flags in linux-gnulibc1 file (#3804) * Disable testing as tests are failing the same as in CMake * Use the current toolchain for examples as default (#3810) * Fix misc. warnings from GCC when compiling with -fsanitize=undefined (#3787) * Set NVHPC maximum optimization level to -O1 for now (#3800) * Set NVHPC maximum optimization level to -O1 for now Compiling HDF5 with NVHPC 23.5 - 23.9 results in test failures in 4 different test files that need to be resolved. Since those tests pass with an optimization level of -O1 (and -O0) and it is currently unclear whether the test failures are due to issues in HDF5 or issues in the 'nvc' compiler, set the maximum optimization level for NVHPC to -O1 until the test failures are resolved. * Disable nvhpc Java testing in CMake and amend known issues * Re-enable testing of Autotools nvhpc * Update some doxygen links to local refs (#3814) * Rework MPI Info FAPL preserve PR to use VFD 'ctl' operations (#3782) * Removed the use of C wrappers from H5P APIs. (#3824) * fix seg fault on frontier/cray * fix seg fault on frontier/cray * fix seg fault on frontier/cray * removed the use of h5pclose_c * removed the use of h5pclose_c * Fortran Wrappers H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f (#3801) * Added H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f * Added H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f tests * Create test for H5Pget_dxpl_mpio (#3825) * Create test and add to testphdf5 * Renamed h5fuse.sh to h5fuse (#3834) * provide an alternative to mapfile for older bash * Disable FP exceptions in H5T init code (#3837) The H5T floating-point datatype initialization code can raise exceptions when handling signaling NaNs. This change disables FE_INVALID exceptions during initialization. Also removes the -ieee=full change for NAG Fortran as that shouldn't be necessary anymore. Fixes #3831 * Add intel oneapi windows build to CI CMake (#3836) * Remove printf format warning on Windows oneAPI. (#3838) * Correct ENV variables (#3841) * Remove Autotools sed hack (#3848) configure.ac contains a sed line that cleans up incorrect library flags which was added to paper over some bugs in earlier versions of the Autotools. These issues are not a problem with the current versions of the Autootols. The sed line causes problems on MacOS, so it has been removed. Fixes #3843 * Make filter unregister callbacks safe for VOL connectors (#3629) * Make filter callbacks use top-level API functions When using VOL connectors, H5I_iterate may not provide valid object pointers to its callback. This change keeps existing functionality in H5Zunregister() without using potentially unsafe pointers. * Filter callbacks use internal API * Skip MPI work on non-native VOL * Add extra space in comments for consistency (#3852) * Add extra space in comments for consistency * uncomment tfloatsattrs test * Update Actions badges to link to relevant workflow (#3850) * Add CMake long double cross-compile defaults (#3683) HDF5 performs a couple of checks at build time to see if long double values can be converted correctly (IBM's Power architecture uses a special format for long doubles). These checks were performed using TRY_RUN, which is a problem when cross-compiling. These checks now use default values appropriate for most non-Power systems when cross-compiling. The cache values can be pre-set if necessary, which will preempt both the TRY_RUN and the default. Affected values: H5_LDOUBLE_TO_LONG_SPECIAL (default no) H5_LONG_TO_LDOUBLE_SPECIAL (default no) H5_LDOUBLE_TO_LLONG_ACCURATE (default yes) H5_LLONG_TO_LDOUBLE_CORRECT (default yes) H5_DISABLE_SOME_LDOUBLE_CONV (default no) Fixes GitHub #3585 * Updates for building and testing VOL connectors * Fix issue with HDF5_VOL_ALLOW_EXTERNAL CMake variable * Initialize parallel testing with MPI_THREAD_MULTIPLE when testing API * Add CMake variable to allow specifying a VOL connector's package name * Remove call to MPI_Init in serial API tests While previously necessary, it now interferes with VOL connectors that may need to be initialized with MPI_THREAD_MULTIPLE * Fixes for CI and presets (#3853) * Change dest for doxygen (#3856) * Implement selection vector I/O with collective chunk filling (#3826) * Changes for ECP-344: Implement selection vector I/O with collective chunk filling. Also fix a bug in H5FD__mpio_write_vector() to account for fixed size optimization when computing max address. * Fixes based on PR review comments: For H5Dchunk.c: fix H5MM_xfree() For H5FDmpio.c: 1) Revert the fix to H5FD__mpio_write_vector() 2) Apply the patch from Neil on the proper length of s_sizes reported by H5FD__mpio_vector_build_types() * Put back the logic of dividing up the work among all the mpi ranks similar to the original H5D__chunk_collective_fill() routine. * Add a test to verify the fix for the illegal reference problem in H5FD__mpio_write_vector(). * Do not publish compression headers or docs (#3865) * Fix typo: look -> loop (#3866) * Moved the README to markdown and expanded its overview of the files, file generation, and other Fortran wrapper development practices as mentioned in the HDF5 architectural document. I added a new figure and included the SVG file and the original xfig file it was generated from. (#3862) * Add HDF5_DISABLE_TESTS_REGEX option to skip tests (#3859) * Fix typo in error message for `MPI_Type_dup`. (#3867) * Complete the `if command line option` sentence. (#3868) * Fix h5dump segmentation fault when --vfd-value option is used (#3873) * Updated URL in funding.yml (#3882) Using new shortened URL, might look better. * Remove unused variable from unmerged changes * Update src/H5Tinit_float.c

jhendersonHDF added Merge - To 1.14 Priority - 2. Medium ⏹ It would be nice to have this in the next release Component - Build CMake, Autotools Type - Task Actions that don't fit into any other type category labels Oct 30, 2023

jhendersonHDF requested review from lrknox, derobins, byrnHDF, fortnern, qkoziol, vchoi-hdfgroup, bmribler, glennsong09, mattjala and brtnfld as code owners October 30, 2023 20:52

jhendersonHDF commented Oct 30, 2023

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byrnHDF approved these changes Oct 30, 2023

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brtnfld reviewed Oct 30, 2023

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brtnfld approved these changes Oct 30, 2023

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jhendersonHDF mentioned this pull request Oct 30, 2023

Add processing of NVHPC flags in linux-gnulibc1 file #3804

Merged

jhendersonHDF force-pushed the nvhpc_opt branch from 218a570 to cea46a0 Compare October 31, 2023 18:13

jhendersonHDF force-pushed the nvhpc_opt branch from 8d49707 to edde9ef Compare November 1, 2023 18:53

jhendersonHDF added 3 commits November 1, 2023 13:53

Disable nvhpc Java testing in CMake and amend known issues

ff9d26b

Re-enable testing of Autotools nvhpc

edde9ef

lrknox approved these changes Nov 1, 2023

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lrknox merged commit 64e239c into HDFGroup:develop Nov 1, 2023
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jhendersonHDF deleted the nvhpc_opt branch November 1, 2023 20:32

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Set NVHPC maximum optimization level to -O1 for now #3800

Set NVHPC maximum optimization level to -O1 for now #3800

jhendersonHDF commented Oct 30, 2023

jhendersonHDF commented Oct 30, 2023

jhendersonHDF Oct 30, 2023

jhendersonHDF commented Oct 30, 2023

brtnfld Oct 30, 2023

jhendersonHDF Oct 30, 2023

brtnfld Oct 30, 2023

brtnfld left a comment

jhendersonHDF commented Oct 30, 2023

jhendersonHDF commented Oct 31, 2023

lrknox commented Nov 1, 2023

		@@ -106,7 +107,8 @@ if test "X-nvc" = "X-$cc_vendor" -o "X-nvcc" = "X-$cc_vendor"; then
		################

		HIGH_OPT_CFLAGS="-O1" # -O2+ currently has test failures.

Set NVHPC maximum optimization level to -O1 for now #3800

Set NVHPC maximum optimization level to -O1 for now #3800

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