Segmentation fault in testphdf5 on 32-bit


#1

I’m doing test builds of HDF5 1.10.7 for Fedora Rawhide and noticed the following:

============================
Test log for testphdf5

===================================
PHDF5 TESTS START

MPI-process 2. hoMPI-process 4. hostname=buildhw-x86-11.iad2.fedoraproject.org
stname=buildhw-x86-11.iad2.fedoraproject.org
MPI-process 5. hostnaMPI-process 1. hostname=MPI-process 3. hostname=me=buildhw-x86-11.iad2.fedoraproject.org
buildhw-x86-11.iad2.fedoraproject.org
For help use: /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.10 release 7
For help use: /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.10 release 7
For help use: /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.10 release 7
buildhw-x86-11.iad2.fedoraproject.org
For help use: /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.10 release 7
For help use: /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.10 release 7
MPI-process 0. hostname=buildhw-x86-11.iad2.fedoraproject.org
For help use: /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5 -help
Linked with hdf5 version 1.10 release 7
Test filenames aTest filenames are:
Test filenames are:Test filenames are:
Test filenames are:
*** Hint ***
You can use enre:
ParaTest.h5
ParaTest.h5
Testing – fapl_mpio duplicate (mpiodup)
ParaTest.h5
Testing – fapl_mpio duplicate (mpiodup)
ParaTest.h5
Testing – fapl_mpio duplicate (mpiodup)
vironment variable HDF5_PARAPREFIParaTest.h5
Testing – fapl_mpio duplicate (mpiodup)
X to run parallel test files in a
different Testing – fapl_mpio duplicate (mpiodup)
directory or to add file type prefix. e.g.,
HDF5_PARAPREFIX=pfs:/PFS/user/me
export HDF5_PARAPREFIX
*** End of Hint ***
Test filenames are:
ParaTest.h5
Testing – fapl_mpio duplicate (mpiodup)
Testing – dataset using split communicators (split)
Testing – dataset using split communicators (split)
Testing – dataset using split communicators (split)
Testing – dataset using split communicators (split)
Testing – dataset using split communicators (split)
Testing – dataset using split communicators (split)
Testing – Coll Metadata file property settings (props)
Testing – Coll Metadata file property settings (props)
Testing – Coll Metadata file property settings (props)
Testing – Coll Metadata file property settings (props)
Testing – Coll Metadata file property settings (props)
Testing – Coll Metadata file property settings (props)
Testing – dataset independent write (idsetw)
Testing – dataset independent write (idsetw)
Testing – dataset independent write (idsetw)
Testing – dataset independent write (idsetw)
Testing – dataset independent write (idsetw)
Testing – dataset independent write (idsetw)
Testing – dataset independent read (idsetr)
Testing – dataset independent read (idsetr)
Testing – dataset independent read (idsetr)
Testing – dataset independent read (idsetr)
Testing – dataset independent read (idsetr)
Testing – dataset independent read (idsetr)
Testing – dataset collective write (cdsetw)
Testing – dataset collective write (cdsetw)
Testing – dataset collective write (cdsetw)
Testing – dataset collective write (cdsetw)
Testing – dataset collective write (cdsetw)
Testing – dataset collective write (cdsetw)
Testing – dataset collective read (cdsetr)
Testing – dataset collective read (cdsetr)
Testing – dataset collective read (cdsetr)
Testing – dataset collective read (cdsetr)
Testing – dataset collective read (cdsetr)
Testing – dataset collective read (cdsetr)
[buildhw-x86-11:4046468] *** Process received signal ***
[buildhw-x86-11:4046468] Signal: Segmentation fault (11)
[buildhw-x86-11:4046468] Signal code: Address not mapped (1)
[buildhw-x86-11:4046468] Failing at address: 0x57eef140
[buildhw-x86-11:4046441] *** Process received signal ***
[buildhw-x86-11:4046441] Signal: Segmentation fault (11)
[buildhw-x86-11:4046441] Signal code: Address not mapped (1)
[buildhw-x86-11:4046441] Failing at address: 0x57eef140
[buildhw-x86-11:4046444] *** Process received signal ***
[buildhw-x86-11:4046444] Signal: Segmentation fault (11)
[buildhw-x86-11:4046444] Signal code: Address not mapped (1)
[buildhw-x86-11:4046444] Failing at address: 0x57eef140
[buildhw-x86-11:4046448] *** Process received signal ***
[buildhw-x86-11:4046448] Signal: Segmentation fault (11)
[buildhw-x86-11:4046448] Signal code: Address not mapped (1)
[buildhw-x86-11:4046448] Failing at address: 0x57eef140
[buildhw-x86-11:4046455] *** Process received signal ***
[buildhw-x86-11:4046455] Signal: Segmentation fault (11)
[buildhw-x86-11:4046455] Signal code: Address not mapped (1)
[buildhw-x86-11:4046455] Failing at address: 0x57eef140
[buildhw-x86-11:4046468] [ 0] linux-gate.so.1(__kernel_rt_sigreturn+0x0)[0xf7f9c580]
[buildhw-x86-11:4046468] [ 1] [buildhw-x86-11:4046441] [ 0] linux-gate.so.1(__kernel_rt_sigreturn+0x0)[0xf7f96580]
[buildhw-x86-11:4046441] [ 1] [buildhw-x86-11:4046444] [ 0] linux-gate.so.1(__kernel_rt_sigreturn+0x0)[0xf7fc8580]
[buildhw-x86-11:4046444] [ 1] [buildhw-x86-11:4046448] [ 0] linux-gate.so.1(__kernel_rt_sigreturn+0x0)[0xf7f78580]
[buildhw-x86-11:4046448] [ 1] [buildhw-x86-11:4046455] [ 0] linux-gate.so.1(__kernel_rt_sigreturn+0x0)[0xf7f22580]
[buildhw-x86-11:4046455] [ 1] /usr/lib/openmpi/lib/libmpi.so.40(PMPI_Type_size_x+0x45)[0xf7a4c1e5]
[buildhw-x86-11:4046441] [ 2] /usr/lib/openmpi/lib/libmpi.so.40(PMPI_Type_size_x+0x45)[0xf7a7e1e5]
[buildhw-x86-11:4046444] [ 2] /usr/lib/openmpi/lib/libmpi.so.40(PMPI_Type_size_x+0x45)[0xf79d81e5]
[buildhw-x86-11:4046455] [ 2] /usr/lib/openmpi/lib/libmpi.so.40(PMPI_Type_size_x+0x45)[0xf7a2e1e5]
[buildhw-x86-11:4046448] [ 2] /usr/lib/openmpi/lib/libmpi.so.40(PMPI_Type_size_x+0x45)[0xf7a521e5]
[buildhw-x86-11:4046468] [ 2] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(+0x302596)[0xf7e0b596]
[buildhw-x86-11:4046468] [ 3] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(+0x302596)[0xf7d91596]
[buildhw-x86-11:4046455] [ 3] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(+0x302596)[0xf7de7596]
[buildhw-x86-11:4046448] [ 3] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(+0x302596)[0xf7e37596]
[buildhw-x86-11:4046444] [ 3] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(+0x302596)[0xf7e05596]
[buildhw-x86-11:4046441] [ 3] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5FD_read+0x179)[0xf7c541c9]
[buildhw-x86-11:4046444] [ 4] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5FD_read+0x179)[0xf7c221c9]
[buildhw-x86-11:4046441] [ 4] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5FD_read+0x179)[0xf7c281c9]
[buildhw-x86-11:4046468] [ 4] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5FD_read+0x179)[0xf7bae1c9]
[buildhw-x86-11:4046455] [ 4] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5FD_read+0x179)[0xf7c041c9]
[buildhw-x86-11:4046448] [ 4] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5F__accum_read+0x242)[0xf7b84692]
[buildhw-x86-11:4046455] [ 5] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5F__accum_read+0x242)[0xf7c2a692]
[buildhw-x86-11:4046444] [ 5] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5F__accum_read+0x242)[0xf7bda692]
[buildhw-x86-11:4046448] [ 5] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5F__accum_read+0x242)[0xf7bf8692]
[buildhw-x86-11:4046441] [ 5] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5F__accum_read+0x242)[0xf7bfe692]
[buildhw-x86-11:4046468] [ 5] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5PB_read+0x758)[0xf7cf1858]
[buildhw-x86-11:4046448] [ 6] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5PB_read+0x758)[0xf7d0f858]
[buildhw-x86-11:4046441] [ 6] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5PB_read+0x758)[0xf7d41858]
[buildhw-x86-11:4046444] [ 6] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5PB_read+0x758)[0xf7c9b858]
[buildhw-x86-11:4046455] [ 6] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5F_block_read+0xc9)[0xf7b918a9]
[buildhw-x86-11:4046455] [ 7] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5PB_read+0x758)[0xf7d15858]
[buildhw-x86-11:4046468] [ 6] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5F_block_read+0xc9)[0xf7c0b8a9]
[buildhw-x86-11:4046468] [ 7] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5F_block_read+0xc9)[0xf7c378a9]
[buildhw-x86-11:4046444] [ 7] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5F_block_read+0xc9)[0xf7be78a9]
[buildhw-x86-11:4046448] [ 7] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5F_block_read+0xc9)[0xf7c058a9]
[buildhw-x86-11:4046441] [ 7] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5D__mpio_select_read+0x57)[0xf7e2d737]
[buildhw-x86-11:4046444] [ 8] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5D__mpio_select_read+0x57)[0xf7ddd737]
[buildhw-x86-11:4046448] [ 8] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5D__mpio_select_read+0x57)[0xf7e01737]
[buildhw-x86-11:4046468] [ 8] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5D__mpio_select_read+0x57)[0xf7dfb737]
[buildhw-x86-11:4046441] [ 8] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5D__mpio_select_read+0x57)[0xf7d87737]
[buildhw-x86-11:4046455] [ 8] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(+0x2ff743)[0xf7d8e743]
[buildhw-x86-11:4046455] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(+0x2ff743)[0xf7e02743]
[buildhw-x86-11:4046441] [ 9] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(+0x2f88b8)[0xf7dfb8b8]
[buildhw-x86-11:4046441] [10] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(+0x2ff743)[0xf7e08743]
[buildhw-x86-11:4046468] [ 9] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(+0x2f88b8)[0xf7e018b8]
[buildhw-x86-11:4046468] [10] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(+0x2ff743)[0xf7e34743]
[buildhw-x86-11:4046444] [ 9] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(+0x2f88b8)[0xf7e2d8b8]
[buildhw-x86-11:4046444] [10] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(+0x2ff743)[0xf7de4743]
[buildhw-x86-11:4046448] [ 9] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(+0x2f88b8)[0xf7ddd8b8]
[buildhw-x86-11:4046448] [10] [ 9] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(+0x2f88b8)[0xf7d878b8]
[buildhw-x86-11:4046455] [10] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5D__contig_collective_read+0x43)[0xf7e2dba3]
[buildhw-x86-11:4046444] [11] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5D__contig_collective_read+0x43)[0xf7d87ba3]
[buildhw-x86-11:4046455] [11] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5D__contig_collective_read+0x43)[0xf7dddba3]
[buildhw-x86-11:4046448] [11] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5D__contig_collective_read+0x43)[0xf7dfbba3]
[buildhw-x86-11:4046441] [11] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5D__contig_collective_read+0x43)[0xf7e01ba3]
[buildhw-x86-11:4046468] [11] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5D__read+0x523)[0xf7b57fd3]
[buildhw-x86-11:4046455] [12] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5D__read+0x523)[0xf7badfd3]
[buildhw-x86-11:4046448] [12] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5D__read+0x523)[0xf7bcbfd3]
[buildhw-x86-11:4046441] [12] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5D__read+0x523)[0xf7bfdfd3]
[buildhw-x86-11:4046444] [12] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5D__read+0x523)[0xf7bd1fd3]
[buildhw-x86-11:4046468] [12] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5Dread+0x164)[0xf7bae774]
[buildhw-x86-11:4046448] [13] /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5(+0x10be3)[0x56592be3]
[buildhw-x86-11:4046448] [14] /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5(+0x5636)[0x56587636]
[buildhw-x86-11:4046448] [15] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5Dread+0x164)[0xf7bcc774]
[buildhw-x86-11:4046441] [13] /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5(+0x10be3)[0x565d6be3]
[buildhw-x86-11:4046441] [14] /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5(+0x5636)[0x565cb636]
[buildhw-x86-11:4046441] [15] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5Dread+0x164)[0xf7bd2774]
[buildhw-x86-11:4046468] [13] /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5(+0x10be3)[0x565a6be3]
[buildhw-x86-11:4046468] [14] /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5(+0x5636)[0x5659b636]
[buildhw-x86-11:4046468] [15] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5Dread+0x164)[0xf7bfe774]
[buildhw-x86-11:4046444] [13] /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5(+0x10be3)[0x565e6be3]
[buildhw-x86-11:4046444] [14] /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5(+0x5636)[0x565db636]
[buildhw-x86-11:4046444] [15] /builddir/build/BUILD/hdf5-1.10.7/openmpi/src/.libs/libhdf5.so.103(H5Dread+0x164)[0xf7b58774]
[buildhw-x86-11:4046455] [13] /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5(+0x10be3)[0x5665abe3]
[buildhw-x86-11:4046455] [14] /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5(+0x5636)[0x5664f636]
[buildhw-x86-11:4046455] [15] /lib/libc.so.6(__libc_start_main+0xed)[0xf77889dd]
[buildhw-x86-11:4046455] [16] /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5(+0x5f25)[0x5664ff25]
/lib/libc.so.6(__libc_start_main+0xed)[0xf78029dd]
[buildhw-x86-11:4046468] [16] /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5(+0x5f25)[0x5659bf25]
[buildhw-x86-11:4046468] *** End of error message ***
/lib/libc.so.6(__libc_start_main+0xed)[0xf782e9dd]
[buildhw-x86-11:4046444] [16] /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5(+0x5f25)[0x565dbf25]
[buildhw-x86-11:4046444] *** End of error message ***
/lib/libc.so.6(__libc_start_main+0xed)[0xf77fc9dd]
[buildhw-x86-11:4046441] [16] /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5(+0x5f25)[0x565cbf25]
[buildhw-x86-11:4046441] *** End of error message ***
/lib/libc.so.6(__libc_start_main+0xed)[0xf77de9dd]
[buildhw-x86-11:4046448] [16] /builddir/build/BUILD/hdf5-1.10.7/openmpi/testpar/.libs/testphdf5(+0x5f25)[0x56587f25]
[buildhw-x86-11:4046448] *** End of error message ***
[buildhw-x86-11:4046455] *** End of error message ***

Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.


mpiexec noticed that process rank 1 with PID 0 on node buildhw-x86-11 exited on signal 11 (Segmentation fault).

Command exited with non-zero status 139
0.18user 0.29system 0:00.48elapsed 99%CPU (0avgtext+0avgdata 19512maxresident)k
0inputs+16648outputs (2129major+8521minor)pagefaults 0swaps
Finished testing testphdf5

This is with openmpi 4.1.1rc1 on Fedora Rawhide i686


#2

Thank you for reporting! We will try to take a look.

Elena