Hi there all,
We're using SU2 with OpenMPI 4.0.3, gcc 8.5.0 on Redhat 7.9. We compiled
all component for using on HPC system.
When I use SU2 with QuickStart config file with OpenMPI, it gives error
like in attached file.
Command is:
|mpirun -np 8 --allow-run-as-root SU2_CFD inv_NACA0012.cfg|
--
İyi çalışmalar,
Aziz Öğütlü
Eduline Bilişim Sanayi ve Ticaret Ltd. Şti.www.eduline.com.tr
Merkez Mah. Ayazma Cad. No:37 Papirus Plaza
Kat:6 Ofis No:118 Kağıthane - İstanbul - Türkiye 34406
Tel : +90 212 324 60 61 Cep: +90 541 350 40 72
[headnode:3423 :0:3423] Caught signal 11 (Segmentation fault: address not
mapped to object at address 0x30)
[headnode:3426 :0:3426] Caught signal 11 (Segmentation fault: address not
mapped to object at address 0x30)
[headnode:3424 :0:3424] Caught signal 11 (Segmentation fault: address not
mapped to object at address 0x30)
[headnode:3427 :0:3427] Caught signal 11 (Segmentation fault: address not
mapped to object at address 0x30)
[headnode:3420 :0:3420] Caught signal 11 (Segmentation fault: address not
mapped to object at address 0x30)
[headnode:3425 :0:3425] Caught signal 11 (Segmentation fault: address not
mapped to object at address 0x30)
[headnode:3422 :0:3422] Caught signal 11 (Segmentation fault: address not
mapped to object at address 0x30)
[headnode:3421 :0:3421] Caught signal 11 (Segmentation fault: address not
mapped to object at address 0x30)
==== backtrace (tid: 3421) ====
0 0x000000000004d455 ucs_debug_print_backtrace() ???:0
1 0x0000000000043b08 ompi_file_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/file/file.c:153
2 0x0000000000043b08 ompi_file_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/file/file.c:153
3 0x0000000000064336 PMPI_File_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/mpi/c/profile/pfile_close.c:60
4 0x00000000005ff508 CFileWriter::OpenMPIFile() ???:0
5 0x000000000060f4ce CSU2BinaryFileWriter::Write_Data() ???:0
6 0x00000000005aa7a0 COutput::WriteToFile() ???:0
7 0x00000000005ac166 COutput::SetResult_Files() ???:0
8 0x00000000004fbf02 CSinglezoneDriver::Output() ???:0
9 0x00000000004fc86a CSinglezoneDriver::StartSolver() ???:0
10 0x0000000000472c29 main() ???:0
11 0x0000000000022555 __libc_start_main() ???:0
12 0x0000000000494f87 _start() ???:0
==== backtrace (tid: 3427) ====
0 0x000000000004d455 ucs_debug_print_backtrace() ???:0
1 0x0000000000043b08 ompi_file_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/file/file.c:153
2 0x0000000000043b08 ompi_file_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/file/file.c:153
3 0x0000000000064336 PMPI_File_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/mpi/c/profile/pfile_close.c:60
4 0x00000000005ff508 CFileWriter::OpenMPIFile() ???:0
5 0x000000000060f4ce CSU2BinaryFileWriter::Write_Data() ???:0
6 0x00000000005aa7a0 COutput::WriteToFile() ???:0
7 0x00000000005ac166 COutput::SetResult_Files() ???:0
8 0x00000000004fbf02 CSinglezoneDriver::Output() ???:0
9 0x00000000004fc86a CSinglezoneDriver::StartSolver() ???:0
10 0x0000000000472c29 main() ???:0
11 0x0000000000022555 __libc_start_main() ???:0
12 0x0000000000494f87 _start() ???:0
=================================
==== backtrace (tid: 3425) ====
0 0x000000000004d455 ucs_debug_print_backtrace() ???:0
1 0x0000000000043b08 ompi_file_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/file/file.c:153
2 0x0000000000043b08 ompi_file_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/file/file.c:153
3 0x0000000000064336 PMPI_File_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/mpi/c/profile/pfile_close.c:60
4 0x00000000005ff508 CFileWriter::OpenMPIFile() ???:0
5 0x000000000060f4ce CSU2BinaryFileWriter::Write_Data() ???:0
6 0x00000000005aa7a0 COutput::WriteToFile() ???:0
7 0x00000000005ac166 COutput::SetResult_Files() ???:0
8 0x00000000004fbf02 CSinglezoneDriver::Output() ???:0
9 0x00000000004fc86a CSinglezoneDriver::StartSolver() ???:0
10 0x0000000000472c29 main() ???:0
11 0x0000000000022555 __libc_start_main() ???:0
12 0x0000000000494f87 _start() ???:0
=================================
==== backtrace (tid: 3423) ====
0 0x000000000004d455 ucs_debug_print_backtrace() ???:0
1 0x0000000000043b08 ompi_file_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/file/file.c:153
2 0x0000000000043b08 ompi_file_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/file/file.c:153
3 0x0000000000064336 PMPI_File_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/mpi/c/profile/pfile_close.c:60
4 0x00000000005ff508 CFileWriter::OpenMPIFile() ???:0
5 0x000000000060f4ce CSU2BinaryFileWriter::Write_Data() ???:0
6 0x00000000005aa7a0 COutput::WriteToFile() ???:0
7 0x00000000005ac166 COutput::SetResult_Files() ???:0
8 0x00000000004fbf02 CSinglezoneDriver::Output() ???:0
9 0x00000000004fc86a CSinglezoneDriver::StartSolver() ???:0
10 0x0000000000472c29 main() ???:0
11 0x0000000000022555 __libc_start_main() ???:0
12 0x0000000000494f87 _start() ???:0
=================================
==== backtrace (tid: 3426) ====
0 0x000000000004d455 ucs_debug_print_backtrace() ???:0
1 0x0000000000043b08 ompi_file_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/file/file.c:153
2 0x0000000000043b08 ompi_file_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/file/file.c:153
3 0x0000000000064336 PMPI_File_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/mpi/c/profile/pfile_close.c:60
4 0x00000000005ff508 CFileWriter::OpenMPIFile() ???:0
5 0x000000000060f4ce CSU2BinaryFileWriter::Write_Data() ???:0
6 0x00000000005aa7a0 COutput::WriteToFile() ???:0
7 0x00000000005ac166 COutput::SetResult_Files() ???:0
8 0x00000000004fbf02 CSinglezoneDriver::Output() ???:0
9 0x00000000004fc86a CSinglezoneDriver::StartSolver() ???:0
10 0x0000000000472c29 main() ???:0
11 0x0000000000022555 __libc_start_main() ???:0
12 0x0000000000494f87 _start() ???:0
==== backtrace (tid: 3420) ====
0 0x000000000004d455 ucs_debug_print_backtrace() ???:0
1 0x0000000000043b08 ompi_file_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/file/file.c:153
2 0x0000000000043b08 ompi_file_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/file/file.c:153
3 0x0000000000064336 PMPI_File_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/mpi/c/profile/pfile_close.c:60
4 0x00000000005ff508 CFileWriter::OpenMPIFile() ???:0
5 0x000000000060f4ce CSU2BinaryFileWriter::Write_Data() ???:0
6 0x00000000005aa7a0 COutput::WriteToFile() ???:0
7 0x00000000005ac166 COutput::SetResult_Files() ???:0
8 0x00000000004fbf02 CSinglezoneDriver::Output() ???:0
9 0x00000000004fc86a CSinglezoneDriver::StartSolver() ???:0
10 0x0000000000472c29 main() ???:0
11 0x0000000000022555 __libc_start_main() ???:0
12 0x0000000000494f87 _start() ???:0
=================================
==== backtrace (tid: 3424) ====
0 0x000000000004d455 ucs_debug_print_backtrace() ???:0
1 0x0000000000043b08 ompi_file_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/file/file.c:153
2 0x0000000000043b08 ompi_file_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/file/file.c:153
3 0x0000000000064336 PMPI_File_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/mpi/c/profile/pfile_close.c:60
4 0x00000000005ff508 CFileWriter::OpenMPIFile() ???:0
5 0x000000000060f4ce CSU2BinaryFileWriter::Write_Data() ???:0
6 0x00000000005aa7a0 COutput::WriteToFile() ???:0
7 0x00000000005ac166 COutput::SetResult_Files() ???:0
8 0x00000000004fbf02 CSinglezoneDriver::Output() ???:0
9 0x00000000004fc86a CSinglezoneDriver::StartSolver() ???:0
10 0x0000000000472c29 main() ???:0
11 0x0000000000022555 __libc_start_main() ???:0
12 0x0000000000494f87 _start() ???:0
=================================
==== backtrace (tid: 3422) ====
0 0x000000000004d455 ucs_debug_print_backtrace() ???:0
1 0x0000000000043b08 ompi_file_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/file/file.c:153
2 0x0000000000043b08 ompi_file_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/file/file.c:153
3 0x0000000000064336 PMPI_File_close()
/var/tmp/OFED_topdir/BUILD/openmpi-4.0.3rc4/ompi/mpi/c/profile/pfile_close.c:60
4 0x00000000005ff508 CFileWriter::OpenMPIFile() ???:0
5 0x000000000060f4ce CSU2BinaryFileWriter::Write_Data() ???:0
6 0x00000000005aa7a0 COutput::WriteToFile() ???:0
7 0x00000000005ac166 COutput::SetResult_Files() ???:0
8 0x00000000004fbf02 CSinglezoneDriver::Output() ???:0
9 0x00000000004fc86a CSinglezoneDriver::StartSolver() ???:0
10 0x0000000000472c29 main() ???:0
11 0x0000000000022555 __libc_start_main() ???:0
12 0x0000000000494f87 _start() ???:0
=================================
=================================
[headnode:03421] *** Process received signal ***
[headnode:03421] Signal: Segmentation fault (11)
[headnode:03421] Signal code: (-6)
[headnode:03421] Failing at address: 0xd5d
[headnode:03421] [ 0] /lib64/libpthread.so.0(+0xf630)[0x2ad6190d6630]
[headnode:03421] [ 1]
/usr/mpi/gcc/openmpi-4.0.3rc4/lib64/libmpi.so.40(ompi_file_close+0x18)[0x2ad61834ab08]
[headnode:03421] [ 2]
/usr/mpi/gcc/openmpi-4.0.3rc4/lib64/libmpi.so.40(PMPI_File_close+0x16)[0x2ad61836b336]
[headnode:03421] [ 3] SU2_CFD[0x5ff508]
[headnode:03421] [ 4] SU2_CFD[0x60f4ce]
[headnode:03421] [ 5] SU2_CFD[0x5aa7a0]
[headnode:03421] [ 6] SU2_CFD[0x5ac166]
[headnode:03421] [ 7] SU2_CFD[0x4fbf02]
[headnode:03421] [ 8] SU2_CFD[0x4fc86a]
[headnode:03421] [headnode:03427] *** Process received signal ***
[headnode:03427] Signal: Segmentation fault (11)
[headnode:03427] Signal code: (-6)
[headnode:03427] Failing at address: 0xd63
[headnode:03427] [ 0] /lib64/libpthread.so.0(+0xf630)[0x2aeafde82630]
[headnode:03427] [ 1]
/usr/mpi/gcc/openmpi-4.0.3rc4/lib64/libmpi.so.40(ompi_file_close+0x18)[0x2aeafd0f6b08]
[headnode:03427] [ 2]
/usr/mpi/gcc/openmpi-4.0.3rc4/lib64/libmpi.so.40(PMPI_File_close+0x16)[0x2aeafd117336]
[headnode:03427] [ 3] SU2_CFD[0x5ff508]
[headnode:03427] [ 4] SU2_CFD[0x60f4ce]
[headnode:03427] [ 5] SU2_CFD[0x5aa7a0]
[headnode:03427] [ 6] SU2_CFD[0x5ac166]
[headnode:03427] [ 7] SU2_CFD[0x4fbf02]
[headnode:03427] [ 8] SU2_CFD[0x4fc86a]
[headnode:03427] [ 9] SU2_CFD[0x472c29]
[headnode:03427] [headnode:03425] *** Process received signal ***
[headnode:03425] Signal: Segmentation fault (11)
[headnode:03425] Signal code: (-6)
[headnode:03425] Failing at address: 0xd61
[headnode:03425] [ 0] /lib64/libpthread.so.0(+0xf630)[0x2b0642f60630]
[headnode:03425] [ 1]
/usr/mpi/gcc/openmpi-4.0.3rc4/lib64/libmpi.so.40(ompi_file_close+0x18)[0x2b06421d4b08]
[headnode:03425] [ 2]
/usr/mpi/gcc/openmpi-4.0.3rc4/lib64/libmpi.so.40(PMPI_File_close+0x16)[0x2b06421f5336]
[headnode:03425] [ 3] SU2_CFD[0x5ff508]
[headnode:03425] [ 4] SU2_CFD[0x60f4ce]
[headnode:03425] [ 5] SU2_CFD[0x5aa7a0]
[headnode:03425] [ 6] SU2_CFD[0x5ac166]
[headnode:03425] [ 7] SU2_CFD[0x4fbf02]
[headnode:03425] [ 8] SU2_CFD[0x4fc86a]
[headnode:03425] [ 9] SU2_CFD[0x472c29]
[headnode:03425] [10] [headnode:03423] *** Process received signal ***
[headnode:03423] Signal: Segmentation fault (11)
[headnode:03423] Signal code: (-6)
[headnode:03423] Failing at address: 0xd5f
[headnode:03423] [ 0] /lib64/libpthread.so.0(+0xf630)[0x2ac7bd1f9630]
[headnode:03423] [ 1]
/usr/mpi/gcc/openmpi-4.0.3rc4/lib64/libmpi.so.40(ompi_file_close+0x18)[0x2ac7bc46db08]
[headnode:03423] [ 2]
/usr/mpi/gcc/openmpi-4.0.3rc4/lib64/libmpi.so.40(PMPI_File_close+0x16)[0x2ac7bc48e336]
[headnode:03423] [ 3] SU2_CFD[0x5ff508]
[headnode:03423] [ 4] SU2_CFD[0x60f4ce]
[headnode:03423] [ 5] SU2_CFD[0x5aa7a0]
[headnode:03423] [ 6] SU2_CFD[0x5ac166]
[headnode:03423] [ 7] SU2_CFD[0x4fbf02]
[headnode:03423] [ 8] SU2_CFD[0x4fc86a]
[headnode:03423] [ 9] SU2_CFD[0x472c29]
[headnode:03423] [10] =================================
[headnode:03426] *** Process received signal ***
[headnode:03426] Signal: Segmentation fault (11)
[headnode:03426] Signal code: (-6)
[headnode:03426] Failing at address: 0xd62
[headnode:03426] [ 0] /lib64/libpthread.so.0(+0xf630)[0x2b8ffe591630]
[headnode:03426] [ 1]
/usr/mpi/gcc/openmpi-4.0.3rc4/lib64/libmpi.so.40(ompi_file_close+0x18)[0x2b8ffd805b08]
[headnode:03426] [ 2]
/usr/mpi/gcc/openmpi-4.0.3rc4/lib64/libmpi.so.40(PMPI_File_close+0x16)[0x2b8ffd826336]
[headnode:03426] [ 3] SU2_CFD[0x5ff508]
[headnode:03426] [ 4] [headnode:03420] *** Process received signal ***
[headnode:03420] Signal: Segmentation fault (11)
[headnode:03420] Signal code: (-6)
[headnode:03420] Failing at address: 0xd5c
[headnode:03420] [ 0] /lib64/libpthread.so.0(+0xf630)[0x2aafebcfa630]
[headnode:03420] [ 1]
/usr/mpi/gcc/openmpi-4.0.3rc4/lib64/libmpi.so.40(ompi_file_close+0x18)[0x2aafeaf6eb08]
[headnode:03420] [ 2]
/usr/mpi/gcc/openmpi-4.0.3rc4/lib64/libmpi.so.40(PMPI_File_close+0x16)[0x2aafeaf8f336]
[headnode:03420] [ 3] SU2_CFD[0x5ff508]
[headnode:03420] [ 4] SU2_CFD[0x60f4ce]
[headnode:03424] *** Process received signal ***
[headnode:03424] Signal: Segmentation fault (11)
[headnode:03424] Signal code: (-6)
[headnode:03424] Failing at address: 0xd60
[headnode:03424] [ 0] /lib64/libpthread.so.0(+0xf630)[0x2ac4f79aa630]
[headnode:03424] [ 1]
/usr/mpi/gcc/openmpi-4.0.3rc4/lib64/libmpi.so.40(ompi_file_close+0x18)[0x2ac4f6c1eb08]
[headnode:03424] [ 2]
/usr/mpi/gcc/openmpi-4.0.3rc4/lib64/libmpi.so.40(PMPI_File_close+0x16)[0x2ac4f6c3f336]
[headnode:03424] [ 3] SU2_CFD[0x5ff508]
[headnode:03424] [ 4] SU2_CFD[0x60f4ce]
[headnode:03424] [ 5] [headnode:03422] *** Process received signal ***
[headnode:03422] Signal: Segmentation fault (11)
[headnode:03422] Signal code: (-6)
[headnode:03422] Failing at address: 0xd5e
[headnode:03422] [ 0] /lib64/libpthread.so.0(+0xf630)[0x2b7058b17630]
[headnode:03422] [ 1]
/usr/mpi/gcc/openmpi-4.0.3rc4/lib64/libmpi.so.40(ompi_file_close+0x18)[0x2b7057d8bb08]
[headnode:03422] [ 2]
/usr/mpi/gcc/openmpi-4.0.3rc4/lib64/libmpi.so.40(PMPI_File_close+0x16)[0x2b7057dac336]
[headnode:03422] [ 3] SU2_CFD[0x5ff508]
[headnode:03422] [ 4] SU2_CFD[0x60f4ce]
[headnode:03422] [ 5] SU2_CFD[0x5aa7a0]
[headnode:03422] [ 9] SU2_CFD[0x472c29]
[headnode:03421] [10] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2ad619305555]
[headnode:03421] [11] SU2_CFD[0x494f87]
[headnode:03421] *** End of error message ***
[10] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2aeafe0b1555]
[headnode:03427] [11] SU2_CFD[0x494f87]
[headnode:03427] *** End of error message ***
SU2_CFD[0x60f4ce]
[headnode:03426] [ 5] SU2_CFD[0x5aa7a0]
[headnode:03426] [ 6] SU2_CFD[0x5ac166]
[headnode:03426] [ 7] SU2_CFD[0x4fbf02]
[headnode:03426] [ 8] SU2_CFD[0x4fc86a]
[headnode:03426] [ 9] SU2_CFD[0x472c29]
[headnode:03426] [10] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b8ffe7c0555]
[headnode:03426] [11] SU2_CFD[0x494f87]
[headnode:03426] *** End of error message ***
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b064318f555]
[headnode:03425] [11] SU2_CFD[0x494f87]
[headnode:03425] *** End of error message ***
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2ac7bd428555]
[headnode:03423] [11] SU2_CFD[0x494f87]
[headnode:03423] *** End of error message ***
[headnode:03420] [ 5] SU2_CFD[0x5aa7a0]
[headnode:03420] [ 6] SU2_CFD[0x5ac166]
[headnode:03420] [ 7] SU2_CFD[0x4fbf02]
[headnode:03420] [ 8] SU2_CFD[0x4fc86a]
[headnode:03420] [ 9] SU2_CFD[0x472c29]
[headnode:03420] [10] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2aafebf29555]
[headnode:03420] [11] SU2_CFD[0x494f87]
[headnode:03420] *** End of error message ***
SU2_CFD[0x5aa7a0]
[headnode:03424] [ 6] SU2_CFD[0x5ac166]
[headnode:03424] [ 7] SU2_CFD[0x4fbf02]
[headnode:03424] [ 8] SU2_CFD[0x4fc86a]
[headnode:03424] [ 9] SU2_CFD[0x472c29]
[headnode:03424] [10] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2ac4f7bd9555]
[headnode:03424] [11] SU2_CFD[0x494f87]
[headnode:03424] *** End of error message ***
[ 6] SU2_CFD[0x5ac166]
[headnode:03422] [ 7] SU2_CFD[0x4fbf02]
[headnode:03422] [ 8] SU2_CFD[0x4fc86a]
[headnode:03422] [ 9] SU2_CFD[0x472c29]
[headnode:03422] [10] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b7058d46555]
[headnode:03422] [11] SU2_CFD[0x494f87]
[headnode:03422] *** 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.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 6 with PID 0 on node headnode exited on signal
11 (Segmentation fault).
--------------------------------------------------------------------------
