Romio is imported from a not update mpich. Could you give the latest mpich a try ?
That will be helpful to figure out whether this bug has already been fixed. Cheers, Gilles Nicolas Joly <nj...@pasteur.fr> wrote: >On Fri, Jun 17, 2016 at 10:15:28AM +0200, Vincent Huber wrote: >> Dear Mr. Joly, >> >> >> I have tried your code on my MacBook Pro (cf. infra for details) to detail >> that behavior. > >Thanks for testing. > >> Looking at openmpi-1.10.3/ompi/mca/io/romio/romio/adio/comon/ad_fstype.c to >> get the list of file system I can test, I have tried the following: >> >> mpirun -np 2 ./sample ufs:data.txt > >Works. > >> mpirun -np 2 ./sample nfs:data.txt > >Crash with SIGSEGV in ADIOI_NFS_ReadStrided() > >Made a quick and dirty test by replacing ADIOI_NFS_ReadStrided by >ADIOI_GEN_ReadStrided() in ADIO_NFS_operations structure >(ad_nfs/ad_nfs.c) ... and this fixed the problem. > >> mpirun -np 2 ./sample pfs:data.txt >> mpirun -np 2 ./sample piofs:data.txt >> mpirun -np 2 ./sample panfs:data.txt >> mpirun -np 2 ./sample hfs:data.txt >> mpirun -np 2 ./sample xfs:data.txt >> mpirun -np 2 ./sample sfs:data.txt >> mpirun -np 2 ./sample pvfs:data.txt >> mpirun -np 2 ./sample zoidfs:data.txt >> mpirun -np 2 ./sample ftp:data.txt >> mpirun -np 2 ./sample lustre:data.txt >> mpirun -np 2 ./sample bgl:data.txt >> mpirun -np 2 ./sample bglockless:data.txt > >I don't have access to this filesystems ... The tool fails when >trying to open the file, that's the corresponding assert that fire. > >> mpirun -np 2 ./sample testfs:data.txt > >This one crash with SIGSEGV but in ADIOI_Flatten(). > >I also tried with ompio and it seems to work. > >mpirun --mca io ompio -np 2 ./sample data.txt >rank0 ... 000000000022222222224444444444 >rank1 ... 111111111133333333335555555555 > >> The only one to not crash is ufs. >> That is not the answer you are looking for but my two cents? > >Thanks. > >> gcc --version >> Configured with: >> --prefix=/Applications/Xcode.app/Contents/Developer/usr >> --with-gxx-include-dir=/usr/include/c++/4.2.1 >> Apple LLVM version 7.0.0 (clang-700.0.72) >> Target: x86_64-apple-darwin15.5.0 >> Thread model: posix >> >> >> et >> >> >> mpirun --version >> mpirun (Open MPI) 1.10.2 >> >> >> ? >> >> >> 2016-06-14 17:42 GMT+02:00 Nicolas Joly <nj...@pasteur.fr>: >> >> >> > >> > Hi, >> > >> > At work, i do have some mpi codes that make use of custom datatypes to >> > call MPI_File_read with MPI_BOTTOM ... It mostly works, except when >> > the underlying filesystem is NFS where if crash with SIGSEGV. >> > >> > The attached sample (code + data) works just fine with 1.10.1 on my >> > NetBSD/amd64 workstation using the UFS romio backend, but crash if >> > switched to NFS : >> > >> > njoly@issan [~]> mpirun --version >> > mpirun (Open MPI) 1.10.1 >> > njoly@issan [~]> mpicc -g -Wall -o sample sample.c >> > njoly@issan [~]> mpirun -n 2 ./sample ufs:data.txt >> > rank1 ... 111111111133333333335555555555 >> > rank0 ... 000000000022222222224444444444 >> > njoly@issan [~]> mpirun -n 2 ./sample nfs:data.txt >> > [issan:20563] *** Process received signal *** >> > [issan:08879] *** Process received signal *** >> > [issan:20563] Signal: Segmentation fault (11) >> > [issan:20563] Signal code: Address not mapped (1) >> > [issan:20563] Failing at address: 0xffffffffb1309240 >> > [issan:08879] Signal: Segmentation fault (11) >> > [issan:08879] Signal code: Address not mapped (1) >> > [issan:08879] Failing at address: 0xffffffff881b0420 >> > [issan:08879] [ 0] [issan:20563] [ 0] 0x7dafb14a52b0 >> > <__sigtramp_siginfo_2> at /usr/lib/libc.so.12 >> > [issan:20563] *** End of error message *** >> > 0x78b9886a52b0 <__sigtramp_siginfo_2> at /usr/lib/libc.so.12 >> > [issan:08879] *** End of error message *** >> > -------------------------------------------------------------------------- >> > mpirun noticed that process rank 0 with PID 20563 on node issan exited on >> > signal 11 (Segmentation fault). >> > -------------------------------------------------------------------------- >> > njoly@issan [~]> gdb sample sample.core >> > GNU gdb (GDB) 7.10.1 >> > [...] >> > Core was generated by `sample'. >> > Program terminated with signal SIGSEGV, Segmentation fault. >> > #0 0x000078b98871971f in memcpy () from /usr/lib/libc.so.12 >> > [Current thread is 1 (LWP 1)] >> > (gdb) bt >> > #0 0x000078b98871971f in memcpy () from /usr/lib/libc.so.12 >> > #1 0x000078b974010edf in ADIOI_NFS_ReadStrided () from >> > /usr/pkg/lib/openmpi/mca_io_romio.so >> > #2 0x000078b97400bacf in MPIOI_File_read () from >> > /usr/pkg/lib/openmpi/mca_io_romio.so >> > #3 0x000078b97400bc72 in mca_io_romio_dist_MPI_File_read () from >> > /usr/pkg/lib/openmpi/mca_io_romio.so >> > #4 0x000078b988e72b38 in PMPI_File_read () from /usr/pkg/lib/libmpi.so.12 >> > #5 0x00000000004013a4 in main (argc=2, argv=0x7f7fff7b0f00) at sample.c:63 >> > >> > Thanks. >> > >> > -- >> > Nicolas Joly >> > >> > Cluster & Computing Group >> > Biology IT Center >> > Institut Pasteur, Paris. >> > >> > _______________________________________________ >> > users mailing list >> > us...@open-mpi.org >> > Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users >> > Link to this post: >> > http://www.open-mpi.org/community/lists/users/2016/06/29434.php >> > >> >> >> >> >> >> >> -- >> Docteur Ingénieur de recherche >> CeMoSiS <http://www.cemosis.fr> - vincent.hu...@cemosis.fr >> Tel: +33 (0)3 68 8*5 02 06* >> IRMA - 7, rue René Descartes >> 67 000 Strasbourg > >> _______________________________________________ >> users mailing list >> us...@open-mpi.org >> Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users >> Link to this post: >> http://www.open-mpi.org/community/lists/users/2016/06/29476.php > >-- >Nicolas Joly > >Cluster & Computing Group >Biology IT Center >Institut Pasteur, Paris. >_______________________________________________ >users mailing list >us...@open-mpi.org >Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users >Link to this post: >http://www.open-mpi.org/community/lists/users/2016/06/29477.php
