[Pkg-openmpi-maintainers] Bug#592326: Bug#592326: Failure of AZTEC test case run.

Wed Sep 1 13:50:42 UTC 2010

Hi Rachel,

I'm not very familiar with Fortran, so I'm most likely of not too much
help here. I added Jeff to CC, maybe he can shed some lights into this.

Am Montag, den 09.08.2010, 12:59 +0300 schrieb Rachel Gordon:
> package:  openmpi
> 
> dpkg --search openmpi
> gromacs-openmpi: /usr/share/doc/gromacs-openmpi/copyright
> gromacs-dev: /usr/lib/libmd_mpi_openmpi.la
> gromacs-dev: /usr/lib/libgmx_mpi_d_openmpi.la
> gromacs-openmpi: /usr/share/lintian/overrides/gromacs-openmpi
> gromacs-openmpi: /usr/lib/libmd_mpi_openmpi.so.5
> gromacs-openmpi: /usr/lib/libmd_mpi_d_openmpi.so.5.0.0
> gromacs-dev: /usr/lib/libmd_mpi_openmpi.so
> gromacs-dev: /usr/lib/libgmx_mpi_d_openmpi.so
> gromacs-openmpi: /usr/lib/libmd_mpi_openmpi.so.5.0.0
> gromacs-openmpi: /usr/bin/mdrun_mpi_d.openmpi
> gromacs-openmpi: /usr/lib/libgmx_mpi_d_openmpi.so.5.0.0
> gromacs-openmpi: /usr/share/doc/gromacs-openmpi/README.Debian
> gromacs-dev: /usr/lib/libgmx_mpi_d_openmpi.a
> gromacs-openmpi: /usr/bin/mdrun_mpi.openmpi
> gromacs-openmpi: /usr/share/doc/gromacs-openmpi/changelog.Debian.gz
> gromacs-dev: /usr/lib/libmd_mpi_d_openmpi.la
> gromacs-openmpi: /usr/share/man/man1/mdrun_mpi_d.openmpi.1.gz
> gromacs-dev: /usr/lib/libgmx_mpi_openmpi.a
> gromacs-openmpi: /usr/lib/libgmx_mpi_openmpi.so.5.0.0
> gromacs-dev: /usr/lib/libmd_mpi_d_openmpi.so
> gromacs-openmpi: /usr/lib/libmd_mpi_d_openmpi.so.5
> gromacs-dev: /usr/lib/libgmx_mpi_openmpi.la
> gromacs-openmpi: /usr/share/man/man1/mdrun_mpi.openmpi.1.gz
> gromacs-openmpi: /usr/share/doc/gromacs-openmpi
> gromacs-dev: /usr/lib/libmd_mpi_openmpi.a
> gromacs-dev: /usr/lib/libgmx_mpi_openmpi.so
> gromacs-openmpi: /usr/lib/libgmx_mpi_openmpi.so.5
> gromacs-openmpi: /usr/lib/libgmx_mpi_d_openmpi.so.5
> gromacs-dev: /usr/lib/libmd_mpi_d_openmpi.a
> 
> 
> Dear support,
> I am trying to run a test case of AZTEC library named 
> az_tutorial_with_MPI.f . The example uses gfortran + MPI. The
> compilation and linkage stage goes O.K., generating an executable 
> 'sample'. But when I try to run sample (on 1 or more
> processors) the run crushes immediately.
> 
> The compilation and linkage stage is done as follows:
> 
> gfortran -O  -I/shared/include -I/shared/include/openmpi/ompi/mpi/cxx 
> -I../lib -DMAX_MEM_SIZE=16731136
> -DCOMM_BUFF_SIZE=200000 -DMAX_CHUNK_SIZE=200000  -c -o 
> az_tutorial_with_MPI.o az_tutorial_with_MPI.f
> gfortran az_tutorial_with_MPI.o -O -L../lib -laztec  -lm -L/shared/lib 
> -lgfortran -lmpi -lmpi_f77 -o sample

Generally, when compiling programs for use with MPI, you should use the
compiler wrappers which do all the magic. In Debian's case this is
mpif77.openmpi and mpi90.openmpi, respectively. Could you give that a
try?

> The run:
> /shared/home/gordon/Aztec_lib.dir/app>mpirun -np 1 sample
> 
> [cluster:12046] *** Process received signal ***
> [cluster:12046] Signal: Segmentation fault (11)
> [cluster:12046] Signal code: Address not mapped (1)
> [cluster:12046] Failing at address: 0x100000098
> [cluster:12046] [ 0] /lib/libc.so.6 [0x7fd4a2fa8f60]
> [cluster:12046] [ 1] /shared/lib/libmpi.so.0(MPI_Comm_size+0x6e) 
> [0x7fd4a376c34e]
> [cluster:12046] [ 2] sample [0x4178aa]
> [cluster:12046] [ 3] sample [0x402a07]
> [cluster:12046] [ 4] sample [0x402175]
> [cluster:12046] [ 5] sample [0x401c52]
> [cluster:12046] [ 6] sample [0x448edc]
> [cluster:12046] [ 7] /lib/libc.so.6(__libc_start_main+0xe6) 
> [0x7fd4a2f951a6]
> [cluster:12046] [ 8] sample [0x401a49]
> [cluster:12046] *** End of error message ***
> --------------------------------------------------------------------------
> mpirun noticed that process rank 0 with PID 12046 on node cluster exited 
> on signal 11 (Segmentation fault).
> 
> Here is some information about the machine:
> 
> uname -a
> Linux cluster 2.6.26-2-amd64 #1 SMP Sun Jun 20 20:16:30 UTC 2010 x86_64 
> GNU/Linux
> 
> 
> lsb_release -a
> No LSB modules are available.
> Distributor ID: Debian
> Description:    Debian GNU/Linux 5.0.5 (lenny)
> Release:        5.0.5
> Codename:       lenny
> 
> gcc --version
> gcc (Debian 4.3.2-1.1) 4.3.2
> 
> gfortran --version
> GNU Fortran (Debian 4.3.2-1.1) 4.3.2
> 
> ldd sample
>          linux-vdso.so.1 =>  (0x00007fffffffe000)
>          libgfortran.so.3 => /usr/lib/libgfortran.so.3 (0x00007fd29db16000)
>          libm.so.6 => /lib/libm.so.6 (0x00007fd29d893000)
>          libmpi.so.0 => /shared/lib/libmpi.so.0 (0x00007fd29d5e7000)
>          libmpi_f77.so.0 => /shared/lib/libmpi_f77.so.0 
> (0x00007fd29d3af000)
>          libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007fd29d198000)
>          libc.so.6 => /lib/libc.so.6 (0x00007fd29ce45000)
>          libopen-rte.so.0 => /shared/lib/libopen-rte.so.0 
> (0x00007fd29cbf8000)
>          libopen-pal.so.0 => /shared/lib/libopen-pal.so.0 
> (0x00007fd29c9a2000)
>          libdl.so.2 => /lib/libdl.so.2 (0x00007fd29c79e000)
>          libnsl.so.1 => /lib/libnsl.so.1 (0x00007fd29c586000)
>          libutil.so.1 => /lib/libutil.so.1 (0x00007fd29c383000)
>          libpthread.so.0 => /lib/libpthread.so.0 (0x00007fd29c167000)
>          /lib64/ld-linux-x86-64.so.2 (0x00007fd29ddf1000)
> 
> 
> Let me just mention that the C+MPI test case of the AZTEC library 
> 'az_tutorial.c' runs with no problem.
> Also, az_tutorial_with_MPI.f runs O.K. on my 32bit LINUX cluster running 
> gcc,g77 and MPICH, and on my SGI 16 processors
> Ithanium 64 bit machine.

The IA64 architecture is supported by Open MPI, so this should be OK.

> Thank you for your help,

Best regards,
Manuel