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Subject: Re: [OMPI users] openMPI shared with NFS, but says different version
From: Cristobal Navarro (axischire_at_[hidden])
Date: 2010-07-27 19:11:32


i compiled with absolute path in case:
fcluster_at_agua:~$ /opt/openmpi-1.4.2/bin/mpicc testMPI/hello.c -o
testMPI/hola
fcluster_at_agua:~$ mpirun --hostfile myhostfile -np 5 testMPI/hola
[agua:03547] mca: base: component_find: unable to open
/opt/openmpi-1.4.2/lib/openmpi/mca_btl_ofud: perhaps a missing symbol, or
compiled for a different version of Open MPI? (ignored)
[agua:03547] mca: base: component_find: unable to open
/opt/openmpi-1.4.2/lib/openmpi/mca_btl_openib: perhaps a missing symbol, or
compiled for a different version of Open MPI? (ignored)
[agua:03548] mca: base: component_find: unable to open
/opt/openmpi-1.4.2/lib/openmpi/mca_btl_ofud: perhaps a missing symbol, or
compiled for a different version of Open MPI? (ignored)
[agua:03548] mca: base: component_find: unable to open
/opt/openmpi-1.4.2/lib/openmpi/mca_btl_openib: perhaps a missing symbol, or
compiled for a different version of Open MPI? (ignored)
[agua:03549] mca: base: component_find: unable to open
/opt/openmpi-1.4.2/lib/openmpi/mca_btl_ofud: perhaps a missing symbol, or
compiled for a different version of Open MPI? (ignored)
[agua:03549] mca: base: component_find: unable to open
/opt/openmpi-1.4.2/lib/openmpi/mca_btl_openib: perhaps a missing symbol, or
compiled for a different version of Open MPI? (ignored)
[agua:03550] mca: base: component_find: unable to open
/opt/openmpi-1.4.2/lib/openmpi/mca_btl_ofud: perhaps a missing symbol, or
compiled for a different version of Open MPI? (ignored)
[agua:03550] mca: base: component_find: unable to open
/opt/openmpi-1.4.2/lib/openmpi/mca_btl_openib: perhaps a missing symbol, or
compiled for a different version of Open MPI? (ignored)
[agua:03551] mca: base: component_find: unable to open
/opt/openmpi-1.4.2/lib/openmpi/mca_btl_ofud: perhaps a missing symbol, or
compiled for a different version of Open MPI? (ignored)
[agua:03551] mca: base: component_find: unable to open
/opt/openmpi-1.4.2/lib/openmpi/mca_btl_openib: perhaps a missing symbol, or
compiled for a different version of Open MPI? (ignored)
--------------------------------------------------------------------------
mpirun noticed that process rank 4 with PID 3551 on node agua exited on
signal 11 (Segmentation fault).
--------------------------------------------------------------------------

and it segfaulted. the machine stoped and threw many errors on its screen,
cannot copy them because they didnt show in ssh.

On Tue, Jul 27, 2010 at 7:07 PM, Cristobal Navarro <axischire_at_[hidden]>wrote:

> Thanks Gus,
>
> but i already had the paths
>
> fcluster_at_agua:~$ echo $PATH
>
> /opt/openmpi-1.4.2/bin:/opt/cfc/sge/bin/lx24-amd64:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
> fcluster_at_agua:~$ echo $LD_LIBRARY_PATH
> /opt/openmpi-1.4.2/lib:
> fcluster_at_agua:~$
>
> even weird, errors come sometimes from the master node (agua)
>
>
> On Tue, Jul 27, 2010 at 6:59 PM, Gus Correa <gus_at_[hidden]> wrote:
>
>> Hi Cristobal
>>
>> Try using the --prefix option of mpiexec.
>> "man mpiexec" is your friend!
>>
>> Alternatively, append the OpenMPI directories to your
>> PATH *and* LD_LIBRARY_PATH on your .bashrc/.csrhc file
>> See this FAQ:
>> http://www.open-mpi.org/faq/?category=running#adding-ompi-to-path
>>
>> I hope it helps,
>> Gus Correa
>>
>> Cristobal Navarro wrote:
>>
>>> Hi,
>>> Even when executing a hello world openmpi, i get this error, which is
>>> then ignored.
>>> fcluster_at_fuego:~$ mpirun --hostfile myhostfile -np 5 testMPI/hola
>>> [agua:02357] mca: base: component_find: unable to open
>>> /opt/openmpi-1.4.2/lib/openmpi/mca_btl_ofud: perhaps a missing symbol, or
>>> compiled for a different version of Open MPI? (ignored)
>>> [agua:02354] mca: base: component_find: unable to open
>>> /opt/openmpi-1.4.2/lib/openmpi/mca_btl_ofud: perhaps a missing symbol, or
>>> compiled for a different version of Open MPI? (ignored)
>>> [agua:02356] mca: base: component_find: unable to open
>>> /opt/openmpi-1.4.2/lib/openmpi/mca_btl_ofud: perhaps a missing symbol, or
>>> compiled for a different version of Open MPI? (ignored)
>>> [agua:02358] mca: base: component_find: unable to open
>>> /opt/openmpi-1.4.2/lib/openmpi/mca_btl_ofud: perhaps a missing symbol, or
>>> compiled for a different version of Open MPI? (ignored)
>>> [agua:02355] mca: base: component_find: unable to open
>>> /opt/openmpi-1.4.2/lib/openmpi/mca_btl_ofud: perhaps a missing symbol, or
>>> compiled for a different version of Open MPI? (ignored)
>>> [agua:02358] mca: base: component_find: unable to open
>>> /opt/openmpi-1.4.2/lib/openmpi/mca_btl_openib: perhaps a missing symbol, or
>>> compiled for a different version of Open MPI? (ignored)
>>> [agua:02355] mca: base: component_find: unable to open
>>> /opt/openmpi-1.4.2/lib/openmpi/mca_btl_openib: perhaps a missing symbol, or
>>> compiled for a different version of Open MPI? (ignored)
>>> [agua:02354] mca: base: component_find: unable to open
>>> /opt/openmpi-1.4.2/lib/openmpi/mca_btl_openib: perhaps a missing symbol, or
>>> compiled for a different version of Open MPI? (ignored)
>>> [agua:02356] mca: base: component_find: unable to open
>>> /opt/openmpi-1.4.2/lib/openmpi/mca_btl_openib: perhaps a missing symbol, or
>>> compiled for a different version of Open MPI? (ignored)
>>> [agua:02357] mca: base: component_find: unable to open
>>> /opt/openmpi-1.4.2/lib/openmpi/mca_btl_openib: perhaps a missing symbol, or
>>> compiled for a different version of Open MPI? (ignored)
>>> Process 3 on agua out of 5
>>> Process 4 on agua out of 5
>>> Process 1 on agua out of 5
>>> Process 2 on agua out of 5
>>> Process 0 on agua out of 5
>>>
>>>
>>> /opt/openmpi-1.4.2/ is shared through NFS.
>>>
>>> master node did had an older openmpi version before installing 1.4.2, but
>>> i removed them all with
>>> sudo apt-get --purge remove libopenmpi1 libopenmpi-dev openmpi-bin
>>> openmpi-dev openmpi-common
>>> i checked for /usr/lib64/openmpi and for /usr/lib/openmpi and
>>> deleted them.
>>>
>>> however, when compiling again i keep getting this error,
>>> something must be remaining from the older version of openmpi, but i
>>> really dont know where that remaining could be.
>>> any help, welcome
>>>
>>>
>>> ------------------------------------------------------------------------
>>>
>>> _______________________________________________
>>> users mailing list
>>> users_at_[hidden]
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>
>>
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