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Subject: Re: [OMPI users] problem with .bashrc stetting of openmpi
From: sunita_at_[hidden]
Date: 2010-08-16 02:14:55


Hi,

> sunita_at_[hidden] wrote:
>> Dear Open-mpi users,
>>
>> I installed openmpi-1.4.1 in my user area and then set the path for
>> openmpi in the .bashrc file as follow. However, am still getting
>> following
>> error message whenever am starting the parallel molecular dynamics
>> simulation using GROMACS. So every time am starting the MD job, I need
>> to
>> source the .bashrc file again.
>>
>> Earlier in some other machine I did the same thing and was not getting
>> any
>> problem.
>>
>> Could you guys suggest what would be the problem?
>>
>>
> Have you set OPAL_PREFIX to /home/sunitap/soft/openmpi?
How to set OPAL_PREFIX?
During the installation of openmpi, I ran configure with
--prefix=/home/sunitap/soft/openmpi
Did you mean this?
>
> If you do a ldd on mdrun_mpi does libmpi.so.0 come up not found?

I got libmpi.so.0 not found. The output I got is
=========
ldd `which mdrun_mpi`
        libxml2.so.2 => /usr/lib64/libxml2.so.2 (0x00000039e1800000)
        libnsl.so.1 => /lib64/libnsl.so.1 (0x00000039dd600000)
        libm.so.6 => /lib64/libm.so.6 (0x00000039d5e00000)
        libSM.so.6 => /usr/lib64/libSM.so.6 (0x00000039d9600000)
        libICE.so.6 => /usr/lib64/libICE.so.6 (0x00000039da600000)
        libX11.so.6 => /usr/lib64/libX11.so.6 (0x00000039d7200000)
        libmpi.so.0 => not found
        libopen-rte.so.0 => not found
        libopen-pal.so.0 => not found
        libdl.so.2 => /lib64/libdl.so.2 (0x00000039d6200000)
        libutil.so.1 => /lib64/libutil.so.1 (0x00000039e4a00000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00000039d6600000)
        libc.so.6 => /lib64/libc.so.6 (0x00000039d5a00000)
        libz.so.1 => /usr/lib64/libz.so.1 (0x00000039d6a00000)
        libXau.so.6 => /usr/lib64/libXau.so.6 (0x00000039d6e00000)
        libXdmcp.so.6 => /usr/lib64/libXdmcp.so.6 (0x00000039d7600000)
        /lib64/ld-linux-x86-64.so.2 (0x00000039d5600000)
=========
> If so and there truly is a libmpi.so.0 in /home/sunitap/soft/openmpi/lib
> you may want to make sure the bitness of libmpi.so.0 and mdrun_mpi are
> the same by
> doing a file command on both.
>
----------------------------
The file command on both gives following output.
file ~/soft/gromacs/bin/mdrun_mpi
/home/sunitap/soft/gromacs/bin/mdrun_mpi: ELF 64-bit LSB executable, AMD
x86-64, version 1 (SYSV), for GNU/Linux 2.6.9, dynamically linked (uses
shared libs), for GNU/Linux 2.6.9, not stripped

file /home/sunitap/soft/openmpi/lib/libmpi.so.0
/home/sunitap/soft/openmpi/lib/libmpi.so.0: symbolic link to
`libmpi.so.0.0.1'
----------------------------

Thanks.
Sunita
> --td
>> ============.bashrc============
>> #path for openmpi
>> export PATH=$PATH:/home/sunitap/soft/openmpi/bin
>> export CFLAGS="-I/home/sunitap/soft/openmpi/include"
>> export LDFLAGS="-L/home/sunitap/soft/openmpi/lib"
>> export LD_LIBRARY_PATH=/home/sunitap/soft/openmpi/lib:$LD_LIBRARY_PATH
>>
>> ============== error message ==============
>> mdrun_mpi: error while loading shared libraries: libmpi.so.0: cannot
>> open
>> shared object file: No such file or directory
>>
>> ============================================
>>
>> Thanks for any help.
>> Best regards,
>> Sunita
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>
>
> --
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> Developer Tools Engineering | +1.650.633.7054
> Oracle * - Performance Technologies*
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