Re: [OMPI users] problem with .bashrc stetting of openmpi

2010-08-16 Thread Eugene Loh




sun...@chem.iitb.ac.in wrote:

  
sun...@chem.iitb.ac.in 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.
  

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?
  

No.  The "OPAL_PREFIX" steps occurs after you configure, build, and
install OMPI.  At the time that you run MPI programs, set the
"OPAL_PREFIX" environment variable to /home/sunitap/soft/openmpi.  The
syntax depends on your shell.  E.g., for csh:

setenv OPAL_PREFIX /home/sunitap/soft/openmpi

The sequence might be something like this:

./configure --prefix=/home/sunitap/soft/openmpi
make
make install
cd /home/sunitap/soft/openmpi/examples
mpicc connectivity_c.c
setenv OPAL_PREFIX /home/sunitap/soft/openmpi
mpirun -n 2 ./connectivity_c

though I didn't check all those commands out.




Re: [OMPI users] problem with .bashrc stetting of openmpi

2010-08-16 Thread Addepalli, Srirangam V
Try 

env | grep LD_LIBRARY_PATH

Does it show /home/sunitap/soft/openmpi/lib in your library path.

I have a similar installation. This is how my LD_LIBRARY_PATH looks.

LD_LIBRARY_PATH=/lustre/work/apps/gromacs-testgar/lib:/lustre/work/apps/gromacs-mkl/lib:/lustre/work/apps/openmpi-testgar/lib:/opt/intel/Compiler/11.1/064/lib/intel64:/opt/intel/Compiler/11.1/064/mkl/lib/em64t:/opt/intel/Compiler/11.1/064/lib/intel64:/opt/intel/Compiler/11.1/064/mkl/lib/em64t:/opt/gridengine/lib/lx26-amd64

Rangam

From: users-boun...@open-mpi.org [users-boun...@open-mpi.org] On Behalf Of 
sun...@chem.iitb.ac.in [sun...@chem.iitb.ac.in]
Sent: Monday, August 16, 2010 1:24 AM
To: Open MPI Users
Subject: Re: [OMPI users] problem with .bashrc stetting of openmpi

> Hello Sunitha,
> If you have admin privileges on this system add library path to
>  /etc/ld.so.conf
I don't have admin privileges.
>
> eg: echo "/home/sunitap/soft/openmpi/lib" >> /etc/ld.so.conf
>
> ldconfig
>
> Rangam
> 
> From: users-boun...@open-mpi.org [users-boun...@open-mpi.org] On Behalf Of
> sun...@chem.iitb.ac.in [sun...@chem.iitb.ac.in]
> Sent: Monday, August 16, 2010 12:28 AM
> To: Open MPI Users
> Subject: Re: [OMPI users] problem with .bashrc stetting of openmpi
>
> Hi,
>
>> hello Sunita,
>>
>> what linux distribution is this?
> The linux distribution is Red Hat Enterprise Linux Server release 5.5
> (Tikanga)
>>
>> On Fri, Aug 13, 2010 at 1:57 AM, <sun...@chem.iitb.ac.in> wrote:
>>
> Thanks,
> Sunita
>
>>> 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?
>>>
>>> .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
>>> us...@open-mpi.org
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
> ___
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>


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Re: [OMPI users] problem with .bashrc stetting of openmpi

2010-08-16 Thread sunita
> Hello Sunitha,
> If you have admin privileges on this system add library path to
>  /etc/ld.so.conf
I don't have admin privileges.
>
> eg: echo "/home/sunitap/soft/openmpi/lib" >> /etc/ld.so.conf
>
> ldconfig
>
> Rangam
> 
> From: users-boun...@open-mpi.org [users-boun...@open-mpi.org] On Behalf Of
> sun...@chem.iitb.ac.in [sun...@chem.iitb.ac.in]
> Sent: Monday, August 16, 2010 12:28 AM
> To: Open MPI Users
> Subject: Re: [OMPI users] problem with .bashrc stetting of openmpi
>
> Hi,
>
>> hello Sunita,
>>
>> what linux distribution is this?
> The linux distribution is Red Hat Enterprise Linux Server release 5.5
> (Tikanga)
>>
>> On Fri, Aug 13, 2010 at 1:57 AM, <sun...@chem.iitb.ac.in> wrote:
>>
> Thanks,
> Sunita
>
>>> 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?
>>>
>>> .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
>>> us...@open-mpi.org
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
> ___
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>




Re: [OMPI users] problem with .bashrc stetting of openmpi

2010-08-16 Thread sunita
Hi,


> sun...@chem.iitb.ac.in 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 (0x0039e180)
libnsl.so.1 => /lib64/libnsl.so.1 (0x0039dd60)
libm.so.6 => /lib64/libm.so.6 (0x0039d5e0)
libSM.so.6 => /usr/lib64/libSM.so.6 (0x0039d960)
libICE.so.6 => /usr/lib64/libICE.so.6 (0x0039da60)
libX11.so.6 => /usr/lib64/libX11.so.6 (0x0039d720)
libmpi.so.0 => not found
libopen-rte.so.0 => not found
libopen-pal.so.0 => not found
libdl.so.2 => /lib64/libdl.so.2 (0x0039d620)
libutil.so.1 => /lib64/libutil.so.1 (0x0039e4a0)
libpthread.so.0 => /lib64/libpthread.so.0 (0x0039d660)
libc.so.6 => /lib64/libc.so.6 (0x0039d5a0)
libz.so.1 => /usr/lib64/libz.so.1 (0x0039d6a0)
libXau.so.6 => /usr/lib64/libXau.so.6 (0x0039d6e0)
libXdmcp.so.6 => /usr/lib64/libXdmcp.so.6 (0x0039d760)
/lib64/ld-linux-x86-64.so.2 (0x0039d560)
=
> 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
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>
>
> --
> Oracle
> Terry D. Dontje | Principal Software Engineer
> Developer Tools Engineering | +1.650.633.7054
> Oracle * - Performance Technologies*
> 95 Network Drive, Burlington, MA 01803
> Email terry.don...@oracle.com 
>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users




Re: [OMPI users] problem with .bashrc stetting of openmpi

2010-08-16 Thread Addepalli, Srirangam V
Hello Sunitha,
If you have admin privileges on this system add library path to
 /etc/ld.so.conf

eg: echo "/home/sunitap/soft/openmpi/lib" >> /etc/ld.so.conf

ldconfig

Rangam

From: users-boun...@open-mpi.org [users-boun...@open-mpi.org] On Behalf Of 
sun...@chem.iitb.ac.in [sun...@chem.iitb.ac.in]
Sent: Monday, August 16, 2010 12:28 AM
To: Open MPI Users
Subject: Re: [OMPI users] problem with .bashrc stetting of openmpi

Hi,

> hello Sunita,
>
> what linux distribution is this?
The linux distribution is Red Hat Enterprise Linux Server release 5.5
(Tikanga)
>
> On Fri, Aug 13, 2010 at 1:57 AM, <sun...@chem.iitb.ac.in> wrote:
>
Thanks,
Sunita

>> 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?
>>
>> .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
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users


___
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Re: [OMPI users] problem with .bashrc stetting of openmpi

2010-08-16 Thread Manik Mayur
Hi Sunita,

have you tried running "ldconfig"?

Manik Mayur




2010/8/16  :
> Hi,
>
>> hello Sunita,
>>
>> what linux distribution is this?
> The linux distribution is Red Hat Enterprise Linux Server release 5.5
> (Tikanga)
>>
>> On Fri, Aug 13, 2010 at 1:57 AM,  wrote:
>>
> Thanks,
> Sunita
>
>>> 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?
>>>
>>> .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
>>> us...@open-mpi.org
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>>
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>


Re: [OMPI users] problem with .bashrc stetting of openmpi

2010-08-16 Thread sunita
Hi,

> hello Sunita,
>
> what linux distribution is this?
The linux distribution is Red Hat Enterprise Linux Server release 5.5
(Tikanga)
>
> On Fri, Aug 13, 2010 at 1:57 AM,  wrote:
>
Thanks,
Sunita

>> 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?
>>
>> .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
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users




Re: [OMPI users] problem with .bashrc stetting of openmpi

2010-08-13 Thread Gus Correa

Hi Sunita

My guess is that you are picking a wrong mpiexec,
because of the way you set your PATH.
What do you get from "which mpiexec"?

Try *pre-pending" the OpenMPI path to the existing PATH,
instead of appending it (that's what you did with the LD_LIBRARY_PATH):

export PATH=/home/sunitap/soft/openmpi/bin:$PATH

My $0.02
Gus Correa
-
Gustavo Correa
Lamont-Doherty Earth Observatory - Columbia University
Palisades, NY, 10964-8000 - USA
-

sun...@chem.iitb.ac.in 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?

.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

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Re: [OMPI users] problem with .bashrc stetting of openmpi

2010-08-13 Thread Jeff Squyres
You might want to make sure that this .bashrc is both the same and is 
executated properly upon both interactive and non-interactive logins on all the 
systems that you are running on.


On Aug 13, 2010, at 1:57 AM, sun...@chem.iitb.ac.in 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?
> 
> .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
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users


-- 
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jsquy...@cisco.com
For corporate legal information go to:
http://www.cisco.com/web/about/doing_business/legal/cri/




Re: [OMPI users] problem with .bashrc stetting of openmpi

2010-08-13 Thread Terry Dontje

sun...@chem.iitb.ac.in 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?

If you do a ldd on mdrun_mpi does libmpi.so.0 come up not found?
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.

--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
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--
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Terry D. Dontje | Principal Software Engineer
Developer Tools Engineering | +1.650.633.7054
Oracle * - Performance Technologies*
95 Network Drive, Burlington, MA 01803
Email terry.don...@oracle.com 



Re: [OMPI users] problem with .bashrc stetting of openmpi

2010-08-13 Thread Cristobal Navarro
hello Sunita,

what linux distribution is this?

On Fri, Aug 13, 2010 at 1:57 AM,  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?
>
> .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
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>