[gmx-users] running job parallel

[Bharati Singh]

Hi Team,

Thanks for your reply.

I had tried following method to install gromacs-4.0.7 -

$ module load intel_all/impi/default

$ ./configure --enable-mpi --with-fft=fftw2
LDFLAGS="-L/sfs1/lib/sfftw-2.1.5/lib/"
CPPFLAGS="-I/sfs1/lib/sfftw-2.1.5/include" LIBS="-lsfftw" F77=mpif77
--prefix=/sfs3/home/bharati/gromacs

$ make
$ make install

Following the command to submit the job in queue:

bsub -q normal4c -n 4 mpirun -srun /sfs3/home/bharati/gromacs/bin/mdrun -pd
-v -s Ag6A12_equil.tpr -o Ag6A12_equil.trr -c Ag6A12_equil.gro -e
Ag6A12_equil.edr -g Ag6A12_equil.log


When I submit the job for more than one processors in queue, it gets
terminated immediately without error. It is not creating any file etc..

Thanks & Regards,

On Tue, May 3, 2011 at 2:40 PM, Saikat Banerjee <banskt.saikat at gmail.com>wrote:

> Hi,
>
> Have you checked the error log? Please post the error log.
>
> Have you configured GROMACS using --enable-mpi?
>
> Thanks,
> Saikat
>
> On Tue, May 3, 2011 at 2:35 PM, Bharati Singh <bharati0307 at gmail.com>wrote:
>
>> Hi Team,
>>
>> I have LSF in my cluster ,I have installed gromacs-4.0.7 on Sampige. It is
>> working fine as a serial(on 1 processor) ,when I submit the job for more
>> than one processors in queue, it gets terminated immediately.Can you suggest
>> me something about it, please
>>
>> Thanks & Regards,
>>
>> --
>> Bharati Singh
>> System Administrator
>> Centre for Computational Materials Science(CCMS)
>> Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR),
>> Bangalore - 560 064
>> India.
>> mob.   : 08970898515
>> Phone : +91 80 2208 2944   + Ext. 26 & 28
>> Fax     : +91 80 2208 2906
>> Email  : bharati_singh at jncasr.ac.in <amit at jncasr.ac.in>
>>
>>
>> http://www.jncasr.ac.in/ccms
>> http://www.jncasr.ac.in/
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
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>
>
>
> --
> -------------------------------------------------------------------
> Saikat Banerjee
> Integrated Ph.D student
> Prof B. Bagchi's group
> Room no. 210
> Solid State and Structural Chemistry Unit (SSCU)
> Indian Institute of Science
> Bangalore-560012
>
>   Ph: +91-80-22933305 (lab)
>       +91-80-23602338 (lab)
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>
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>       banskt at yahoo.co.in
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>
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-- 
Bharati Singh
System Administrator
Centre for Computational Materials Science(CCMS)
Jawaharlal Nehru Centre for Advanced Scientific Research(JNCASR),
Bangalore - 560 064
India.
mob.   : 08970898515
Phone : +91 80 2208 2944   + Ext. 26 & 28
Fax     : +91 80 2208 2906
Email  : bharati_singh at jncasr.ac.in <amit at jncasr.ac.in>


http://www.jncasr.ac.in/ccms
http://www.jncasr.ac.in/
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