[gmx-users] running job parallel

[Mark Abraham]

On 3/05/2011 7:37 PM, Bharati Singh wrote:
> 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..

That set of commands should create mdrun_mpi. Why are you not using it?

If this mdrun really is the one produced by the above configuration, the 
symptoms suggest some kind of (dynamic) linking problem, but we have no 
way to be more specific. It's not GROMACS-related.

Mark

>
> Thanks & Regards,
>
> On Tue, May 3, 2011 at 2:40 PM, Saikat Banerjee 
> <banskt.saikat at gmail.com <mailto: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 <mailto: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 <mailto:amit at jncasr.ac.in>
>
>
>         http://www.jncasr.ac.in/ccms
>         http://www.jncasr.ac.in/
>
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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)
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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 <mailto:amit at jncasr.ac.in>
>
>
> http://www.jncasr.ac.in/ccms
> http://www.jncasr.ac.in/

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