[gmx-users] running job parallel
Mark Abraham
Mark.Abraham at anu.edu.au
Tue May 3 15:29:07 CEST 2011
On 3/05/2011 8:19 PM, Bharati Singh wrote:
> Mentioned method is working in another user's home directory on same
> machine, then I dont think the problem with linking.
Please be specific... I can think of three different things you might
mean by the "mentioned method", and when you've not troubled to address
the specific points I've raised, I'm not going to be troubled to guess
what you do mean :-)
Mark
> On Tue, May 3, 2011 at 3:34 PM, Mark Abraham
> <Mark.Abromeaham at anu.edu.au <mailto:Mark.Abromeaham at anu.edu.au>> wrote:
>
> 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)
>> +91-80-23602338 (lab)
>> +91-9980228606 (mobile)
>>
>> Alternate e-mail:
>> saikat at sscu.iisc.ernet.in <mailto:saikat at sscu.iisc.ernet.in>
>> banskt at yahoo.co.in <mailto:banskt at yahoo.co.in>
>> -------------------------------------------------------------------
>>
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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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>
>
>
>
> --
> 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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