[gmx-users] running job parallel

[Bharati Singh]

 Mentioned method is working in another user's home directory on same
machine, then I dont think the problem with linking.



On Tue, May 3, 2011 at 3:34 PM, Mark Abraham <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>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/
>>>
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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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>
>
>
> --
> 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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-- 
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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