[gmx-users] running job parallel

Wed May 4 06:39:39 CEST 2011

Hi Mark,

Sorry for your inconvenience
As you said some kind of (dynamic) linking problem, Is it possible to
resolve it?

Thanks & Regards,
Bharati

On Tue, May 3, 2011 at 6:59 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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>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)
>>>       +91-9980228606  (mobile)
>>>
>>>   Alternate e-mail:
>>>       saikat at sscu.iisc.ernet.in
>>>       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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-- 
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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