[gmx-users] running job parallel

Bharati Singh bharati0307 at gmail.com
Wed May 4 06:56:40 CEST 2011 

Thank you Mark, for your valuable suggestion.

Regards,
Bharati


On Wed, May 4, 2011 at 10:18 AM, Mark Abraham <mark.abraham at anu.edu.au>wrote:

>
>
> On 04/05/11, *Bharati Singh * <bharati0307 at gmail.com> wrote:
>
> Hi Mark,
>
> Sorry for your inconvenience
> As you said some kind of (dynamic) linking problem, Is it possible to
> resolve it?
>
>
> Yes, but you will need someone who can troubleshoot what has and has not
> worked on your system. We do not have any relevant knowledge, so can't help.
> Using configure --disable-shared might help.
>
> Mark
>
>
> 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/
>>>>>
>>>>>  --
>>>>> 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)
>>>>       +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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>



-- 
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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