[gmx-users] running job parallel
Mark Abraham
mark.abraham at anu.edu.au
Wed May 4 06:48:55 CEST 2011
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
> > > > > > >
> > > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > > > > >
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> > > > > > >
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> > > > > >
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> > > > > >
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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
> > > > > >
> > > > > > -------------------------------------------------------------------
> > > > > >
> > > > > >
> > > > > >
> > > > > > --
> > > > > >
> > > > > > gmx-users mailing list gmx-users at gromacs.org
> > > > > >
> > > > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > > > >
> > > > > > Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
> > > > > > before posting!
> > > > > >
> > > > > > Please don't post (un)subscribe requests to the
> > > > > > list. Use the
> > > > > >
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> > > > > >
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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 <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
> > > >
> > > > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > > >
> > > > Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search
> > > > before posting!
> > > >
> > > > Please don't post (un)subscribe requests to the list. Use the
> > > >
> > > > www interface or send it to gmx-users-request at gromacs.org.
> > > >
> > > > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > >
> > > --
> > >
> > > 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
> >
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> >
> > Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >
> > Please don't post (un)subscribe requests to the list. Use the
> >
> > www interface or send it to gmx-users-request at gromacs.org.
> >
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
>
>
>
>
> --
> 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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