On 04/05/11, Bharati Singh <bharati0...@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.abra...@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.abromea...@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.sai...@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 <bharati0...@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_si...@jncasr.ac.in > > > > > > > <a...@jncasr.ac.in> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > http://www.jncasr.ac.in/ccms > > > > > > > > > > > > > > http://www.jncasr.ac.in/ > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > > > gmx-users mailing list > > > > > > > gmx-users@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-requ...@gromacs.org. > > > > > > > > > > > > > > Can't post? Read > > > > > > > http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > ------------------------------------------------------------------- > > > > > > > > > > > > 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: > > > > > > > > > > > > sai...@sscu.iisc.ernet.in > > > > > > > > > > > > ban...@yahoo.co.in > > > > > > > > > > > > ------------------------------------------------------------------- > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > > > > > gmx-users mailing list > > > > > > gmx-users@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-requ...@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_si...@jncasr.ac.in > > > > > <a...@jncasr.ac.in> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > http://www.jncasr.ac.in/ccms > > > > > > > > > > http://www.jncasr.ac.in/ > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > > > > > gmx-users mailing list gmx-users@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-requ...@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_si...@jncasr.ac.in <a...@jncasr.ac.in> > > > > > > > > > > > > > > > > > > http://www.jncasr.ac.in/ccms > > > > > > http://www.jncasr.ac.in/ > > > > > > > > > > > > > > > > > > > > > > > > > > -- > > > > gmx-users mailing list gmx-users@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-requ...@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_si...@jncasr.ac.in <a...@jncasr.ac.in> > > > http://www.jncasr.ac.in/ccms > > http://www.jncasr.ac.in/ > > >
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