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.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/
-- 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
