Thank you Mark, for your valuable suggestion. Regards, Bharati
On Wed, May 4, 2011 at 10:18 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > > > 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/ > > > -- > 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
