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 <[email protected] <mailto:[email protected]>> 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. MarkThanks & Regards, On Tue, May 3, 2011 at 2:40 PM, Saikat Banerjee <[email protected] <mailto:[email protected]>> 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 <[email protected] <mailto:[email protected]>> 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 SinghSystem 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 : [email protected] <mailto:[email protected]> http://www.jncasr.ac.in/ccms http://www.jncasr.ac.in/ -- gmx-users mailing list [email protected] <mailto:[email protected]> 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 [email protected] <mailto:[email protected]>. 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: [email protected] <mailto:[email protected]> [email protected] <mailto:[email protected]> ------------------------------------------------------------------- -- gmx-users mailing list [email protected] <mailto:[email protected]> 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 [email protected] <mailto:[email protected]>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- Bharati SinghSystem 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 : [email protected] <mailto:[email protected]> http://www.jncasr.ac.in/ccms http://www.jncasr.ac.in/-- gmx-users mailing list [email protected] <mailto:[email protected]> 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 [email protected] <mailto:[email protected]>. 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 : [email protected] <mailto:[email protected]> http://www.jncasr.ac.in/ccms http://www.jncasr.ac.in/
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