I am using 24 processors and it is same for all steps. this is the command in use:
---------------- tpbconv_mpi -f run.trr -s run.tpr -e run.edr -extend 1000 -o ext_11 nohup /opt/ScaleMP/mpich2/1.0.8/bin/mpirun -machinefile $PBS_NODEFILE -np 24 /opt/gromacs4/bin/mdrun_mpi -v -deffnm ext_11 -------------------------------------------------------------- similar for next steps. regards anupam > On 18/08/11, Anupam Nath Jha <anu...@mbu.iisc.ernet.in> wrote: > >> >> >> Dear all >> >> I am running a MD (Gromacs - 4.5.3) in VSMP cluster with 24nodes. >> >> I am writing log files for different ns (1-10) in different files i.e. >> different >> files for each nano second . The performance goes like following: >> >> -------------------------- >> for 1st ns: >> >> (Mnbf/s) (GFlops) (ns/day) (hour/ns) >> Performance: 1444.719 85.902 3.946 6.082 >> Finished mdrun on node 0 Tue Aug 16 21:46:02 2011 >> >> at 2nd ns: >> >> (Mnbf/s) (GFlops) (ns/day) (hour/ns) >> Performance: 560.393 33.322 1.531 15.679 >> Finished mdrun on node 0 Wed Aug 17 13:27:38 2011 >> ------------------ >> >> and in case of 3rd ns: >> it didn't complete the all steps and went in next. >> >> Is it the problem with the gromacs? >> > > > Probably not. Assuming you have kept everything else constant, it is likely > that > other activity on the machine or file system is delaying you somehow. However, > in the absence of much basic information (like how many processors you are > trying to use) we can't suppose much. Copying and pasting command lines is > useful. > > Mark > > -- > This message has been scanned for viruses and > dangerous content by MailScanner, and is > believed to be clean. > > -- > 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 -- Science is facts; just as houses are made of stone, so is science is made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science. Anupam Nath Jha Saraswathi Vishveshwara Lab Molecular Biophysics Unit IISc,Bangalore-560012 Karnataka Ph. no.-22932611 -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- 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
