Dear Justin, Thanks for the suggestion. Do we need to install FFTW libraries also while installing gromacs as I think FFT pack got installed as default when the gromacs is installed by the system admin using yum i.e. yum install gromacs.
yum install gromacs_openmpi / yum install gromacs_mpich2, because when i asked my system administrator he mentioned that he installed mpich2 version of gromacs, but when i tried to locate g_mdrun_mpich2, i could not find it in the path, instead i found g_mdrun_openmpi and so i tried to run the job with g_mdrun_openmpi, but could not run the job. So it is difficult now to figure out why I could not use g_mdrun_openmpi, even though the file exists in the path:/usr/lib64/openmpi/bin/g_mdrun_openmpi Ram On Wed, May 18, 2011 at 3:00 PM, Justin A. Lemkul <[email protected]> wrote: > > > ram bio wrote: >> >> Dear Gromacs Users, >> >> I am trying to run a gromacs mdrun job (pbs script) on the cluster >> (RHEL operating system) using the recently installed gromacs version >> 4.5.3, but i think i could not run it paralleled on the nodes, as it >> is taking a long time to finish the job. >> >> The information regarding the installed gromacs on the server is as >> follows: >> >> Scheduler: Moab/Torque >> Mpi Version: Mpich2 >> OS: RHEL 5.5 >> Compiler: gcc version 4.4 enterprise linux 5 >> FFT – FFT Pack >> >> I am running a batch job using the script as under: >> >> #PBS -S /bin/bash >> #PBS -N aarontest >> #PBS -o aaronout.txt >> #PBS -j oe >> #PBS -l nodes=2:ppn=4 >> #PBS -l walltime=336:00:00 >> >> #cat $PBS_NODEFILE >> NP=`wc -l < $PBS_NODEFILE` >> cd $PBS_O_WORKDIR >> #export MPI_GROUP_MAX=128 >> >> >> /usr/local/bin/mpirun -np 8 /usr/bin/g_mdrun -nt 8 -deffnm testnpt3ns >> -v dlb yes -rdd 1.2 >> >> Please let me know your suggestions for correcting the error. >> > > MPI and threading are mutually exclusive; you can't launch a multi-thread > process (mdrun -nt) via mpirun. The mdrun executable must be MPI-enabled to > run on this system. Perhaps the pre-compiled binary is not, in which case > you should install from source with --enable-mpi and --disable-threads. > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list [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]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list [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]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
