Hi, You should really use fftw, it's *much* faster! (Btw: fftpack comes with Gromacs.)
I'm not sure what versions of Gromacs are available through the RHEL packages, but as installing from source is not very difficult (especially for a sysadmin) you might be better of with getting a fresh installation. You can find the instructions here: http://www.gromacs.org/Downloads/Installation_Instructions Cheers, -- Szilárd On Wed, May 18, 2011 at 10:24 PM, ram bio <[email protected]> wrote: > 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 > -- 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
