Thanks for your reply. I have also tried installing with _mpi suffix Here is the output of ldd:
gromacs3.3/bin$ ldd mdrun_mpi linux-vdso.so.1 => (0x00007fff4658c000) libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x00007f7d7afe9000) libfftw3f.so.3 => /usr/lib/libfftw3f.so.3 (0x00007f7d7ac76000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f7d7a9f3000) libmpich.so.3 => /usr/lib/libmpich.so.3 (0x00007f7d7a603000) libopa.so.1 => /usr/lib/libopa.so.1 (0x00007f7d7a402000) libmpl.so.1 => /usr/lib/libmpl.so.1 (0x00007f7d7a1fd000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f7d79ff5000) libcr.so.0 => /usr/lib/libcr.so.0 (0x00007f7d79deb000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f7d79bce000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f7d79847000) /lib64/ld-linux-x86-64.so.2 (0x00007f7d7b216000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f7d79642000) -------------------------------------------------------------------------------------------------------------------- gromacs3.3/bin$ ldd mdrun_mpi | grep mpi libmpich.so.3 => /usr/lib/libmpich.so.3 (0x00007fc78fb5c000) It seems that gromacs has been compiled with mpich. On Tue, Nov 20, 2012 at 4:15 AM, Justin Lemkul <[email protected]> wrote: > > > On 11/19/12 12:09 PM, Parisa Rahmani wrote: > >> Dear gmx users >> >> I have a problem with running parallel jobs on my Debian system(Openmpi >> installed on it), >> **Linux debian 3.2.0-1-amd64 #1 SMP , UTC 2012 x86_64 GNU/Linux** >> I am using gmx 3.3.3, because of the *lambda dynamics* method which is >> >> implemented in it. >> >> AS I know ,in gmx 3.x, the number of processors supplied for the >> subsequent >> mdrun needed to match the input file. but when i use **grompp -np 6 & >> mpirun -np 6 mdrun** the following error appears : >> >> ERROR : run input file md.tpr was made for 6 nodes, >> while mdrun expected it to be for 1 nodes. >> >> through search of mailing list i found similar problems, but non of >> the solutions worked for my case. >> >> wihtout -np option in grompp the error disappears, and then with each >> of these commands >> >> ** >> >> 1)mpirun -np 6 mdrun -deffnm md >> >> 2)mpirun -np 6 mdrun -deffnm md -N 6 >> >> 3)mpirun -np 6 mdrun -np 6 -deffnm md >> >> 4)mdrun -np 6 -s md -N 6 >> >> >> **it uses 6 processors(each one at nearly 100%), but the simulation >> time is the same as for 1 processor. >> >> I have no problem with parallel jobs on our cluster(gmx 3.3.3 & >> openmpi), with following command: >> >> ** >> grompp -np 6 -f ... >> mpiexec mdrun ...(number of processors is specified in the bash file) >> ** >> , >> but i can't run it on my 6 core system. >> >> Also, I have no problem with newer version of gmx (4.5.x), but i >> should use this version, and Hope someone can help me. >> >> > Have you properly compiled an MPI-enabled mdrun? The default executable > name should be mdrun_mpi. It should be linked against libmpi, so running > ldd on the mdrun executable should tell you. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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<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
