Did you build a parallel GROMACS? If so, how? Do MPI test programs run? Mark
----- Original Message ----- From: Manik Mayur <[email protected]> Date: Saturday, August 14, 2010 15:14 Subject: [gmx-users] Parallel mdrun not working on gentoo linux To: Discussion list for GROMACS users <[email protected]> > Hi All, > > I am trying to build gromacs-4.0.7 on my gentoo box. My non-parallel > version of mdrun is working without any issues but when I try to run > the parallel version of mdrun, it kind of hangs (even no help info). > Some details- > > 1) $uname -a > Linux bingo 2.6.34-gentoo-r1 #7 SMP Fri Aug 13 10:18:23 IST 2010 i686 > Intel(R) Core(TM)2 Quad CPU Q8200 @ 2.33GHz GenuineIntel GNU/Linux > > 2) openmpi -version : 1.4.1 (through emerge) > > 3) $ ldd /usr/local/bin/mdrun_mpi > linux-gate.so.1 => (0xb77f6000) > libmd_mpi.so.5 => /usr/local/gromacs/lib/libmd_mpi.so.5 (0xb76ee000) > libgmx_mpi.so.5 => /usr/local/gromacs/lib/libgmx_mpi.so.5 > (0xb7460000) libxml2.so.2 => /usr/lib/libxml2.so.2 (0xb7321000) > libz.so.1 => /lib/libz.so.1 (0xb730d000) > libnsl.so.1 => /lib/libnsl.so.1 (0xb72f5000) > libfftw3f.so.3 => /usr/lib/libfftw3f.so.3 (0xb71b2000) > libm.so.6 => /lib/libm.so.6 (0xb718d000) > libSM.so.6 => /usr/lib/libSM.so.6 (0xb7184000) > libuuid.so.1 => /lib/libuuid.so.1 (0xb717f000) > libICE.so.6 => /usr/lib/libICE.so.6 (0xb7166000) > libX11.so.6 => /usr/lib/libX11.so.6 (0xb7041000) > libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb7025000) > libXau.so.6 => /usr/lib/libXau.so.6 (0xb7021000) > libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0xb701b000) > libdl.so.2 => /lib/libdl.so.2 (0xb7017000) > libmpi.so.0 => /usr/lib/libmpi.so.0 (0xb6f84000) > libopen-rte.so.0 => /usr/lib/libopen-rte.so.0 (0xb6f3d000) > libopen-pal.so.0 => /usr/lib/libopen-pal.so.0 (0xb6ed2000) > libutil.so.1 => /lib/libutil.so.1 (0xb6ece000) > libpthread.so.0 => /lib/libpthread.so.0 (0xb6eb5000) > libc.so.6 => /lib/libc.so.6 (0xb6d6f000) > /lib/ld-linux.so.2 (0xb77f7000) > > Please somebody tell me what is the problem? > > Thanks, > > Manik Mayur > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
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