[gmx-users] Parallel mdrun not working on gentoo linux

[Mark Abraham]

Did you build a parallel GROMACS? If so, how? Do MPI test programs run?

Mark

----- Original Message -----
From: Manik Mayur <manik.mayur at gmail.com>
Date: Saturday, August 14, 2010 15:14
Subject: [gmx-users] Parallel mdrun not working on gentoo linux
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> 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
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