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

Manik Mayur manik.mayur at gmail.com
Sat Aug 14 07:13:16 CEST 2010

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?


Manik Mayur

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