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

[Manik Mayur]

comments inline..

2010/8/14 Mark Abraham <mark.abraham at anu.edu.au>:
> Did you build a parallel GROMACS? If so, how? Do MPI test programs run?

I used the following command..

./configure --enable-mpi --disable-nice --with-fft=fftw3 --program-suffix=_mpi
make mdrun
make install-mdrun

and yes, mpi test programs are running fine.

further, $mdrun_mpi just results in a blinking cursor at newline
(earlier it displayed an array of info strings)

> Mark

-Manik

>
> ----- 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
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> 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 gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> --
> gmx-users mailing list    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>