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

[Mark Abraham]

----- Original Message -----
From: Manik Mayur <manik.mayur at gmail.com>
Date: Monday, August 16, 2010 3:02
Subject: Re: [gmx-users] Parallel mdrun not working on gentoo linux
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

> 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)

That's weird. Sounds like a dynamic linking error. Is there another version of MPI installed? (Get rid of it.) Try enforcing static linking.

Or, try these http://gentoo-portage.com/sci-chemistry/gromacs

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
> >> --
> >> 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
> >
> -- 
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100816/74aab802/attachment.html>