[gmx-users] more- mdrun on Beowulf cluster

[Yu Sun (Denis)]

Dear David,

Now everything is fine. I used all the "without--" in the configure.
Thank you

Yu

At 08:51 PM 1/12/04 +0100, you wrote:
>On Mon, 2004-01-12 at 21:27, Yu Sun (Denis) wrote:
> > I recompile and install the gromacs on my home directory. And type
> > mpprun -map 4 mdrun <options...>
> >
> > this time it gives error:
> >     error while loading shared libraries: libXm.so.1
> >
>Sorry about this...
>You need to add a configure flag
>--without-motif-libraries --without-motif-includes
>and maybe as well
>--without-x
>
> >
> > At 02:23 PM 1/12/04 -0500, you wrote:
> > >At 07:14 PM 1/12/04 +0100, you wrote:
> > >>On Mon, 2004-01-12 at 20:05, Yu Sun (Denis) wrote:
> > >> > Dear Gmx-usrs,
> > >> >
> > >> > We want to run mdrun  (sequential verison) job on the specific 
> node of our
> > >> > cluster.
> > >> > When I run mdrun as follows:
> > >> >
> > >> > mpprun -map 1 mdrun  <options ..>
> > >> >
> > >> > it gives me the following error msg:
> > >> >
> > >> >     error while loading shared libraries libmd.so.2
> > >> >     cannot open shared object file: No such file or directory
> > >> >
> > >> > But when I run directly without mpprun
> > >> > mdrun <options ...>
> > >> > There are no problems.
> > >>Is this also on the Beowulf node? Most likely your gromacs installation
> > >>is not NFS mounted in the cluster, or you should source GMXRC or you
> > >>should compile statically.
> > >
> > >This is on the cluster head node. I can know it  by using beostatus
> > >
> > >
> > >
> > >> >
> > >> > For other programs, I can use mpprun  to assign job to specific node
> > >> > without problem.
> > >> >
> > >> > Do you have any ideas?
> > >> >
> > >> > Thank you !
> > >> >
> > >> >
> > >> >
> > >> > Yu Sun  (Denis)
> > >> > Postdoc
> > >> > Department of Bioengineering
> > >> > Clemson, SC 29631
> > >> > Tel. (864)656-1352
> > >> > email: yus at clemson.edu
> > >> >
> > >> > _______________________________________________
> > >> > gmx-users mailing list
> > >> > gmx-users at gromacs.org
> > >> > http://www.gromacs.org/mailman/listinfo/gmx-users
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> > >>--
> > >>David.
> > >>________________________________________________________________________
> > >>David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> > >>Dept. of Cell and Molecular Biology, Uppsala University.
> > >>Husargatan 3, Box 596,          75124 Uppsala, Sweden
> > >>phone:  46 18 471 4205          fax: 46 18 511 755
> > >>spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > >>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > >>
> > >>_______________________________________________
> > >>gmx-users mailing list
> > >>gmx-users at gromacs.org
> > >>http://www.gromacs.org/mailman/listinfo/gmx-users
> > >>Please don't post (un)subscribe requests to the list. Use the
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> > >
> > >
> > >_______________________________________________
> > >gmx-users mailing list
> > >gmx-users at gromacs.org
> > >http://www.gromacs.org/mailman/listinfo/gmx-users
> > >Please don't post (un)subscribe requests to the list. Use the www
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> >
> >
> > _______________________________________________
> > gmx-users mailing list
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>--
>David.
>________________________________________________________________________
>David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596,          75124 Uppsala, Sweden
>phone:  46 18 471 4205          fax: 46 18 511 755
>spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
>_______________________________________________
>gmx-users mailing list
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