AMBER Archive (2008)

Subject: Re: AMBER: AMBER Parallel test error

From: sudipta sinha (sudipta.mml_at_gmail.com)
Date: Wed May 07 2008 - 11:09:28 CDT

Have u tried the run from an user account?

regards
sudipta

On Tue, May 6, 2008 at 7:08 PM, jitrayut jitonnom <jitrayut.018_at_gmail.com>
wrote:

> Dear Ross.
>
> I am sorry for the early reply. I have checked it again but it 's still
> found the problem but not the localhost problem any more. Here is the error
> i found when i uses make test.parallel
>
> [root_at_chemoinfo test]# make test.parallel
> export TESTsander=/usr/local/src/amber9/exe/sander.MPI; make
> test.sander.BASIC
> make[1]: Entering directory `/usr/local/src/amber9/test'
> cd dmp; ./Run.dmp
> /usr/local/src/amber9/exe/sander.MPI: error while loading shared
> libraries: liborte.so.0: cannot open shared object file: No such file or
> directory
> ./Run.dmp: Program error
> make[1]: *** [test.sander.BASIC] Error 1
> make[1]: Leaving directory `/usr/local/src/amber9/test'
> make: *** [test.sander.BASIC.MPI] Error 2
>
> To solve with this problem is difficult for me since I am new for unix
> installation and I need some learning. So, if anyone can give me some advice
> in practical way. It would help me very much.
>
> Thanks.
>
> Jitrayut
>
>
> 2008/5/6, jitrayut jitonnom <jitrayut.018_at_gmail.com>:
>
> > Dear Ross Walker,
> >
> > Thank you for you suggestion. As you mention, I forgot to add the line
> > 127.0.0.1 localhost at /etc/host so that why i got error. Besides, when
> > i try sander.MPI it show a missing library file liborte.so.0 as follow:
> >
> > sander.MPI: error while loading shared libraries: liborte.so.0: cannot
> > open shared object file: No such file or directory
> >
> > how can I remove this error ?
> >
> > Thanks.
> >
> > Jitrayut
> >
> >
> > 2008/5/6, Ross Walker <ross_at_rosswalker.co.uk>:
> > >
> > > Hi Jitrayut,
> > >
> > >
> > >
> > > This is a problem with your MPI implementation. You should check the
> > > documentation for the version of MPI you are using. If someone manages your
> > > machine or queuing system then check with them to see what specific
> > > requirements there are for running parallel jobs on your system.
> > >
> > >
> > >
> > > You should also try some of the simple mpi examples that came with the
> > > mpi implementation you are using since if you can't get these to run there
> > > will be no chance of getting amber to run in parallel.
> > >
> > >
> > >
> > > Note from the error message you may need to check that the line:
> > >
> > >
> > >
> > > 127.0.0.1 localhost.localdomain localhost
> > >
> > >
> > >
> > > Exists in /etc/hosts
> > >
> > >
> > >
> > > Although you should also carefully check the mpi documentation to make
> > > sure there is nothing else you need to add.
> > >
> > >
> > >
> > > Good luck,
> > >
> > > Ross
> > >
> > >
> > >
> > > *From:* owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] *On
> > > Behalf Of *jitrayut jitonnom
> > > *Sent:* Monday, May 05, 2008 11:38 AM
> > > *To:* amber_at_scripps.edu
> > > *Subject:* AMBER: AMBER Parallel test error
> > >
> > >
> > >
> > > Dear Amber users,
> > >
> > >
> > >
> > > I can't complete the parallel test with the command and errors belows,
> > > So, what is my problem and how to solve this problem ?
> > >
> > >
> > >
> > >
> > > [root_at_chemoinfo test]# make test.parallel
> > > export TESTsander=/usr/local/src/amber9/exe/sander.MPI; make
> > > test.sander.BASIC
> > > make[1]: Entering directory `/usr/local/src/amber9/test'
> > > cd dmp; ./Run.dmp
> > > This test not set up for parallel
> > > cannot run in parallel with #residues < #pes
> > > cd adenine; ./Run.adenine
> > > This test not set up for parallel
> > > cannot run in parallel with #residues < #pes
> > > ==============================================================
> > > cd cytosine; ./Run.cytosine
> > > ssh: localhost: Name or service not known
> > > [chemoinfo.science.cmu.ac.th:13300] ERROR: A daemon on node localhost
> > > failed to start as expected.
> > > [chemoinfo.science.cmu.ac.th:13300] ERROR: There may be more
> > > information available from
> > > [chemoinfo.science.cmu.ac.th:13300] ERROR: the remote shell (see
> > > above).
> > > [chemoinfo.science.cmu.ac.th:13300] ERROR: The daemon exited
> > > unexpectedly with status 255.
> > > ./Run.cytosine: Program error
> > > make[1]: *** [test.sander.BASIC] Error 1
> > >
> > >
> > > Jitrayut
> > >
> >
> >
>

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