AMBER Archive (2008)

Subject: Re: AMBER: AMBER Parallel test error

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Thu May 08 2008 - 04:10:49 CDT

Dear amber user,

Can I ask you about how to install OpenMPI or MPICH for the lasted version?
Yes, as I know just use ./configure and then make. But in this
sander parallel I use the older version of OpenMPI 1.0.2 where contains the
Make file but for the lasted version they don't give a Make file just only
Make.in and Make.as. May be I don't know or misunderstanding about MPI
installation. So, some help for newbies unix users like me would be
appreciated.

Jitrayut
,

2008/5/7, sudipta sinha <sudipta.mml_at_gmail.com>:
>
> 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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