AMBER Archive (2008)

Subject: Re: AMBER: AMBER Parallel test error

From: jitrayut jitonnom (jitrayut.018_at_gmail.com)
Date: Tue May 06 2008 - 08:09:10 CDT

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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