AMBER Archive (2008)

Subject: RE: AMBER: AMBER Parallel test error

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon May 05 2008 - 14:42:09 CDT

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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