AMBER Archive (2008)

Subject: RE: AMBER: launching a job works with sander.MPI and fail with pmemd.MPI

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Dec 15 2008 - 09:18:04 CST

Hi Therese,

First thing to check. PMEMD when built in parallel (which I assume you did)
is called pmemd, not pmemd.MPI. Hence you should be getting a file not found
error - which in parallel may be masking itself as a lamboot failure.

Also I would make sure you do the following to run cleanly in your script:

export AMBERHOME=/foo/bar/amber10
lamboot
mpirun -np 4 $AMBERHOME/exe/pmemd -O -i ...
lamhalt

Then you can nohup the entire script. You should probably make sure you kill
any existing lambood or lamd instances on your machine first though since
some will probably be left over from earlier runs. You should also make sure
that pmemd was built with the same version of lam as your mpirun refers to.
Makes sure you run the test cases:

export DO_PARALLEL='mpirun -np 4'
lamboot
cd $AMBERHOME/test/
make test.pmemd
lamhalt

Good luck,
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of Thérèse Malliavin
> Sent: Monday, December 15, 2008 6:42 AM
> To: amber_at_scripps.edu
> Cc: terez_at_pasteur.fr
> Subject: AMBER: launching a job works with sander.MPI and fail with
> pmemd.MPI
>
> Dear AMBER Netters,
>
> I have a question about the use of PMEMD. It is probably a trivial
> question, but, as I did not find an answer neither on the Web pages
> neither in the manuals, I am asking it to you.
>
> I am doing the parallel calculations with sander.MPI using a lamd deamon
> and the command nohup to launch the job, so I am doing:
>
> . /Bis/shared/centos-3_x86_64/etc/custom.d/amber9_intel8.1_lam-
> 7.1.2_intel-8.1.sh
> lamboot
>
> before starting the AMBER calculations. The typical command line for
> sander.MPI is then:
>
> mpirun -np 4 ${AMBERHOME}/exe/sander.MPI -O -i mdr1.in -o mdr1.out -inf
> mdr1.inf -x mdr1.crd -c eq7.rst -p prmtop -r mdr1.rst
>
> But, if I replace in the command line sander.MPI by pmemd.MPI:
>
> mpirun -np 4 ${AMBERHOME}/exe/pmemd.MPI -O -i mdr1.in -o mdr1.out -inf
> mdr1.inf -x mdr1.crd -c eq7.rst -p prmtop -r mdr1.rst
>
> I get an error saying that lamboot was not started.
>
> I am trying to do these calculation on an 64 bits 8-proc Linux machine,
> running under centos-3. The lam used is the version 7.1.2_intel-8.1.
>
> Also, I am only using features which should exist in PMEMD according to
> the AMBER manual.
>
> Do you have any idea what I could check or what to find information to fix
> this problem?
>
> Thank you in abvance for your help,
>
> Therese Malliavin
> Unite de Bioinformatique Structurale
> Institut Pasteur, Paris
> France
>
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