AMBER Archive (2008)

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

From: Thérèse Malliavin (terez_at_pasteur.fr)
Date: Tue Dec 16 2008 - 06:57:05 CST

Hi Ross,

Thank you for your mail. Finally, I tried to use AMBER 10 in place of
AMBER 9, and pmemd runs without any problem. Now, I have another naive
question. I already realized that pmemd runs significantly faster than
sander even on 4 processors. But, if I compare the results obtained
by sander and pmemd starting from the same system, as for example the
total energy, the two runs seem not to be so much correlated. So, I would
like to know whether we have to expect that pmemd or sander should produce
the same numbers if the runs start from the same system. The
differences observed come probably from a different architecture of the
two programs, could you please tell me little bit more about that?

Thank you for your help,

Best regards,

Therese

On Mon, 15 Dec 2008, Ross Walker wrote:

> 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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