AMBER Archive (2008)

Subject: Re: AMBER: Optimal compiling of amber on XT3

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Oct 30 2008 - 05:22:35 CDT

if it's an xt4 like kraken, I also have configure scripts for sander
and ambertools.

On Thu, Oct 30, 2008 at 1:59 AM, Robert Duke <rduke_at_email.unc.edu> wrote:
> Note that the only xt3 I have used has catamount, and that is what the
> configure script options I gave are for. The xt4 was very different with
> compute node linux - I hand-developed a script for franklin at nersc for
> this which is probably the same thing that Ross has. The only info I have
> been able to find on sapphire indicates it is a catamount xt3, but ERDC was
> supposed to get an XT4 at some point in 2008. Should you actually have an
> xt4, either Ross' script or my old script from franklin would be best
> (please just request if you need it).
> Regards - Bob Duke
>
> ----- Original Message ----- From: "Ross Walker" <ross_at_rosswalker.co.uk>
> To: <amber_at_scripps.edu>
> Sent: Thursday, October 30, 2008 1:33 AM
> Subject: RE: AMBER: Optimal compiling of amber on XT3
>
>
>> Hi Patrick,
>>
>>> I'm trying to compile AMBER on a Cray XT3 at the ERDC MSRC
>>> (sapphire). What are the optimal settings for libraries, mpi/mpich/
>>> mpich2, compiler, etc. for AMBER? Am I right that the test programs
>>> in the configure script will not run on the login node?
>>
>> Most Cray's have their own custom MPI library and compiler script (ftn)
>> that
>> acts as a wrapper to the Portland Group compilers. See
>> http://ambermd.org/amber10.bench1.html for benchmarks on NICS Kraken (an
>> XT4) along with the config.h file I used for PMEMD. Note this should work
>> on
>> an XT3 if you are using compute node linux. If it is using Catamount then
>> you may need to tweak the configure script a bit depending on whether the
>> compiler wrapping script is different / the paths are different etc.
>>
>> To run the test cases you just submit a job to the main queue. E.g.
>>
>> ---------------------------------
>> #!/bin/csh
>> #PBS -A YOUR_ACCOUNT_NUMBER
>> #PBS -N run_pmemd_tests
>> #PBS -j oe
>> #PBS -l walltime=01:00:00,size=4
>> #PBS -M your_at_email.com
>>
>> cd /lustre/scratch/username/amber10/test/
>> date
>>
>> setenv AMBERHOME '/lustre/scratch/username/amber10/
>> setenv DO_PARALLEL 'aprun -n 4 -N4'
>>
>> make test.pmemd </dev/null
>>
>> ----------------------------------
>>
>> Then just qsub this and when it is done you should get the test output in
>> the log file corresponding to the job. Any possible failures you can check
>> by going into the test directories and looking for the .dif files.
>>
>> Good luck,
>> Ross
>>
>>
>> /\
>> \/
>> |\oss Walker
>>
>> | Assistant Research Professor |
>> | San Diego Supercomputer Center |
>> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
>> | http://www.rosswalker.co.uk | PGP Key available on request |
>>
>> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
>> be read every day, and should not be used for urgent or sensitive issues.
>>
>>
>>
>>
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>
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