AMBER Archive (2008)

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

From: Robert Duke (
Date: Thu Oct 30 2008 - 00:59:21 CDT

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" <>
To: <>
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
> 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 -N run_pmemd_tests
> #PBS -j oe
> #PBS -l walltime=01:00:00,size=4
> #PBS -M
> 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:- |
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