AMBER Archive (2008)

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

From: Ross Walker (
Date: Thu Oct 30 2008 - 00:33:35 CDT

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.

#PBS -N run_pmemd_tests
#PBS -j oe
#PBS -l walltime=01:00:00,size=4

cd /lustre/scratch/username/amber10/test/

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,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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