Re: amber-developers: latest tarballs for AmberTools and Amber10

From: Scott Brozell <>
Date: Tue, 1 Apr 2008 08:54:12 -0800 (PST)


On Mon, 31 Mar 2008, David A. Case wrote:

> On Mon, Mar 31, 2008, Lachele Foley wrote:
> >
> > We put our common-area executables in a directory that is not writable by
> > the compute nodes. This is important to us since we're likely to have
> > homemade programs running about, and wish to minimize unintended overwrites.
> > So... while $AMBERHOME is visible to all the nodes, any test that requires a
> > node writing to $AMBERHOME/anything will fail for us, and the diff will be
> > against an empty file. Programs that merely send output to the scheduler
> > will work.
> Why not just make a link between your (local) AMBERHOME/exe and the
> common-area executables directory? Then you could write to $AMBERHOME, yet
> still run jobs from the common area.
> Just a thought...might not work. But the tests are run in the amber10/test
> tree, and it's not easy to imagine how this can very easily be made into a
> read-only location.
Probably Lachele has Amber installed on a non-compute server that
very few can access and that mounts the device on which Amber resides
as writable. This is the situation at OSC, and it does complicate testing
especially since Amber has become bloated. Alternatively others have
different but related issues: Amber contains a testing
suite that is soo long it overruns an interactive cpu time limit
and a suite that requires a variety of parallel footprints, which may
only be available from a batch job, for thorough testing.

The simple solution for these situations is to tar the Amber tree,
untar it on local scratch disk, and test it there from a batch job:

Here is one from Amber 8; it will need updating for Amber 10.
See also amber10/test/nightly_test.

#PBS -S /bin/csh
set echo
set verbose
#setenv AMBERHOME /usr/local/amber/amber8
module load amber9
gtar zcf $TMPDIR/a8.tar test exe dat src/config.h
gtar zxf a8.tar
chmod -R u+rwx *
pbsdcp -r $TMPDIR/* $TMPDIR
#ls -lR
cd $AMBERHOME/test
setenv DO_PARALLEL "mpiexec -verbose"
setenv DO_PARALLEL "mpiexec "
#setenv TESTsander ../../exe/sander
make clean
#setenv TESTsander $AMBERHOME/exe/sander
#make test.sander
make test.parallel
make check
make clean
#setenv TESTsanderLES $AMBERHOME/exe/sander.LES
make test.sander.LES
make check
make clean
#setenv TESTsander $AMBERHOME/exe/pmemd
make test.pmemd
make check

Received on Fri Apr 18 2008 - 21:15:54 PDT
Custom Search