Installing Chaste on Huygens

Support pages are at https://subtrac.sara.nl/userdoc/wiki/huygens

Grid access

If you do not have direct ssh access and are logging in using an e-Science certificate or equivalent then you will need to:

Get a Grid Certificate
Send the Distinguished Name (DN) of your certificate to your DEISA contact
Wait for the certificate details to propogate to other sites
Use a Grid-enabled tool such as gsissh to log in

gsissh-term

If you don't have gsissh installed then there is a Java webstart of gsissh-term available at http://www.grid.lrz-muenchen.de/res/globus/gsissh-term/applet/jws.jnlp

This is able to pull your credentials directly from your browser (which will need to be the one you requested the certificate from or has had the certificate exported too). You may also need to update the cryptography packages. Instructions are at http://www.grid.lrz-muenchen.de/de/mware/globus/client/gsissh_term.html#OtherAuthMeth

Once you have access then you can install an ssh key to allow ssh access

Environment

To set up your environment do:

. /home/hpx1wils/dependencies/profile

which on 09/12/2009 contained:

CHASTE_UTILS=/home/hpx1wils/dependencies
export CHASTE_UTILS
CHASTE_LIBS=$CHASTE_UTILS
export CHASTE_LIBS

PATH=${CHASTE_LIBS}/bin:${CHASTE_UTILS}/bin:$PATH
for util in scons ; do 
 PATH=${PATH}:$CHASTE_UTILS/$util/bin
done
export PATH

module load sara hdf5-mp petsc

module load lapack

After sourcing the profile your module environment should be:

module list

Currently Loaded Modulefiles:
 1) compilerwrappers/yes  5) c++/ibm/10.1          9) hdf5-mp/1.6.7        
 2) gcc/4.2.1             6) fortran/ibm/12.1     10) petsc/2.3.3/real     
 3) java/ibm/1.5          7) subversion/1.5.4     11) lapack/3.1.1         
 4) c/ibm/10.1            8) sara

Compilation

To build with the GNU compilers do:

scons build=GccPower

Interactive Use

You can run short, low processor count parallel jobs on the login node. Instructions are at https://subtrac.sara.nl/userdoc/wiki/huygens/usage/progavail/poe#UsingPOEinteractively

This is useful to run tests on the front-end when building Chaste.

Executable

A pre-built version of the executable is available at

/home/hpx1wils/dependencies/bin/Chaste

An example job script to run the executable can be found at

/home/hpx1wils/dependencies/runchaste.q

There are 101 nodes available for batch usage, each with 32 processors.