TODO: this page needs to be filled out in more detail.

For some other hints, check scripts on the Friesner website.

Queue system

Intel compilers


Recent versions of python

This piggybacks on a local install that Richard has made, and might only be accessible from the Reichman group.

Add this to your bashrc:

if [ ${UNAME_N:0:4} = 'iris' ] ; then
    # 64-bit setup (use python2.6)
    export LD_LIBRARY_PATH=/home/Reichman/darst/loc/lib/:/usr/local/intel-mkl-10.1/lib/em64t/
    # this is where scipy/numpy are
    export PYTHONPATH=/home/Reichman/darst/pymod2.6/
    # 32-bit setup
    export LD_LIBRARY_PATH=/home/Reichman/darst/loc/lib/:/usr/local/Intel_v6/mkl/8.0/lib/32/

PATH = "$PATH:/home/Reichman/darst/loc/bin/"

When you are logged into iris*, use python2.6, *not* python to run things. python directly is the default Red Hat outdated python version. (python2.6 is compiled for 64 bit systems)

When you are logged into aqfctl, use python2.5 to run things, not python. (python2.5 is compiled for 32 bit systems)






Old queue system (obsolete, just for historical purposes)

First you will need to adjust your .bash_profile in your home directory, adding:

export LSF_BINDIR=/usr/local/lsf/bin/
export LSF_ENVDIR=/usr/local/lsf/conf
export LSF_LIBDIR=/usr/local/lsf/lib/
export LSF_SERVERDIR=/usr/local/lsf/etc
export XLSF_UIDDIR=/usr/local/lsf/lib/uid
export MANPATH=/usr/share/man::/root/bin:/usr/local/lsf/5.0/man:/usr/local/lsf/5.0/man:/usr/local/pgi5.0/linux86/5.0/man

Also, if you use gsl you should add the following line:

export LD_LIBRARY_PATH=/usr/local/reichman/lib/:/usr/local/Intel_v6/mkl/8.0/lib/32/

Now you can submit jobs with:

bsub -q Reichman -o output.txt -J run019  python2.5 ../
# -q Reichman is the queue name, should always be the same
# -o is the job output filename (optional, I forget the default is)
# -J is the job name (optional, appears in the queue listing)
# everything after it is the commands that are run, with the current environment 
#     variables, in the current directory, on some node, non-interactively

list your jobs:


list all Reichman queue jobs:

bjobs -u all -q Reichman

CUChem/Environment (last edited 2010-02-12 16:14:01 by RichardDarst)