relax on Beagle2

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Setting up relax on Beagle2

See

  1. http://thread.gmane.org/gmane.science.nmr.relax.user/1821
  2. http://beagle.ci.uchicago.edu/using-beagle/
We got the modelfree analysis running on the Cray computer with a bunch of help from the staff there. 
We basically called in the correct versions of python, scipy, numpy and mpi4py and also implemented a virtual environment to run the relax program in. 
We believe that the virtualenv is necessary because of the architecture of the Cray, and might not be needed for a small cluster. 
 
Below is the commands we used to do this, and the submission script that we have to use for our queue. The specific paths to the modules will be spcific to your system, of course.
 
We run the local_tm script first, then sphere, prolate, oblate and ellipsoid in parallel. 
When they are done, we run the final script. As long as the data, the script and the submission instructions are all in the same directory, we haven't had any problems. 
 
Installation
#loaded version of python and libraries we want to use:
 
module load python/2.7.3
export PATH=/soft/python/2.7/2.7.3/python/bin/:$PATH
export LD_LIBRARY_PATH=/soft/python/2.7/2.7.3/python/lib:$LD_LIBRARY_PATH
export PYTHONPATH=${PYTHONPATH}:/soft/python/2.7/2.7.3/modules/numpy/1.7.0/lib/python2.7/site-packages
export PYTHONPATH=${PYTHONPATH}:/soft/python/2.7/2.7.3/modules/scipy/0.12.0/lib/python2.7/site-packages
export PYTHONPATH=${PYTHONPATH}:/soft/python/2.7/2.7.3/modules/mpi4py/1.3/lib/python2.7/site-packages
 
#install virtualenv
 
wget https://pypi.python.org/packages/source/v/virtualenv/virtualenv-12.1.1.tar.gz#md5=901ecbf302f5de9fdb31d843290b7217
tar -xvf virtualenv-12.1.1.tar.gz
cd virtualenv-12.1.1
python virtualenv.py myVE
virtualenv ENV
 
#inside virtualenv dir I installed relax
 
wget http://download.gna.org/relax/relax-3.3.8.src.tar.bz2
tar xvjf relax-3.3.8.src.tar.bz2
cd relax-3.3.8
python -m compileall .
 
#after that was completed
export LD_LIBRARY_PATH=/lustre/beagle2/ams/python_ins/virtualenv-12.1.1/relax-3.3.8/lib:$LD_LIBRARY_PATH
 
Submission script
#Aftert that I tried to run it on compute nodes via PBS script:
 
#!/bin/bash
#PBS -N test
#PBS -q batch
#PBS -l walltime=00:30:00
#PBS -l mppwidth=64
#PBS -j oe
 
. /opt/modules/default/init/bash
module swap PrgEnv-cray PrgEnv-gnu
module load python/2.7.3
export PATH=/soft/python/2.7/2.7.3/python/bin/:$PATH
export PYTHONPATH=${PYTHONPATH}:/soft/python/2.7/2.7.3/modules/numpy/1.7.0/lib/python2.7/site-packages
export PYTHONPATH=${PYTHONPATH}:/soft/python/2.7/2.7.3/modules/scipy/0.12.0/lib/python2.7/site-packages
export PYTHONPATH=${PYTHONPATH}:/soft/python/2.7/2.7.3/modules/mpi4py/1.3/lib/python2.7/site-packages
export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/lustre/beagle2/ams/python_ins/virtualenv-12.1.1/relax-3.3.8/lib
 
cd $PBS_O_WORKDIR
 
aprun -n 2 python /lustre/beagle2/ams/python_ins/virtualenv-12.1.1/relax-3.3.8/relax --multi='mpi4py' --tee log.localtm /lustre/beagle2/ams/python_ins/SR1_localtm.py

See also