.profile
source .bashrc
.bashrc :
export PATH=$HOME/bin:$PATH #gcc 4.7.2 module add gcc/4.7.2 export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib # Python 2.6.5 on /opt/gridware export PATH=/opt/gridware/python2.6.5/bin:$PATH export LD_LIBRARY_PATH=/opt/gridware/python2.6.5/lib/:$LD_LIBRARY_PATH
Thats it. The /opt/gridware python comes with nose, ipython, and numpy. However numpy is a little broken :
$ ipython $ import numpy $ numpy.test()
Assuming your codes are to be run on the dell cluster, add the following lines to your .bashrc file
#if feature=dell check still needs to be added export PYTHONPATH=~/local_dell/lib/python:~/local_dell/lib/python2.6/site-packages/ export PATH=$HOME/local_dell/bin:$PATH
create the required directories
$ mkdir -p $HOME/local_dell/lib/python2.6/site-packages/ $ mkdir -p $HOME/local_dell/bin
Use for tool for managing and install Python packages. Setuptool provides the easy_install command
$ cd tmp $ wget http://pypi.python.org/packages/source/s/setuptools/setuptools-0.6c11.tar.gz $ tar -xf setuptools-0.6c11.tar.gz $ cd setuptools-0.6c11 $ python setup.py install --prefix=$HOME/local_dell
From the login node (which has http access) simply
$ easy_install --prefix=$HOME/local_dell argparse
$ msub -I -l feature=dell $ cd ~/tmp $ ssh login01 wget http://tenet.dl.sourceforge.net/project/numpy/NumPy/1.6.2/numpy-1.6.2.tar.gz $ mv ../numpy-1.6.2.tar.gz ./ $ tar -xf numpy-1.6.2.tar.gz $ cd numpy-1.6.2 $ export ATLAS=None $ export BLAS=None $ export LAPACK=None $ python setup.py build --fcompiler=gnu95 $ python setup.py install --prefix=$HOME/local_dell
when testing you should get
$ ipython import numpy numpy.test() Ran 3568 tests in 11.266s OK (KNOWNFAIL=5, SKIP=1) Out[3]: <nose.result.TextTestResult run=3568 errors=0 failures=0>
$ msub -I -l feature=dell $ cd ~/tmp $ ssh login01 wget http://tenet.dl.sourceforge.net/project/scipy/scipy/0.10.1/scipy-0.10.1.tar.gz $ mv ../scipy-0.10.1.tar.gz ./ $ tar -xf scipy-0.10.1.tar.gz $ cd scipy-0.10.1/ $ python setup.py build --fcompiler=gnu95 #takes about 10 minutes to build $ python setup.py install --prefix=$HOME/local_dell
testing,
$ cd ~/ $ ipython import scipy scipy.__path__ scipy.test()
which did not work 100 % :(
FAILED (KNOWNFAIL=13, SKIP=41, failures=2) Out[2]: <nose.result.TextTestResult run=5101 errors=0 failures=1>
$ msub -I -l feature=dell $ cd ~/tmp $ ssh login01 wget http://ufpr.dl.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.2.0/matplotlib-1.2.0.tar.gz $ mv ../matplotlib-1.2.0.tar.gz ./ $ tar -xf matplotlib-1.2.0.tar.gz $ cd matplotlib-1.2.0 $ python setup.py install --prefix=$HOME/local_dell
Is already installed, all that is needed is to load the openmpi module; add the following line to .bashrc
module add openmpi-1.6.1-intel