if [[ $NERSC_HOST == "carver" ]]
then
module unload python
module load python/2.7.3
module load numpy
module load scipy
module unload pgi
module load gcc
module load tmux
module swap openmpi openmpi-gcc/1.6
module unload R
module load R-tig/2.15.1
module load git
export DYLD_LIBRARY_PATH=$HOME/me/env/lib/:$DYLD_LIBRARY_PATH
export LD_LIBRARY_PATH=$HOME/me/env/lib/:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/usr/common/tig/R/2.15.1/lib64/R/lib/:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$HOME/me/Library/soplex-1.6.0/lib/:$LD_LIBRARY_PATH
fi
http://www.virtualenv.org/en/latest/virtualenv.html#usage
virtualenv env
source env/bin/activate
First install gmp
wget https://ftp.gnu.org/gnu/gmp/gmp-6.0.0a.tar.xz
tar -xf gmp-6.0.0a.tar.xz
cd gmp-6.0.0a
./configure --prefix="/global/homes/z/zking1/env"
make
make check
http://www.gnu.org/software/glpk/
Try version 4.39 for pyglpk 0.3
You'll have to do something like this, to get it in the right directory:
./configure --prefix="/global/homes/z/zking1/env" --with-gmp
make
make install
pip install cobra
pip install glpk
pip install biopython
Start with a virtualenv
virtualenv env --prompt="me> "
source env/bin/activate
install glpk
pip install git+https://github.com/SBRG/cobrapy_internal.git
pip install biopython psycopg2 glpk
# pip install numpy scipy
Install sympy 0.7.1 (newer versions were causing problems)
pip install https://github.com/sympy/sympy/archive/sympy-0.7.1.tar.gz
- TODO: Try the new SymPy, and benchmark it against other options (e.g. eval)