GWDG Cluster

The following instructions assume that you have a working version of Python v3.4 or higher installed in your $HOME directory. We strongly recommend using Miniconda for the Python installation.

1. (Optional) Uninstall mpi4py if you already have it installed.

source activate {envname}
pip uninstall mpi4py
conda remove mpi4py

2. Load the required modules.

module load intel/compiler/64/2017/17.0.2
module load intel/mkl/64/2017/2.174
module load openmpi/intel/64/1.10.7

3. Change to your python environment and install mpi4py. Make sure that it is installed after loading the above modules, so that mpi4py will be linked to openmpi and mkl.

source activate {envname}
conda install mpi4py

4. Install other required packages.

conda install numpy scipy sqlite
pip install pygtrie

5. Compile the C libraries.

cd lib
make clean
make -f Makefile.gwdg
cd ..

6. Update file path of TEJAAS executable in job submission file located in devtools/test.jobsub
7. Submit job

cd devtools
bsub < test.jobsub

8. (Optional) If you are using interactive node, you can run the job using different simulation parameters (--simparams fmin fmax nsnp ntrans cfrac)

EXPRFILE="/scratch/sbanerj/trans-eQTL/data/GTEx_wholeBlood_Normalzed_NoPEER_lmcorrected.txt"
mpirun -n 8 bin/tejaas --gx ${EXPRFILE} --method rr --null perm --simulate --simparams 0.1 0.9 1000 0 0.001