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pythonanacondapbsqsub

Running qsub with anaconda environment

I have a program that usually runs inside a conda environmet in Linux, because I use it to manage my libraries, with this instructions:

source activate my_environment
python hello_world.py

How can I run hello_world.py in a high computer that works with PBS. Instructions explains to run adapting the code script.sh, shown below, and calling with the instruction qsub.

# script.sh
#!/bin/sh
#PBS -S /bin/sh
#PBS -N job_example
#PBS -l select=24
#PBS -j oe
cd $PBS_O_WORKDIR
mpiexec ./programa_mpi

How do I run hello_world.py with qsub using my anaconda environment?

Solution

  • You'll need to load the Python module before activating your environment and before running your script. 

    module load python3

cd $PBS_O_WORKDIR
source activate my_environment

mpiexec python hello_world.py

    Check the documentation for your institution regarding their Python modules. At my institution, Anaconda was the environment module for Python3, so you could load it as I have shown.