OpenMM Python Virtual Environment

This page documents the creation of a Python virtual environment (virtualenv) containing the OpenMM software on the Caviness HPC system¹⁾. It assumes that the user is adding the software to the workgroup storage.

Prepare to add software in the standard sub-directories of the workgroup storage:

[user@login01 ~]$ workgroup -g my_workgroup
[(my_workgroup:user)@login01 ~]$ mkdir --mode=2775 --parent ${WORKDIR}/sw/tensorflow
[(my_workgroup:user)@login01 ~]$ mkdir --mode=2775 --parent ${WORKDIR}/sw/valet

These commands create any missing directories. All directories created will have group-write and -inherit permissions.

The Intel Python distribution will form the basis for the Keras virtualenv, so add it to the environment:

[(my_workgroup:user)@login01 ~]$ vpkg_require intel-python/2020u2:python3
Adding package `intel-python/2020u2:python3` to your environment
(base) [(my_workgroup:user)@login01 ~]$

Notice the prompt changed: the text (base) now prefixes it, indicating the directory that contains the active Python virtualenv.

The conda search tensorflow command can be used to locate the specific version you wish to install. Two examples are shown: TensorFlow release at least 2.0 with GPU support; and an Intel-optimized version of TensorFlow 2.3.

(base) [frey@login00 ~]$ conda search 'tensorflow>=2.0=gpu*'
Loading channels: done
# Name                       Version           Build  Channel             
tensorflow                     2.0.0 gpu_py27hb041a2f_0  pkgs/main           
tensorflow                     2.0.0 gpu_py36h6b29c10_0  pkgs/main           
tensorflow                     2.0.0 gpu_py37h768510d_0  pkgs/main          
tensorflow                     2.1.0 gpu_py27h9cdf9a9_0  pkgs/main           
tensorflow                     2.1.0 gpu_py36h2e5cdaa_0  pkgs/main           
tensorflow                     2.1.0 gpu_py37h7a4bb67_0  pkgs/main           
tensorflow                     2.2.0 gpu_py36hf933387_0  pkgs/main           
tensorflow                     2.2.0 gpu_py37h1a511ff_0  pkgs/main           
tensorflow                     2.2.0 gpu_py38hb782248_0  pkgs/main 
 
(base) [frey@login00 ~]$ conda search 'tensorflow[version=2.3,channel=intel]'
Loading channels: done
# Name                       Version           Build  Channel             
tensorflow                     2.3.0          py36_0  intel               
tensorflow                     2.3.0          py37_0  intel               
tensorflow                     2.3.0          py38_0  intel 

All versions of the TensorFlow virtualenv will be stored in the common base directory, $WORKDIR/sw/tensorflow; each virtualenv must have a unique name that will become the VALET version of TensorFlow. In this tutorial, the latest version of TensorFlow (with GPU support) is version 2.2.0, but the newest non-GPU version available with Python 3.8 is 2.3.0. An appropriate version for the former would be 2.2.0:gpu and the latter 2.3.0:intel,python3.8. Those versions can be translated to VALET-friendly directory names:

[(my_workgroup:user)@login01 ~]$ vpkg_id2path --version-id=2.2.0:gpu
2.2.0-gpu
[(my_workgroup:user)@login01 ~]$ mkdir --mode=3750 ${WORKDIR}/sw/tensorflow/2.2.0-gpu
 
[(my_workgroup:user)@login01 ~]$ vpkg_id2path --version-id=2.3.0:intel,python3.8
2.3.0-intel-python3.8
[(my_workgroup:user)@login01 ~]$ mkdir --mode=3750 ${WORKDIR}/sw/tensorflow/2.3.0-intel-python3.8

The virtualenvs are created using the --prefix option to specify the directories created above:

(base) [(my_workgroup:user)@login01 ~]$ conda create --prefix=${WORKDIR}/sw/tensorflow/2.2.0-gpu 'tensorflow[version=2.2.0,build=gpu_py38hb782248_0]'
WARNING: A directory already exists at the target location '/work/it_nss/sw/tensorflow/2.2.0-gpu'
but it is not a conda environment.
Continue creating environment (y/[n])? y
 
   :
 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate /work/it_nss/sw/tensorflow/2.2.0-gpu
#
# To deactivate an active environment, use
#
#     $ conda deactivate

We're not going to activate that virtualenv – we will install the other one next:

(base) [(it_nss:frey)@login00 ~]$ conda create --prefix=${WORKDIR}/sw/tensorflow/2.3.0-intel-python3.8 'tensorflow[version=2.3.0,build=py38_0,channel=intel]'
WARNING: A directory already exists at the target location '/work/it_nss/sw/tensorflow/2.3.0-intel-python3.8'
but it is not a conda environment.
Continue creating environment (y/[n])? y
 
   :
 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate /work/it_nss/sw/tensorflow/2.3.0-intel-python3.8
#
# To deactivate an active environment, use
#
#     $ conda deactivate

Ignore that conda activate command as well. Rollback the intel-python environment changes before proceeding:

(base) [(my_workgroup:user)@login01 ~]$ vpkg_rollback
[(my_workgroup:user)@login01 ~]$ 

Notice the (base) has disappeared from the prompt, indicating that the baseline virtualenv has been deactivated.