qmflows 0.2.1

Tutorial and Examples

A tutorial written as a jupyter-notebook is available from: tutorial-qmflows. You can also access direclty more advanced examples.

Dependencies installation

Using the conda environment the following packages should be installed:

• install rdkit using the following command:

  • conda install -y -q --name qmflows -c https://conda.anaconda.org/rdkit rdkit

• install HDF5 using conda:

  • conda install -y -q --name qmflows -c anaconda h5py

Package installation

• Type in your terminal,

  source activate qmflows

• Then

  pip install qmflows --upgrade

Now you are ready to use qmflows.

Latest stable version

If you want to install the latest stable version directly from github you can use the following command:

pip install https://github.com/SCM-NV/qmflows/tarball/master#egg=qmflows

Notes:

• Once the libraries and the virtual environment are installed, you only need to type source activate qmflows each time that you want to use the software.

Remote/Xenon setup

Qmflows supports running jobs over a variety of cluster computing schedulers like Slurm and Torque. You program and run your workflows from your laptop, but the jobs are run at the remote site. For this to work you need to setup Qmflows both locally and remotely. In addition you need to add a Bash script that loads the VirtualEnv and starts the Noodles remote worker. This remote worker acts as a pilot job, reading job descriptions from input and returning the results. If you defined the remote VirtualEnv with the name qmflows, the following Bash script gives an idea of what you need:

#!/bin/bash
# comment/uncomment lines that you need

# If you need ADF, and it is available in a module
module load adf/2016.102
# or if you installed it yourself
# ADFHOME=${HOME}/.local/opt/adf
# source ${ADFHOME}/bin/adfrc.sh

# Point PLAMS to its place
export PLAMSDEFAULTS="${HOME}/.local/src/plams/utils/plams_defaults.py"

# Go to the directory that contains this script
cd "$(dirname "${BASH_SOURCE[0]}")"

# Activate the VirtualEnv
source activate qmflows

# Start the remote worker
python -m noodles.worker ${@:2}

# Bye!
source deactivate