Cerise specialisation for MDStudio and DAS5

This repository contains a Cerise specialisation for MDStudio and DAS5.

It's work in progress.

Running

Install the service via Docker

Get the specialised service from Docker:

docker pull mdstudio/cerise-mdstudio-das5:develop

Start it

docker run --name=cerise-mdstudio-das5 -p 29593-29594:29593-29594 --env CERISE_USERNAME=<username> --env CERISE_PASSWORD=<password> mdstudio/cerise-mdstudio-das5:develop

This will give a warning about the Slurm version not being supported, which you can safely ignore.

If this is the first time you run this Cerise specialisation, it will stage a bunch of files to a directory named .cerise in your home directory on DAS-5. This may take a bit of time, so it may take a moment for the service to start processing jobs. You can submit them right away though.

Note that inserting the user name and password via an environment variable is not ideal, amongst others it leaves a copy of them in your ~/.bash_history (from where you may want to delete it now, although it should be only readable to you yourself). Overlay-mounting a file would be another option, but that means that the username and password are stored on disk. If we start the service from Python using docker-py, then the environment variables would probably be the better option.

Run a job

Now we can submit an example Gromit/GROMACS job, using a virtual environment to keep the dependencies away from the rest of the system:

cd examples/
virtualenv -p python3 venv
. venv/bin/activate
pip3 install bravado
python3 run_md.py

This will take about 2 minutes to complete.

Legal Notes

GROMACS

This repository contains a copy of GROMACS 2016.4 in binary (compiled for DAS5/VU) form. The binaries are in the mdstudio/gromacs/ The GMXRC.* scripts were modified to point to the installed location, according to the instructions in them.

GROMACS is Free Software, available under the GNU Lesser General Public License (LGPL), version 2.1. You can redistribute it and/or modify it under the terms of the LGPL as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version.

Note that GROMACS has its own dependencies, some of which are included in GROMACS itself, with their own licenses. We refer to the LICENSE_GROMACS file (which is simply the COPYING file from the GROMACS source code archive) for details.

other files

This repository is covered by the following license grant:

Copyright 2018 Netherlands eScience Center and VU University Amsterdam

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

   http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.