This repository contains all the static configuration that is generic to all the computer resources in order to carry out the MD simulations with the MDStudio infrastucture and Gromacs.
Note: This is work in progress.
In order to create a new specialization you need to create the following files (and folder) which content and function is explained in detail below,
- api/config.yml
- api/install.sh
- api/files/gmxrc
- known_hosts
- Dockerfile
This file contains all the cerise configuration options necessary to run a job in a remote machine. Do not put any password in this file, instead use environmental variables. see the DAS5 config file for an example.
This file is a bash script containing the commands to install all the infrastucture of cerise, miniconda and all files related to the MD simulation. In the current repository we have a general installation script that can be used as shown by the DAS5 installation script.
We assume that Gromacs is installed in the computational infrasctucture that you intend to use or you can compile and install gromacs in this step. In the DAS5 specialization we compiled Gromacs and stored it in the same repository of the specialization and we clone the binaries during the installation.
This plain text file contains an environmental variable call GMXRC_MDSTUDIO pointing to the absolute path of the GMXRC.bash file of Gromacs. Also, it contains all the calls to the [environment modules] required to call Gromacs. See the DAS5 gmxrc for an example.
This file contains the public key of the host that you want to communicate with. for a detail explanation see the client configuration file.
cerise specializations are docker containers in charge of managing the jobs execute in a remote machine. These containers take care of submitting, monitoring and retrieving all the job-related data for a given molecular dynamics simulation. For most of the application you just need to copy paste the reference DAS5 Dockerfile into your specialization Dockerfile.
This repository contains a modified copy of gromit.sh from gromit in api/files/mdstudio/gromit/gromit_mpi.sh. Gromit is licensed under the GNU General Public License version 2.0 (see the file LICENSE_GROMIT).
The rest of 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.