MedeA

MedeA is an integrated software environment for atomistic materials modeling and simulation by Materials Design Inc.

Available

Roihu-CPU: 1.13.1

License

Commercial, more info from Materials Design.

Usage

These instructions assume the MedeA GUI is already installed on your own computer. The MedeA JobServer and TaskServer run in a container on a Roihu login node, and the TaskServer submits calculations to Slurm. VASP and LAMMPS calculations use Roihu's own vasp and lammps modules.

Set up the servers on Roihu (once)

Log in to the login node where your servers will run. Always use the same node, because the servers run there:

ssh roihu-cpu-login1.csc.fi

Load the MedeA server scripts:

module load medea-servers/3.13.1

Create a work directory and generate the server option files JobServer.options and TaskServer.options:

mkdir -p /scratch/<project>/$USER/medea
cd /scratch/<project>/$USER/medea
medea-init-servers.py --jobserver-port 32077 --taskserver-port 23077 --batch-project <project>

Replace <project> with your CSC project (e.g. project_2001234); Slurm jobs are billed to it. The login node is shared with other users, so choose your own two port numbers instead of 32077 and 23077 (any free ports between 1024 and 65535).

The generated TaskServer.options submits jobs with these settings. Edit the file if you need different ones:

Line	Meaning
`-batch_project <project>`	Billing project (Slurm `--account`), set by `--batch-project`
`-batch_queue small`	Slurm partition
`-nprocessors 128`	Maximum cores per task
`-ntasks 4`	Maximum concurrent tasks

Start and stop the servers

Run these on the same login node, in your work directory, with the module loaded:

module load medea-servers/3.13.1
cd /scratch/<project>/$USER/medea

Start the JobServer and TaskServer:

medea-start-servers.sh

Check that the instances medea-jobserver and medea-taskserver are running:

apptainer instance list

Stop the servers when you no longer need them:

medea-stop-servers.sh

Open an SSH tunnel from your computer

On your own computer, forward a local port to your JobServer port (here 32077):

ssh -N -f -L localhost:32001:localhost:32077 roihu-cpu-login1.csc.fi

The JobServer web page is now at http://localhost:32001/index.html.

Close the tunnel:

pkill -f "ssh -N -f -L localhost:32001:localhost:32077 roihu-cpu-login1.csc.fi"

Connect the GUI to Roihu

Start the MedeA GUI, then go to File » Preferences » JobServers and add a JobServer with name Roihu and address http://localhost:32001.

Each time you work with MedeA: start the servers on Roihu (step 2), open the tunnel (step 3), then start the GUI.

Troubleshooting

Servers do not start or a port is in use: choose other ports, run medea-init-servers.py again with them, and use the new JobServer port in the SSH tunnel.
Where are my files? Job data is in <workdir>/JobServer/Jobs and task run directories in <workdir>/TaskServer.