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Update README.md
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mkrack committed Oct 20, 2023
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Expand Up @@ -153,24 +153,6 @@ All containers provide as further binaries:
- `xyz2dcd` (convert `.xyz` files to `.dcd` files and optionally include cell information from CP2K's `.cell` file)
- `graph` (FES post-processing tool for Metadynamics runs)

### Running MPI outside the container

For multi-node runs on HPC cluster systems, it is required to use the MPI of the host system

```
export OMP_NUM_THREADS=2
mpiexec -n 4 docker run -it --shm-size=1g -v $PWD:/mnt -u $(id -u $USER):$(id -g $USER) mkrack/cp2k:2023.2_mpich_generic_psmp cp2k -i H2O-32.inp
```

to achieve best performance, but incompabilities, e.g. because of proprietary drivers or installations, might disable runing the pre-built container with the host MPI.
If the host system has installed SLURM as a scheduler, `srun` can (should) be used instead of `mpirun` (or `mpiexec`)

```
srun docker run -it --shm-size=1g -v $PWD:/mnt -u $(id -u $USER):$(id -g $USER) mkrack/cp2k:2023.2_mpich_generic_psmp cp2k -i H2O-32.inp
```

With SLURM, `srun` is usually the proper way to launch a production run in batch mode.

### Building your own CP2K docker container

You can build your own CP2K docker container, e.g. using the Docker file `Dockerfile.2023.2_mpich_generic_psmp` for the CP2K version 2023.2, by running
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