search

bioexcel / gromacs-docker

Dockerfile for GROMACS
MIT License
45 stars 19 forks source link

Enabling MPI in Gromacs docker image #21

Open areyesromero opened 2 years ago

areyesromero commented 2 years ago

Dear all,

the command "docker run gromacs/gromacs gmx_mpi" generates the following output:

docker: Error response from daemon: OCI runtime create failed: container_linux.go:380: starting container process caused: exec: "gmx_mpi": executable file not found in $PATH: unknown.
ERRO[0001] error waiting for container: context canceled

this error seems to suggest that the image I have pulled from here (https://hub.docker.com/r/gromacs/gromacs) has not been compiled with MPI to enable parallelizations.

Any suggestion to work around it?

Best regards

Atilio

douglowe commented 2 years ago

Hi @areyesromero,

The gromacs version in the docker image is MPI-enabled. However the selector script (to chose the most suitable binary for your architecture) is called gmx not gmx_mpi. If you run docker run gromacs/gromacs gmx --version you'll see that it contains the MPI library.