Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add slurm batch scripts #57

Open
jchodera opened this issue May 21, 2017 · 2 comments
Open

Add slurm batch scripts #57

jchodera opened this issue May 21, 2017 · 2 comments

Comments

@jchodera
Copy link
Member

We should add LSF and slurm batch scripts to examples.

@jchodera
Copy link
Member Author

Here's a rudimentary example modified from one of @Lnaden's scripts, though this one seems to depend on MPS:

#!/bin/bash
#BSUB -W 24:00
#BSUB -o abl-imatinib-explicit.%J.log
#BSUB -env "all, LSB_START_JOB_MPS=Y"
#BSUB -n 4 -R "rusage[ngpus_excl_p=1,mem=8]"
#BSUB -m ls-gpu
#BSUB -J "abl-imatinib-explicit"

# Run the simulation with verbose output:
#source activate yank16
export PREFIX="explicit"
build_mpirun_configfile  "yank script --yaml=$PREFIX.yaml"
mpiexec.hydra -f hostfile -configfile configfile

@jchodera
Copy link
Member Author

jchodera commented Nov 6, 2017

I think the LSF part is done now and the slurm part is left.

@jchodera jchodera changed the title Add LSF and slurm batch scripts Add slurm batch scripts Nov 6, 2017
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Development

No branches or pull requests

1 participant