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This tutorial assumes you’ve generated ForceBalance inputs using my valence-fitting repository through step 04 and have the corresponding fb-fit, parameters-to-optimize, and scripts directories.

Preparing Files

Copy over

  • fb-fit/

    • forcefield/force-field.offxml

    • optimize.in

    • targets.tar.gz

    • oe_license.txt (probably not needed, but I had it)

  • parameters-to-optimize/

  • scripts/

The valence-fitting scripts produce the directory fb-fit/targets, so either tar them up to use the list above or wait for the whole directory to transfer.

Preparing Scripts

The scripts/hpc3_master.sh script is a template file, so you next have to modify it with your account/environment details. Specifically, I updated the #SBATCH -p line to use the free queue instead of the standard queue, and I added my UCI email to the --mail-user line. At least for my first attempt, I also commented out the COMPRESSED_CONDA_ENVIRONMENT stuff, leaving me with a somewhat simpler script than the one currently in the repo:

#!/bin/bash
#SBATCH -J valence-fit
#SBATCH -p free
#SBATCH -t 72:00:00
#SBATCH --nodes=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=10000mb
#SBATCH --account dmobley_lab
#SBATCH --export ALL
#SBATCH --mail-user=bwestbr1@uci.edu
#SBATCH --constraint=fastscratch

rm -rf /tmp/$SLURM_JOB_NAME
source $HOME/.bashrc
mamba activate valence-fitting

rsync  -avzIi  $SLURM_SUBMIT_DIR/optimize.in  $SLURM_TMPDIR/$SLURM_JOB_NAME
rsync  -avzIi  $SLURM_SUBMIT_DIR/targets.tar.gz  $SLURM_TMPDIR/$SLURM_JOB_NAME
rsync  -avzIi  $SLURM_SUBMIT_DIR/forcefield  $SLURM_TMPDIR/$SLURM_JOB_NAME

tar -xzf targets.tar.gz

datadir=$(pwd)
mkdir -p $SLURM_SUBMIT_DIR/worker_logs
echo $(hostname) > $SLURM_SUBMIT_DIR/host

export OMP_NUM_THREADS=1
export MKL_NUM_THREADS=1

if ForceBalance.py optimize.in ; then
   tar -czvf optimize.tmp.tar.gz optimize.tmp
   rsync  -avzIi --exclude="optimize.tmp" --exclude="optimize.bak" --exclude="fb_193*" --exclude="targets*" $TMPDIR/*
$SLURM_SUBMIT_DIR > copy.log
   rm -rf $TMPDIR
fi

echo "All done"

Because I wanted to run the submission scripts from the fb-fit directory instead of the scripts directory, I also edited the call to wq_worker_local.sh in scripts/submit_hpc3_worker_local.sh to point to ../scripts/wq_worker_local.sh. I also commented out the CONDA_ENVIRONMENT stuff therein and ran the script from the proper conda environment. Some of these changes will probably be reflected in the repository in the future.

Submitting

With these preparations done, you can run

sbatch ../scripts/hpc3_master.sh

Once that starts running, it will create a host file containing the HOST argument for submit_hpc3_worker_local.sh. You can obtain the PORT argument from the ForceBalance optimize.in file. Then, run the worker script with

../scripts/submit_hpc3_worker_local.sh HOST PORT

Or for a “one-liner”

../scripts/submit_hpc3_worker_local.sh $(sed 1q host) $(awk '/port/ {print $NF}' optimize.in)

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