runner.pbs

#!/bin/bash -l
#PBS -l walltime=0:10:00
#PBS -l mem=5gb

# In the comments above, we request 10 minutes of wallclock time and 5GB RAM.
# This should be enough to debug, install environments and launch jobs.

# author: Benjamin Rombaut
# contact: benjamin.rombaut[at]ugent.be
# last update: 2024-02-18

# Using -v, we can pass arguments that will be filled in in the variables in the
# script. For example:
#
# $ qsub runner.pbs -v CLUSTER=donphan
#
# will make sure the variable $CLUSTER contains the value "donphan" within the script.

# echo $PBS_O_WORKDIR

# if [ -d $PBS_O_WORKDIR ]; then
# 	# navigate to the folder where the script is located
# 	cd $PBS_O_WORKDIR
# fi

echo "Working dir: $PWD"

# Navigate to the folder "venvs" in the VSC_DATA directory
ROOT_VENVS=$VSC_DATA/venvs/
# pip respects the TMPDIR environment variable
# otherwise ~/.cache/pip will soon take all available VSC_HOME space
# no TMPDIR is set by default, so we set it to a temporary
export TMPDIR=${TMPDIR:-$VSC_DATA/tmp}

if [ ! -d $ROOT_VENVS ]; then
	mkdir $ROOT_VENVS
fi

# If the CLUSTER argument is empty, throw an error
if [ -z $CLUSTER ]; then
	# detect cluster from loaded cluster module
	CLUSTER=$(module list 2>&1 | grep -oP '(?<=cluster/)[^/ ]+')
	# CLUSTER=$SLURM_CLUSTERS
	echo "No CLUSTER argument provided, detected cluster '$CLUSTER'"
fi
if [[ -z $INSTALL && -z $ACTIVATE && -z $CONDA ]]; then
	echo "Provide an INSTALL or ACTIVATE argument: INSTALL=folder/with/requirements.txt_and_modules.sh qsub runner.pbs" 1>&2
	exit 1
fi
if [[ -z $PIP_ARGS ]]; then
	PIP_ARGS="$INSTALL"
fi


if [ ! -z $INSTALL ]; then
	# install a new virtual environment

	NAME=`basename $(readlink -f $INSTALL)`

	# This is the name of the virtual environment we will construct.
	# The name depends on the chosen cluster.
	VENV_NAME=venv_${NAME}_${CLUSTER}
	VENV_PATH="${ROOT_VENVS}/${VENV_NAME}/"

	# Load the modules
	source $INSTALL/modules.sh

    # Create the virtual environment and install packages
	# If this virtual environment already exists, delete it.
	if [ -d $VENV_PATH ]; then
		rm -r $VENV_PATH
	fi
    python -m venv $VENV_PATH
    source $VENV_PATH/bin/activate
	if [ ! -z "$PIP_ARGS" ]; then
        python -m pip install $PIP_ARGS
    fi
	echo "Virtual environment $VENV_PATH installed."
	# TODO: add `pip install -e .` for local packages
elif [ ! -z $ACTIVATE ]; then
	NAME=`basename $(readlink -f $ACTIVATE)`

	# This is the name of the virtual environment we will construct.
	# The name depends on the chosen cluster.
	VENV_NAME=venv_${NAME}_${CLUSTER}
	VENV_PATH="${ROOT_VENVS}/${VENV_NAME}/"
    # Load the modules
	# cd $ACTIVATE
	source $ACTIVATE/modules.sh
	# Activate the virtual environment
	if  [ -f $VENV_PATH/bin/activate ]; then
        source $VENV_PATH/bin/activate
    fi
	echo "Virtual environment $VENV_PATH activated."
elif [ ! -z $CONDA ]; then
	# activate a conda environment
	source ~/.bashrc
	conda activate $CONDA
	echo "Virtual environment $CONDA activated."
fi
if [ ! -z "$SCRIPT" ]; then
	# Navigate to the script folder
	# if script ends with .py, use python
	# if [[ "$SCRIPT" == *.py ]]; then
	# 	SCRIPT="python $SCRIPT"
	# elif [[ "$SCRIPT" == *.sh ]]; then
	# 	# just use bash
	# 	SCRIPT="bash $SCRIPT"
	# fi
	# Run the script (or an absolute script path) with the arguments
	$SCRIPT $@
fi