Generic HPC Install Script

build/hpc_install.sh

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+# Cluster specific setup
+if [[ $1 == "longleaf" ]]; then
+    # Setup general purpose user variables needed for Longleaf
+    USERO=$( echo $USER | awk '{ print substr($0, 1, 1) }' )
+    USERN=$( echo $USER | awk '{ print substr($0, 2, 1) }' )
+    USERDIR="/users/$USERO/$USERN/$USER"
+    cd $USERDIR
+
+    # Load required modules
+    module purge
+    module load gcc/9.1.0
+    module load anaconda/2023.03
+    module load git
+elif [[ $1 == "rockfish" ]]; then
+    # Setup general purspose user variables needed for RockFish
+    USERDIR="/scratch4/struelo1/flepimop-code/$USER/"
+
+    # Load required modules
+    module purge
+    module load gcc/9.3.0
+    module load anaconda/2020.07
+    module load git/2.42.0
+else
+    echo "The cluster name '$1' is not recognized, must be one of: 'longleaf', 'rockfish'."
+    exit 1
+fi
+
+# Make sure the credentials is is where we expect and have the right perms
+if [ ! -f "$USERDIR/slack_credentials.sh" ]; then
+    echo "You need to place sensitive credentials in '$USERDIR/slack_credentials.sh'."
+    exit 1
+fi
+chmod 600 $USERDIR/slack_credentials.sh
+source $USERDIR/slack_credentials.sh
+
+# Ensure we have a $FLEPI_PATH
+if [ -z "${FLEPI_PATH}" ]; then
+    echo "An explicit \$FLEPI_PATH was not provided, setting to '$USERDIR/flepiMoP'."
+    export FLEPI_PATH="$USERDIR/flepiMoP"
+fi
+
+# Test that flepiMoP is located there
+if [ ! -d "$FLEPI_PATH" ]; then
+    echo "Did not find flepiMoP at '$FLEPI_PATH', cloning on your behalf."
+    git clone https://github.com/HopkinsIDD/flepiMoP.git $FLEPI_PATH
+elif [ ! -d "$FLEPI_PATH/.git" ]; then
+    echo "The flepiMoP found at '$FLEPI_PATH' is not a git clone, unsure of how to proceed."
+    exit 1
+fi
+
+# Setup the conda environment
+if [ ! -d "$USERDIR/flepimop-env" ]; then
+cat << EOF > $USERDIR/environment.yml
+channels:
+- conda-forge
+- defaults
+dependencies:
+- python=3.10
+- pip
+- r-base>=4.4
+- r-essentials
+- r-devtools
+- pyarrow=17.0.0
+- r-arrow=17.0.0
+# Manually specify this one because of the paths for libudunits2 on longleaf
+- r-sf 
+# This packages are probably missing from the DESCRIPTION of the R packages
+- r-optparse
+- pip:
+    - git+https://github.com/HopkinsIDD/flepiMoP.git#subdirectory=flepimop/gempyor_pkg
+EOF
+conda env create --prefix $USERDIR/flepimop-env --file $USERDIR/environment.yml
+fi
+conda activate $USERDIR/flepimop-env
+conda update --all
+
+# Check the conda environment is valid
+WHICH_PYTHON=$( which python )
+WHICH_R=$( which R )
+WHICH_PYTHON_OKAY=$( echo "$WHICH_PYTHON" | grep "flepimop-env" | wc -l )
+WHICH_R_OKAY=$( echo "$WHICH_R" | grep "flepimop-env" | wc -l )
+if [[ "$WHICH_PYTHON_OKAY" -ne 1 ]]; then
+    echo "The python found is '$WHICH_PYTHON', which does not contain the expected 'flepimop-env'."
+    exit 1
+fi
+if [[ "$WHICH_R_OKAY" -ne 1 ]]; then
+    echo "The R found is '$WHICH_R', which does not contain the expected 'flepimop-env'."
+    exit 1
+fi
+PYTHON_ARROW_VERSION=$( python -c "import pyarrow; print(pyarrow.__version__)" )
+R_ARROW_VERSION=$( Rscript -e "cat(as.character(packageVersion('arrow')))" )
+COMPATIBLE_ARROW_VERSION=$( echo "$R_ARROW_VERSION" | grep "$PYTHON_ARROW_VERSION" | wc -l )
+if [[ "$COMPATIBLE_ARROW_VERSION" -ne 1 ]]; then
+    echo "The R version of arrow is '$R_ARROW_VERSION' and the python version is '$PYTHON_ARROW_VERSION'. These may not be compatible versions."
+fi
+
+# Install the local R packages
+INSTALL_R=$( mktemp )
+cat << EOF > $INSTALL_R
+library(devtools)
+devtools::install_github('HopkinsIDD/flepiMoP', subdir='flepimop/R_packages/flepicommon')
+devtools::install_github('HopkinsIDD/flepiMoP', subdir='flepimop/R_packages/flepiconfig')
+devtools::install_github('HopkinsIDD/flepiMoP', subdir='flepimop/R_packages/inference')
+EOF
+Rscript $INSTALL_R
+rm $INSTALL_R
+
+# Set correct env vars
+export FLEPI_STOCHASTIC_RUN=false
+export FLEPI_RESET_CHIMERICS=TRUE
+export TODAY=`date --rfc-3339='date'`
+
+echo -n "Please set a project path (relative to '$USERDIR'): "
+read PROJECT_PATH
+export PROJECT_PATH="$USERDIR/$PROJECT_PATH"
+
+echo -n "Please set a config path (relative to '$PROJECT_PATH'): "
+read CONFIG_PATH
+export CONFIG_PATH="$PROJECT_PATH/$CONFIG_PATH"
+
+echo -n "Please set a validation date (today is $TODAY): "
+read VALIDATION_DATE
+
+echo -n "Please set a resume location: "
+read RESUME_LOCATION
+
+echo -n "Please set a flepi run index: "
+read FLEPI_RUN_INDEX
+
+# Done
+cat << EOM
+> The HPC install script has successfully finished.
+
+If you are testing if this worked, say installing for the first time, you can use the inference example from the \`flepimop_sample\` repository:
+\`\`\`bash
+cd \$PROJECT_PATH
+Rscript \$FLEPI_PATH/flepimop/main_scripts/inference_main.R -c \$CONFIG_PATH -j 1 -n 1 -k 1
+\`\`\`
+Just make sure to \`rm -r model_output\` after running.
+
+Otherwise make sure this diagnostic info looks correct before continuing:
+* Cluster:         $1
+* User directory:  $USERDIR
+* Flepi path:      $FLEPI_PATH
+* Project path:    $PROJECT_PATH
+* Python:          $WHICH_PYTHON
+* R:               $WHICH_R
+* Python arrow:    $PYTHON_ARROW_VERSION
+* R arrow:         $R_ARROW_VERSION
+* Stochastic run:  $FLEPI_STOCHASTIC_RUN
+* Reset chimerics: $FLEPI_RESET_CHIMERICS
+* Today:           $TODAY
+* Config path:     $CONFIG_PATH
+* Validation date: $VALIDATION_DATE
+* Resume location: $RESUME_LOCATION
+* Flepi run index: $FLEPI_RUN_INDEX
+EOM