startup_tasks.sh

#!/bin/bash
echo "Update sys"
sudo apt-get update && sudo apt-get upgrade -y && sudo apt-get install -y gfortran g++ make cmake libopenmpi-dev openmpi-bin libnetcdff-dev netcdf-bin libfftw3-dev python3-pip python3-pyqt5 flex bison ncl-ncarg nmap
echo "Downloading palm"
mkdir /palmbase
cd /palmbase
wget https://gitlab.palm-model.org/releases/palm_model_system/-/archive/master/palm_model_system-master.tar.gz && tar -xf palm_model_system-master.tar.gz && cd palm_model_system-master/

# echo "Compiling palm"
# mkdir /palmbase/palm && bash install -p /palmbase/palm
# export PATH=/palmbase/palm/bin:${PATH}

cd /mnt/batch/tasks/fsmounts/shared/
mkdir -p palmbase/palm
cd palmbase

wget https://gitlab.palm-model.org/releases/palm_model_system/-/archive/master/palm_model_system-master.tar.gz && tar -xf palm_model_system-master.tar.gz && cd palm_model_system-master/
bash install -p ../palm


echo "Copying basefile"
# cd /palmbase/palm && mkdir -p /palmbase/palm/JOBS/example_cbl/INPUT 
# cp /palmbase/palm_model_system-master/packages/palm/model/tests/cases/example_cbl/INPUT/example_cbl_p3d /palmbase/palm/JOBS/example_cbl/INPUT/

cd ../palm && mkdir -p JOBS/example_cbl/INPUT 
cp ../palm_model_system-master/packages/palm/model/tests/cases/example_cbl/INPUT/example_cbl_p3d JOBS/example_cbl/INPUT/

# sudo chmod -R 777 /palmbase

sudo chmod -R 777 ../