1Nfinal_run.sh

#!/bin/bash
#SBATCH -N 1
#SBATCH -n 64
#SBATCH -w hepnode0
#SBATCH --exclusive
#SBATCH --output=./output/slurm-%j.out


echo "******final_run.sh*******"
cat $0
echo "******final_run.sh*******"


source ./env.sh

message=$2
# days=$3

run ( ) {
	
	if [ $(hostname) != "hepnode0" ]; then
		export UCX_RC_PATH_MTU=2048
		export I_MPI_HYDRA_RMK=slurm
		export I_MPI_PIN=off
		export OMP_NUM_THREADS=1
	fi
	export I_MPI_PIN=off
	case_name=$1
	node=$2
	proc=$3
	# days=$4
	

	adv_exe_absolute_path=$(readlink -f ./build/gmcore_adv_driver.exe)
	swm_exe_absolute_path=$(readlink -f ./build/gmcore_swm_driver.exe)
	normal_exe_absolute_path=$(readlink -f ./build/gmcore_driver.exe)

	prefix="./run/GMCORE-TESTBED/"
	suffix="/namelist"
	namelist_relative_path="${prefix}${case_name}/${suffix}"
	namelist_absolute_path=$(readlink -f ${namelist_relative_path} )
	echo namelist_absolute_path: ${namelist_absolute_path}
	data_path="/data/gomars_output/$(whoami)/${case_name}/N${2}n${3}/"${message}"-$(date +"%y-%m-%d")"
	# now_dir="/data/gomars_output/$(whoami)/${case_name}/N${2}n${3}/"${message}"-$(date +"%y-%m-%d")/opt.nc"
	days=$(grep 'run_days' ${namelist_absolute_path} | sed 's/.*= *\([0-9]*\).*/\1/')

	check_file="/data/gomars_output/public/N${2}n${3}/${case_name}_${days}days/baseline.nc" 
	check_dir="/data/gomars_output/public/N${2}n${3}/" 

	if [ -f "$check_file" ]; then
		echo "exist!"
	else
		echo "not exist, use default path at N1n16!"
		echo "!!! You should notice days!"
		check_file="/data/gomars_output/public/N1n16/${case_name}_${days}days/baseline.nc"
	fi
	cd ..
	current_dir=$(pwd)
	cd gmcore/

	if [ ! -d ${data_path} ]; then    
		mkdir -p ${data_path}
	fi

	pushd ${data_path}
	if [[ $namelist_absolute_path == *"adv"* ]]; then
		echo "adv case"
		exe_absolute_path=$adv_exe_absolute_path
	elif [[ $namelist_absolute_path == *"swm"* ]]; then
		echo "swm case"
		exe_absolute_path=$swm_exe_absolute_path
	else
		echo "normal case"
		exe_absolute_path=$normal_exe_absolute_path
	fi
	# bash -c "mpirun -n $3 -ppn $( expr $3 / $2 ) $exe_absolute_path $namelist_absolute_path" #doesn't work
	mpirun -n $3 -ppn $( expr $3 / $2 ) $exe_absolute_path $namelist_absolute_path
	# mpirun -n $3 -ppn $( expr $3 / $2 ) ${current_dir}/bind_cpu.sh $exe_absolute_path $namelist_absolute_path


	now_dir="/data/gomars_output/$(whoami)/${case_name}/N${2}n${3}/"${message}"-$(date +"%y-%m-%d")/opt.nc"

	popd
	
}


if [ -z $1 ]; then
	echo "Usage: $0 <case_list> <message>"
	exit 1
fi

cmd_array=()

while IFS= read -r cmd
do
	cmd_array+=("$cmd")
done < $1

for cmd in "${cmd_array[@]}"
do
	pushd ./gmcore
	run $cmd $2
	popd
done