#!/bin/bash


#sprawdzanie parametrow skryptu
if [ $# -eq 0 ]; then
        echo "Sposob uzycia: $0 plik.wej"
        exit 1
fi

if [ ! -f "$1" ]; then
        echo "Brak pliku $1"
        exit 1
fi

export NAZWA_ZAD="$1.iqt"


#do sbatch idzie to co miedzy EOF
cat << EOF | sbatch -p infinity
#!/bin/bash --login
#SBATCH --time=3000:00:00
#SBATCH -N1
#SBATCH --ntasks-per-node=1
#SBATCH --mem=90000MB
#SBATCH --job-name=phyml_cat1


#LD_LIBRARY_PATH=$HOME/lib:$LD_LIBRARY_PATH
#export LD_LIBRARY_PATH

#LD_LIBRARY_PATH=/usr/local/easybuild-bem2:$LD_LIBRARY_PATH:/home/ral/opt/openmpi/lib
#export LD_LIBRARY_PATH

#module load openmpi/1.8.4-intel15.0
#module load openmpi/3.1.3-intel16.0.3

#module load mvapich2
#module load mpiexec
#module load OpenMPI/4.1.2-GCC-11.2.0
#libmpi_cxx.so.1

#PATH=$PATH:/home/ral/opt/openmpi
#module load intel/2022a

#nazwa katologu w ktorym bedzie liczenie
export DIR1=$NAZWA_ZAD

cd \$SLURM_SUBMIT_DIR

#mkdir ./\$DIR1

#cd ./\$DIR1


cp \${SLURM_SUBMIT_DIR}/* ./

    
    #uruchomienie
/home/pamac/BEM2/PhyML-CAT/phyml-cat_linux64 -i $1 -d aa -m C20 -f e -v e -c 5 -a e -b -3 -o tlr -s SPR > opis

    

#echo "skonczony proces $NAZWA_ZAD" | mail -s cluster pamac
EOF









