#!/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 normal
#!/bin/bash --login
#SBATCH --time=504:00:00
#SBATCH -N1
#SBATCH --ntasks-per-node=20
#SBATCH --mem=130000MB
#SBATCH --job-name=t5


#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
#./iqtree-2.2.0-Linux/bin/iqtree2  -s $1 -allnni -m MFP -mset Blosum62,cpREV,Dayhoff,DCMut,FLAVI,FLU,HIVb,HIVw,JTT,JTTDCMut,LG,mtART,mtInv,mtMAM,mtMet,mtREV,mtVer,mtZOA,PMB,Q.bird,Q.insect,Q.mammal,Q.pfam,Q.plant,Q.yeast,rtREV,VT,WAG,Poisson,C10,C20,C30,C40,C50,C60,LG4M,LG4X,EX2,EX3,EHO,UL2,UL3,EX_EHO,CF4  -ninit 1000 -ntop 100 -alrt 10000  -nt 20 -safe
#/home/pamac/BEM2/iqtree-2.2.0-Linux/bin/iqtree2  -s $1 -allnni -m MFP -mset C10,C20,C30,LG+C10,LG+C20,LG+C30  -ninit 1000 -ntop 100 -alrt 10000  -nt 20 -safe
/home/pamac/BEM2/iqtree-2.2.0-Linux/bin/iqtree2  -s $1 -allnni -m LG+C20+F+R10  -ninit 1000 -ntop 100 -alrt 10000  -nt 20 -safe

    

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









