% Write the input script "fort.90" with desired parameters
INPUT = 'setup_and_run.sh';
fid = fopen(INPUT,'wt');

fprintf(fid,[...
'#!/bin/bash\n',...
'mkdir -p $SCRATCH/ahoffman/HeLaZ/wk\n',...
...
'cd $SCRATCH/ahoffman/HeLaZ/wk/\n',...
...
'mkdir -p ', BASIC.RESDIR,'\n',...
'cd ',BASIC.RESDIR,'\n',...
'cp $HOME/HeLaZ/wk/fort.90 .\n',...
'cp $HOME/HeLaZ/wk/batch_script.sh .\n',...
...
'sbatch batch_script.sh\n',...
'echo tail -f $SCRATCH/ahoffman/HeLaZ/results/',BASIC.SIMID,'/',BASIC.PARAMS,'/out.txt']);

fclose(fid);
system(['cp setup_and_run.sh ',BASIC.RESDIR,'/.']);

% Write the sbatch script
INPUT = 'batch_script.sh';
fid = fopen(INPUT,'wt');

fprintf(fid,[...
'#!/bin/bash\n',...
'#SBATCH --chdir $SCRATCH/ahoffman/HeLaZ/results/',BASIC.SIMID,'/',BASIC.PARAMS,'\n',...
'#SBATCH --job-name ',CLUSTER.JNAME,'\n',...
'#SBATCH --time ', CLUSTER.TIME,'\n',...
'#SBATCH --nodes ', CLUSTER.NODES,'\n',...
'#SBATCH --cpus-per-task ', CLUSTER.CPUPT,'\n',...
'#SBATCH --ntasks-per-node ', CLUSTER.NTPN,'\n',...
'#SBATCH --mem ', CLUSTER.MEM,'\n',...
'#SBATCH --partition ',CLUSTER.PART,'\n',...
'module purge\n',...
'module load intel/19.0.5\n',...
'module load intel-mpi/2019.5.281\n',...
'module load fftw/3.3.8-mpi-openmp\n',...
'module load hdf5/1.10.6-mpi\n',...
'srun --cpu-bind=cores ./../../../bin/helaz ',num2str(NP_P),' ',num2str(NP_KR)]);

fclose(fid);
system(['cp batch_script.sh ',BASIC.RESDIR,'/.']);

system('scp {fort.90,setup_and_run.sh,batch_script.sh} ahoffman@izar.epfl.ch:/home/ahoffman/HeLaZ/wk');