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Update sapelo_programs.py #49

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9fdc1fd
Update sapelo_programs.py
cgbriggs99 Dec 3, 2025
f0cce22
Update sapelo_programs.py
cgbriggs99 Dec 19, 2025
38a5739
Update sapelo_programs.py
cgbriggs99 Dec 19, 2025
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35 changes: 17 additions & 18 deletions submitscripts/slurm/sapelo_programs.py
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
# use sapelo2 work area (called scratch)
# no need to copy set psi_scratch variable

fermi = """module load Julia/1.8.2-linux-x86_64
module load intel/2023a
fermi = """module load Julia/1.11.6-gfbf-2023b
module load intel/2023b

julia {input_name}

Expand All @@ -29,39 +29,34 @@
# mpi only
# set scratch dir to home area but run from submit_dir

molpro_mpi = """module load intel/2023a

molpro_mpi = """
# to change scratch dir to use local machine scratch
export SCRATCH_DIR=/scratch/$USER/tmp/$SLURM_JOB_ID
mkdir -p $SCRATCH_DIR
export APPTAINER_BIND="$SLURM_SUBMIT_DIR,$SCRATCH_DIR" # This binds the directory into the container so that output can be written.

mpirun -n $NSLOTS apptainer exec /work/jttlab/containers/molpro_mpipr.sif \
molpro.exe input.dat --output $SLURM_SUBMIT_DIR/output.dat --nouse-logfile --directory $SCRATCH_DIR

singularity run /work/jttlab/containers/molpro-2024.1.1-mpi-gapr.sif -n $NSLOTS input.dat --output $SLURM_SUBMIT_DIR/output.dat --nouse-logfile --directory $SCRATCH_DIR
rm $SCRATCH_DIR -r

"""

# mpi only
# copy everything to lscratch to run and set scratch to lscratch

molpro_mpi_lscratch = """module load intel/2023a

molpro_mpi_lscratch = """
# to change scratch dir to use local machine scratch
export SCRATCH_DIR=/lscratch/$USER/tmp/$SLURM_JOB_ID
mkdir -p $SCRATCH_DIR
export APPTAINER_BIND="$SLURM_SUBMIT_DIR,$SCRATCH_DIR" # This binds the directory into the container so that output can be written.

mpirun -n $NSLOTS apptainer exec /work/jttlab/containers/molpro_mpipr.sif \
molpro.exe input.dat --output $SLURM_SUBMIT_DIR/output.dat --nouse-logfile --directory $SCRATCH_DIR
singularity run /work/jttlab/containers/molpro-2024.1.1-mpi-gapr.sif -n $NSLOTS input.dat --output $SLURM_SUBMIT_DIR/output.dat --nouse-logfile --directory $SCRATCH_DIR

rm $SCRATCH_DIR -r

"""

orca_common = """#Set MPI Variables
module load ORCA/5.0.4-gompi-2022a
module load ORCA/6.1.0-OpenMPI-4.1.8-GCC-13.3.0-avx2
export OMP_NUM_THREADS=1

# Set other variables
Expand All @@ -79,12 +74,12 @@
echo " Running calculation..."

cd $scratch_dir
orca {input_name} >& $SLURM_SUBMIT_DIR/{output_name} || exit 1
/apps/eb/ORCA/6.1.0-OpenMPI-4.1.8-GCC-13.3.0-avx2/bin/orca {input_name} >& $SLURM_SUBMIT_DIR/{output_name} || exit 1
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@AlexHeide AlexHeide Dec 3, 2025

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Does module load not add orca to path?

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@cgbriggs99 cgbriggs99 Dec 19, 2025

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It does, but orca complains if you use threads and don't specify the full path. I don't know why they need this.


echo " Saving data and cleaning up..."
# delete any temporary files that my be hanging around.
rm -f *.tmp*
find . -type f -size +50M -exec rm -f {} \;
find . -type f -size +50M -exec rm -f {{}} \;
tar --exclude='*tmp*' --transform "s,^,Job_Data_$SLURM_JOB_ID/," -vzcf $SLURM_SUBMIT_DIR/Job_Data_$SLURM_JOB_ID.tar.gz *

echo " Job complete on `hostname`."
Expand Down Expand Up @@ -148,31 +143,35 @@
rm $scratch_dir -r
"""

cfour_serial = """module=cfour/2.1-intel-2021b-serial
cfour_serial = """module=cfour/2.1-intel-2023a-serial
export OMP_NUM_THREADS=$NSLOTS

scratch_dir=/scratch/$USER/tmp/$SLURM_JOB_ID
mkdir -p $scratch_dir

""" + cfour_common

cfour_serial_lscratch = """module=cfour/2.1-intel-2021b-serial
cfour_serial_lscratch = """module=cfour/2.1-intel-2023a-serial
export OMP_NUM_THREADS=$NSLOTS

scratch_dir=/lscratch/$USER/tmp/$SLURM_JOB_ID
mkdir -p $scratch_dir

""" + cfour_common

cfour_mpi = """module=cfour/2.1-intel-2021b-mpi
cfour_mpi = """
echo "Sapelo no longer has MPI CFOUR. Use the container version instead."
module=cfour/2.1-intel-2023a-mpi
scratch_dir=/scratch/$USER/tmp/$SLURM_JOB_ID
mkdir -p $scratch_dir

echo -e "\t$NSLOTS" > ./ncpu # CFour appears to just claim any and all cpus
echo -e "\t$NSLOTS" > $scratch_dir/ncpu
""" + cfour_common

cfour_mpi_lscratch = """module=cfour/2.1-intel-2021b-mpi
cfour_mpi_lscratch = """
echo "Sapelo no longer has MPI CFOUR. Use the container version instead."
module=cfour/2.1-intel-2023a-mpi
scratch_dir=/lscratch/$USER/tmp/$SLURM_JOB_ID
mkdir -p $scratch_dir

Expand Down