From 9fdc1fdb69df0eaf9aba84f183a2a16e62ccb66f Mon Sep 17 00:00:00 2001
From: Connor Briggs <cgbriggs99@gmail.com>
Date: Wed, 3 Dec 2025 09:44:10 -0500
Subject: [PATCH 1/3] Update sapelo_programs.py

Update software versions and fix an issue with the ORCA format string where `{}` is treated like it needs an argument.
---
 submitscripts/slurm/sapelo_programs.py | 36 +++++++++++++-------------
 1 file changed, 18 insertions(+), 18 deletions(-)

diff --git a/submitscripts/slurm/sapelo_programs.py b/submitscripts/slurm/sapelo_programs.py
index 2b8dd76..3208905 100644
--- a/submitscripts/slurm/sapelo_programs.py
+++ b/submitscripts/slurm/sapelo_programs.py
@@ -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} 
 
@@ -29,16 +29,13 @@
 # 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
 
 """
@@ -46,22 +43,21 @@
 # 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
@@ -79,12 +75,12 @@
 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
 
 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`."
@@ -148,7 +144,7 @@
 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
@@ -156,7 +152,7 @@
 
 """ + 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
@@ -164,7 +160,9 @@
 
 """ + 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
 
@@ -172,7 +170,9 @@
 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
 

From f0cce2232c747bae3feef57178848b97d459d320 Mon Sep 17 00:00:00 2001
From: Connor Briggs <cgbriggs99@gmail.com>
Date: Fri, 19 Dec 2025 15:18:59 -0500
Subject: [PATCH 2/3] Update sapelo_programs.py

---
 submitscripts/slurm/sapelo_programs.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/submitscripts/slurm/sapelo_programs.py b/submitscripts/slurm/sapelo_programs.py
index 3208905..a850b0a 100644
--- a/submitscripts/slurm/sapelo_programs.py
+++ b/submitscripts/slurm/sapelo_programs.py
@@ -35,7 +35,8 @@
 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.
 
-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
+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 \
+-m $(($SLURM_MEM_PER_NODE/10/$NSLOTS))M # Divide by 10 so that it leaves room for extra variables. Word size is normally 8.
 rm $SCRATCH_DIR -r
 
 """
@@ -49,8 +50,8 @@
 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.
 
-
-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
+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 \
+-m $(($SLURM_MEM_PER_NODE/10/$NSLOTS))M # Divide by 10 so that it leaves room for extra variables. Word size is normally 8.
 
 rm $SCRATCH_DIR -r
 

From 38a57392a04b39d9a62f07e2241622daf9f36ddd Mon Sep 17 00:00:00 2001
From: Connor Briggs <cgbriggs99@gmail.com>
Date: Fri, 19 Dec 2025 16:33:44 -0500
Subject: [PATCH 3/3] Update sapelo_programs.py

---
 submitscripts/slurm/sapelo_programs.py | 6 ++----
 1 file changed, 2 insertions(+), 4 deletions(-)

diff --git a/submitscripts/slurm/sapelo_programs.py b/submitscripts/slurm/sapelo_programs.py
index a850b0a..7d1e41e 100644
--- a/submitscripts/slurm/sapelo_programs.py
+++ b/submitscripts/slurm/sapelo_programs.py
@@ -35,8 +35,7 @@
 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.
 
-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 \
--m $(($SLURM_MEM_PER_NODE/10/$NSLOTS))M # Divide by 10 so that it leaves room for extra variables. Word size is normally 8.
+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
 
 """
@@ -50,8 +49,7 @@
 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.
 
-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 \
--m $(($SLURM_MEM_PER_NODE/10/$NSLOTS))M # Divide by 10 so that it leaves room for extra variables. Word size is normally 8.
+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