Update Slurm script for 2.2.2

Author: prehensilecode

example_slurm_job.sh

@@ -1,32 +1,45 @@
 #!/bin/bash
-#SBATCH --partition=gpu
-#SBATCH --time=2:00:00
-#SBATCH --gres=gpu:1
+#SBATCH -p gpu
+#SBATCH --time=18:00:00
+#SBATCH --gpus=4
 #SBATCH --cpus-per-gpu=12
-#SBATCH --mem-per-gpu=30G
+#SBATCH --mem=140G
 
-module load alphafold
+module load alphafold/2.2.2
+module load python/gcc/3.10
 
-# the alphafold modulefile should define:
-# * ALPHAFOLD_DIR -- install location AlphaFold
-# * ALPHAFOLD_DATADIR -- the DOWLOAD_DIR set in scripts/download_all_data.sh
+### Check values of some environment variables
+echo SLURM_JOB_GPUS=$SLURM_JOB_GPUS
+echo ALPHAFOLD_DIR=$ALPHAFOLD_DIR
+echo ALPHAFOLD_DATADIR=$ALPHAFOLD_DATADIR
 
-# Run AlphaFold; default is to use GPUs, i.e. "--use_gpu"
-python3 ${ALPHAFOLD_DIR}/singularity/run_singularity.py \
-  --fasta_paths=T1050.fasta \
-  --max_template_date=2020-05-14 \
-  --preset=reduced_dbs
+###
+### README This runs AlphaFold 2.2.2 on the T1050.fasta file
+###
 
-# AlphaFold should use all GPU devices available to the job.
+# AlphaFold should use all GPU devices available to the job by default.
 # To explicitly specify use of GPUs, and the GPU devices to use, add
 #   --use_gpu --gpu_devices=${SLURM_JOB_GPUS}
-
+#
 # To run the CASP14 evaluation, use:
-#   --preset=casp14
-
-# To benchmark, running multiple JAX model evaluations:
+#   --model_preset=monomer_casp14
+#
+# To benchmark, running multiple JAX model evaluations (NB this 
+# significantly increases run time):
 #   --benchmark
 
-# Copy all output from AlphaFold back to directory where "sbatch" command was issued
-cp -R $TMPDIR $SLURM_SUBMIT_DIR
+# Run AlphaFold; default is to use GPUs, i.e. "--use_gpu" can be omitted.
+python3 ${ALPHAFOLD_DIR}/singularity/run_singularity.py \
+    --use_gpu --gpu_devices=${SLURM_JOB_GPUS} \
+    --data_dir=${ALPHAFOLD_DATADIR} \
+    --fasta_paths=T1050.fasta \
+    --max_template_date=2020-05-14 \
+    --model_preset=monomer_casp14 \
+    --benchmark
+
+echo INFO: AlphaFold returned $?
+
+### Copy Alphafold output back to directory where "sbatch" command was issued.
+mkdir $SLURM_SUBMIT_DIR/Output-$SLURM_JOB_ID
+cp -R $TMPDIR $SLURM_SUBMIT_DIR/Output-$SLURM_JOB_ID