Merge branch 'main' of github.com:prehensilecode/alphafold_singularity

Author: prehensilecode

Singularity.def

@@ -85,11 +85,14 @@ patch -p0 < /app/alphafold/docker/openmm.patch
 # Add SETUID bit to the ldconfig binary so that non-root users can run it.
 chmod u+s /sbin/ldconfig.real
 
+### SETUID bit does not matter: Apptainer does not allow suid commands
+### Workaround below is to use /mnt/out/ld.so.cache for the ld cache file
+
 %environment
 export PATH="/opt/conda/bin:/usr/local/cuda-11.1/bin:$PATH"
 %runscript
 cd /app/alphafold
-ldconfig
+ldconfig -C /mnt/output/ld.so.cache
 exec python /app/alphafold/run_alphafold.py "$@"
 # %startscript
 # cd /app/alphafold

example_slurm_job.sh

@@ -1,22 +1,25 @@
 #!/bin/bash
 #SBATCH --partition=gpu
-#SBATCH --time=18:00:00
+#SBATCH --time=2:00:00
 #SBATCH --gpus=4
 #SBATCH --cpus-per-gpu=12
 #SBATCH --mem=45G
 
 ### NOTE
-### This job script cannot be used without modification for your specific environment.
+#### This job script cannot be used without modification for your specific environment.
 
 module load python/gcc/3.11
-module load alphafold/2.3.1
+module load alphafold/2.3.2
 
 ### Check values of some environment variables
+echo SLURM_GPUS_ON_NODE=$SLURM_GPUS_ON_NODE
+echo SLURM_JOB_GPUS=$SLURM_JOB_GPUS
+echo SLURM_STEP_GPUS=$SLURM_STEP_GPUS
 echo ALPHAFOLD_DIR=$ALPHAFOLD_DIR
 echo ALPHAFOLD_DATADIR=$ALPHAFOLD_DATADIR
 
 ###
-### README This runs AlphaFold 2.3.1 on the T1050.fasta file
+### README This runs AlphaFold 2.3.2 on the T1050.fasta file
 ###
 
 # AlphaFold should use all GPU devices available to the job by default.
@@ -35,11 +38,12 @@ echo ALPHAFOLD_DATADIR=$ALPHAFOLD_DATADIR
 
 # Run AlphaFold; default is to use GPUs
 python3 ${ALPHAFOLD_DIR}/singularity/run_singularity.py \
+    --use_gpu \
     --data_dir=${ALPHAFOLD_DATADIR} \
     --fasta_paths=T1050.fasta \
     --max_template_date=2020-05-14 \
-    --db_preset=reduced_dbs \
-    --model_preset=monomer
+    --model_preset=monomer \
+    --db_preset=reduced_dbs
 
 echo INFO: AlphaFold returned $?
 

run_singularity.py

@@ -52,12 +52,16 @@
 
 flags.DEFINE_bool(
     'use_gpu', True, 'Enable NVIDIA runtime to run with GPUs.')
-flags.DEFINE_boolean(
-    'run_relax', True,
-    'Whether to run the final relaxation step on the predicted models. Turning '
-    'relax off might result in predictions with distracting stereochemical '
-    'violations but might help in case you are having issues with the '
-    'relaxation stage.')
+flags.DEFINE_enum(
+    'models_to_relax', 'best', ['best', 'all', 'none'],
+    'The models to run the final relaxation step on. '
+    'If `all`, all models are relaxed, which may be time '
+    'consuming. If `best`, only the most confident model is '
+    'relaxed. If `none`, relaxation is not run. Turning off '
+    'relaxation might result in predictions with '
+    'distracting stereochemical violations but might help '
+    'in case you are having issues with the relaxation '
+    'stage.')
 flags.DEFINE_bool(
     'enable_gpu_relax', True, 'Run relax on GPU if GPU is enabled.')
 flags.DEFINE_string(
@@ -247,7 +251,7 @@ def main(argv):
       f'--benchmark={FLAGS.benchmark}',
       f'--use_precomputed_msas={FLAGS.use_precomputed_msas}',
       f'--num_multimer_predictions_per_model={FLAGS.num_multimer_predictions_per_model}',
-      f'--run_relax={FLAGS.run_relax}',
+      f'--models_to_relax={FLAGS.models_to_relax}',
       f'--use_gpu_relax={use_gpu_relax}',
       '--logtostderr',
   ])