Commit afb951d4 authored by jarunanp's avatar jarunanp
Browse files

Merge branch 'main' into 'main'

AF 2.2.0, activate unified memory for smaller proteins, increased time request to 24:00

See merge request jarunanp/alphafold_on_euler!2
parents c643f161 f637a04b
......@@ -86,7 +86,7 @@ if (( "$n_lines" <= 2 )); then
OPTIONS="--pdb70_database_path=\$DATA_DIR/pdb70/pdb70 "
elif (( "$n_lines" > 2 )); then
echo " Protein type: multimer"
OPTIONS="--model_preset=multimer --pdb_seqres_database_path=\$DATA_DIR/pdb_seqres/pdb_seqres.txt --uniprot_database_path=$DATA_DIR/uniprot/uniprot.fasta"
OPTIONS="--model_preset=multimer --pdb_seqres_database_path=\$DATA_DIR/pdb_seqres/pdb_seqres.txt --uniprot_database_path=\$DATA_DIR/uniprot/uniprot.fasta \\"
fi
# Determine the sequence length
......@@ -101,7 +101,7 @@ echo " max: $max_aa"
# Estimate the required computing resources
# For simplicity, the two types of GPUs users could select are RTX 2080 Ti with 11GB GPU mem (GPU_MEM_MB>=10240)
# and TITAN RTX with 24GB GPU mem (GPU_MEM_MB >= 20480)
if (( "$sum_aa" < 800 )); then
if (( "$sum_aa" < 200 )); then
RUNTIME="04:00"
NCPUS=12
NGPUS=1
......@@ -111,7 +111,7 @@ if (( "$sum_aa" < 800 )); then
TOTAL_SCRATCH_MB=120000
ENABLE_UNIFIED_MEMORY=0
MEM_FRACTION=1
elif (( "$sum_aa" >= 800 )) && (( "$sum_aa" < 1500 )); then
elif (( "$sum_aa" >= 200 )) && (( "$sum_aa" < 1500 )); then
RUNTIME="24:00"
NCPUS=12
NGPUS=1
......@@ -119,8 +119,8 @@ elif (( "$sum_aa" >= 800 )) && (( "$sum_aa" < 1500 )); then
TOTAL_GPU_MEM_MB=20480
TOTAL_CPU_MEM_MB=120000
TOTAL_SCRATCH_MB=120000
ENABLE_UNIFIED_MEMORY=0
MEM_FRACTION=1
ENABLE_UNIFIED_MEMORY=1
MEM_FRACTION=2
elif (( "$sum_aa" >= 1500 )) && (( "$sum_aa" < 2500 )); then
RUNTIME="24:00"
NCPUS=24
......@@ -179,7 +179,7 @@ cat <<EOF > $RUNSCRIPT
#BSUB -J alphafold
source /cluster/apps/local/env2lmod.sh
module load gcc/6.3.0 openmpi/4.0.2 alphafold/2.1.1
module load gcc/6.3.0 openmpi/4.0.2 alphafold/2.2.0
source /cluster/apps/nss/alphafold/venv_alphafold/bin/activate
# Define paths to databases and out put directory
......
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