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add option for selection of cuda devices #16

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add option for selection of cuda devices #16

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22 changes: 17 additions & 5 deletions run_RF2.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,9 @@ HHDB="$PIPEDIR/pdb100_2021Mar03/pdb100_2021Mar03"
CPU="8" # number of CPUs to use
MEM="64" # max memory (in GB)

# Default value for CUDA_VISIBLE_DEVICES
CUDA_VISIBLE_DEVICES="" # Empty string means all GPUs are visible

WDIR='rf2out'
#mkdir -p $WDIR/log

Expand Down Expand Up @@ -55,10 +58,11 @@ symm="C1"
pair=0
hhpred=0
fastas=()
cuda_device=-1 # Default value, -1 means no specific GPU

## parse command line
USAGESTRING="Usage: $(basename $0) [-o|--outdir name] [-s|--symm symmgroup] [-p|--pair] [-h|--hhpred] input1.fasta ... inputN.fasta"
VALID_ARGS=$(getopt -o o:s:ph --long help,outdir:,symm:,pair,hhpred -- "$@")
USAGESTRING="Usage: $(basename $0) [-o|--outdir name] [-s|--symm symmgroup] [-p|--pair] [-h|--hhpred] [-c|--cuda cuda_device] input1.fasta ... inputN.fasta"
VALID_ARGS=$(getopt -o o:s:phc: --long help,outdir:,symm:,pair,hhpred,cuda: -- "$@")
if [[ $? -ne 0 ]]; then
exit 1;
fi
Expand All @@ -73,6 +77,7 @@ while [ : ]; do
echo " Understands Cn, Dn, T, I, O (with n an integer)."
echo " -p|--pair: If more than one chain is provided, pair MSAs based on taxonomy ID."
echo " -h|--hhpred: Run hhpred to generate templates"
echo " -c|--cuda: Select a CUDA device to run on (Integer)"
exit 1
;;
-p | --pair)
Expand All @@ -91,13 +96,20 @@ while [ : ]; do
WDIR="$2"
shift 2
;;
-c | --cuda)
cuda_device="$2"
shift 2
;;
--)
shift;
break
shift;
break
;;
esac
done

# Set CUDA_VISIBLE_DEVICES environment variable based on the provided cuda_device value
export CUDA_VISIBLE_DEVICES="$cuda_device"

mkdir -p $WDIR/log

argstring=""
Expand Down Expand Up @@ -153,6 +165,6 @@ python $PIPEDIR/network/predict.py \
-prefix $WDIR/models/model \
-model $PIPEDIR/network/weights/RF2_apr23.pt \
-db $HHDB \
-symm $symm #2> $WDIR/log/network.stderr 1> $WDIR/log/network.stdout
-symm $symm #2> $WDIR/log/network.stderr 1> $WDIR/log/network.stdout

echo "Done"