45 lines
1.3 KiB
Bash
Executable File
45 lines
1.3 KiB
Bash
Executable File
#!/bin/bash
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#SBATCH -p gpu
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#SBATCH -J alphafold
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#SBATCH -M gmerlin6
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#SBATCH --gpus=1
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#SBATCH -n 1
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#SBATCH -c 10
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# sLURM Options can be overwritten by specifing in the sbatch command!
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#
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# Alphafold submission script for the merlin cluster
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# Usage: sbatch [slurm_opts] alphafold_merlin.sh [options] fasta_file
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#
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# OPTIONS
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# All alphafold options are set automatically, but can be overwritten.
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# Some common options:
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#
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# --max_template_date=YYYY-MM-DD (default: today)
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# --output_dir (default: current directory
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# --helpfull List all options
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#
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# 2024-02-08 Spencer Bliven, Greta Assmann
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#
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export ALPHAFOLD_DATA=/data/project/bio/shared/alphafold/versions/v2.3.2/latest
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source /opt/psi/MX/alphafold/ALPHAFOLD_VERSION/miniconda/etc/profile.d/conda.sh
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conda activate "${ALPHAFOLD_ENV:?"Error: ALPHAFOLD_ENV not set. Try 'module use MX unstable; module load alphafold'"}"
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export ALPH_TMP_DIR=/scratch/${SLURM_JOBID}
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mkdir -p $ALPH_TMP_DIR
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export TF_FORCE_UNIFIED_MEMORY=1
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export XLA_PYTHON_CLIENT_MEM_FRACTION="4.0"
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echo "hostname=$(hostname)"
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echo "python=$(which python)"
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echo "ALPHAFOLD_DATA=$(realpath "$ALPHAFOLD_DATA")"
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echo "Alphafold version=$(which alphafold_merlin.sh)"
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echo "$ALPHAFOLD_ENV"
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python "${ALPHAFOLD_DIR:?Error loading module}/bin/alphafold_runner.py" -v 0 "$@"
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squeue -j $SLURM_JOB_ID
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rm -rf $ALPH_TMP_DIR
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