From 129f9ff250cdb2e2ef97bf0a1adcdde9369c4f50 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Mon, 26 Aug 2019 13:27:11 -0400
Subject: [PATCH] fix
---
.../GENERATE.WITH_HPC_CLUSTER.sh | 85 +++++++++++++++++++
.../cluster_submit_script_header.mssm_hpc.lsf | 1 +
2 files changed, 86 insertions(+)
create mode 100755 downloads-generation/models_class1_pan/GENERATE.WITH_HPC_CLUSTER.sh
create mode 120000 downloads-generation/models_class1_pan/cluster_submit_script_header.mssm_hpc.lsf
diff --git a/downloads-generation/models_class1_pan/GENERATE.WITH_HPC_CLUSTER.sh b/downloads-generation/models_class1_pan/GENERATE.WITH_HPC_CLUSTER.sh
new file mode 100755
index 00000000..e6c275cf
--- /dev/null
+++ b/downloads-generation/models_class1_pan/GENERATE.WITH_HPC_CLUSTER.sh
@@ -0,0 +1,85 @@
+#!/bin/bash
+#
+# Model select pan-allele MHCflurry Class I models and calibrate percentile ranks.
+#
+# Uses an HPC cluster (Mount Sinai chimera cluster, which uses lsf job
+# scheduler). This would need to be modified for other sites.
+#
+set -e
+set -x
+
+DOWNLOAD_NAME=models_class1_pan
+SCRATCH_DIR=${TMPDIR-/tmp}/mhcflurry-downloads-generation
+SCRIPT_ABSOLUTE_PATH="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/$(basename "${BASH_SOURCE[0]}")"
+SCRIPT_DIR=$(dirname "$SCRIPT_ABSOLUTE_PATH")
+
+mkdir -p "$SCRATCH_DIR"
+
+# Send stdout and stderr to a logfile included with the archive.
+exec > >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt")
+exec 2> >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt" >&2)
+
+# Log some environment info
+echo "Invocation: $0 $@"
+date
+pip freeze
+git status
+
+cd $SCRATCH_DIR/$DOWNLOAD_NAME
+
+export OMP_NUM_THREADS=1
+export PYTHONUNBUFFERED=1
+
+cp $SCRIPT_ABSOLUTE_PATH .
+
+GPUS=$(nvidia-smi -L 2> /dev/null | wc -l) || GPUS=0
+echo "Detected GPUS: $GPUS"
+
+PROCESSORS=$(getconf _NPROCESSORS_ONLN)
+echo "Detected processors: $PROCESSORS"
+
+if [ "$GPUS" -eq "0" ]; then
+ NUM_JOBS=${NUM_JOBS-1}
+else
+ NUM_JOBS=${NUM_JOBS-$GPUS}
+fi
+echo "Num local jobs for model selection: $NUM_JOBS"
+
+UNSELECTED_PATH="$(mhcflurry-downloads path models_class1_pan_unselected)"
+
+for kind in with_mass_spec no_mass_spec
+do
+ # Model selection is always done locally. It's fast enough that it
+ # doesn't make sense to put it on the cluster.
+ MODELS_DIR="$UNSELECTED_PATH/models.${kind}"
+ time mhcflurry-class1-select-pan-allele-models \
+ --data "$MODELS_DIR/train_data.csv.bz2" \
+ --models-dir "$MODELS_DIR" \
+ --out-models-dir models.${kind} \
+ --min-models 8 \
+ --max-models 32 \
+ --num-jobs $NUM_JOBS --max-tasks-per-worker 1 --gpus $GPUS --max-workers-per-gpu 1
+
+ # Percentile rank calibration is run on the cluster.
+ # For now we calibrate percentile ranks only for alleles for which there
+ # is training data. Calibrating all alleles would be too slow.
+ # This could be improved though.
+ time mhcflurry-calibrate-percentile-ranks \
+ --models-dir models.${kind} \
+ --match-amino-acid-distribution-data "$MODELS_DIR/train_data.csv.bz2" \
+ --motif-summary \
+ --num-peptides-per-length 100000 \
+ --allele $(bzcat "$MODELS_DIR/train_data.csv.bz2" | cut -f 1 -d , | grep -v allele | uniq | sort | uniq) \
+ --verbosity 1 \
+ --worker-log-dir "$SCRATCH_DIR/$DOWNLOAD_NAME" \
+ --cluster-parallelism \
+ --cluster-submit-command bsub \
+ --cluster-results-workdir ~/mhcflurry-scratch \
+ --cluster-script-prefix-path $SCRIPT_DIR/cluster_submit_script_header.mssm_hpc.lsf
+done
+
+bzip2 LOG.txt
+for i in $(ls LOG-worker.*.txt) ; do bzip2 $i ; done
+RESULT="$SCRATCH_DIR/${DOWNLOAD_NAME}.$(date +%Y%m%d).tar.bz2"
+tar -cjf "$RESULT" *
+echo "Created archive: $RESULT"
diff --git a/downloads-generation/models_class1_pan/cluster_submit_script_header.mssm_hpc.lsf b/downloads-generation/models_class1_pan/cluster_submit_script_header.mssm_hpc.lsf
new file mode 120000
index 00000000..09aeb92d
--- /dev/null
+++ b/downloads-generation/models_class1_pan/cluster_submit_script_header.mssm_hpc.lsf
@@ -0,0 +1 @@
+../models_class1_pan_unselected/cluster_submit_script_header.mssm_hpc.lsf
\ No newline at end of file
--
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