From f0140df0f54538a93874d3fbef40eebd5f11dbd9 Mon Sep 17 00:00:00 2001
From: Timothy ODonnell <odonnt02@li03c03.chimera.hpc.mssm.edu>
Date: Thu, 3 Oct 2019 10:11:11 -0400
Subject: [PATCH] fix
---
.../GENERATE.WITH_HPC_CLUSTER.sh | 6 +++---
...ster_submit_script_header.mssm_hpc.nogpu.lsf | 17 ++++++++++++++---
2 files changed, 17 insertions(+), 6 deletions(-)
diff --git a/downloads-generation/data_mass_spec_benchmark/GENERATE.WITH_HPC_CLUSTER.sh b/downloads-generation/data_mass_spec_benchmark/GENERATE.WITH_HPC_CLUSTER.sh
index 4a7e849d..5f73e767 100755
--- a/downloads-generation/data_mass_spec_benchmark/GENERATE.WITH_HPC_CLUSTER.sh
+++ b/downloads-generation/data_mass_spec_benchmark/GENERATE.WITH_HPC_CLUSTER.sh
@@ -64,12 +64,12 @@ python write_proteome_peptides.py \
python run_thirdparty_predictors.py \
proteome_peptides.chr1.csv \
--predictor netmhcpan4 \
- --chunk-size 100000 \
+ --chunk-size 10000 \
--allele $(cat alleles.txt) \
--out "predictions/chr1.netmhcpan4" \
--worker-log-dir "$SCRATCH_DIR/$DOWNLOAD_NAME" \
--cluster-parallelism \
- --cluster-max-retries 15 \
+ --cluster-max-retries 3 \
--cluster-submit-command bsub \
--cluster-results-workdir ~/mhcflurry-scratch \
--cluster-script-prefix-path $SCRIPT_DIR/cluster_submit_script_header.mssm_hpc.nogpu.lsf
@@ -106,7 +106,7 @@ python run_thirdparty_predictors.py \
--out "predictions/all.netmhcpan4" \
--worker-log-dir "$SCRATCH_DIR/$DOWNLOAD_NAME" \
--cluster-parallelism \
- --cluster-max-retries 15 \
+ --cluster-max-retries 3 \
--cluster-submit-command bsub \
--cluster-results-workdir ~/mhcflurry-scratch \
--cluster-script-prefix-path cluster_submit_script_header.mssm_hpc.nogpu.lsf
diff --git a/downloads-generation/data_mass_spec_benchmark/cluster_submit_script_header.mssm_hpc.nogpu.lsf b/downloads-generation/data_mass_spec_benchmark/cluster_submit_script_header.mssm_hpc.nogpu.lsf
index 7b85917f..275d650b 100644
--- a/downloads-generation/data_mass_spec_benchmark/cluster_submit_script_header.mssm_hpc.nogpu.lsf
+++ b/downloads-generation/data_mass_spec_benchmark/cluster_submit_script_header.mssm_hpc.nogpu.lsf
@@ -4,8 +4,8 @@
#BSUB -q express # queue
#BSUB -R span[hosts=1] # one node
#BSUB -n 1 # number of compute cores
-#BSUB -W 46:00 # walltime in HH:MM
-#BSUB -R rusage[mem=30000] # mb memory requested
+#BSUB -W 12:00 # walltime in HH:MM
+#BSUB -R rusage[mem=20000] # mb memory requested
#BSUB -o {work_dir}/%J.stdout # output log (%J : JobID)
#BSUB -eo {work_dir}/STDERR # error log
#BSUB -L /bin/bash # Initialize the execution environment
@@ -25,8 +25,19 @@ export NETMHC_BUNDLE_HOME=$HOME/sinai/git/netmhc-bundle
export NETMHC_BUNDLE_TMPDIR=/local/JOBS/netmhctmp-{work_item_num}
export PATH=$NETMHC_BUNDLE_HOME/bin:$PATH
+cd {work_dir}
+
+mkdir -p "$NETMHC_BUNDLE_TMPDIR"
+mkdir -p "$TMPDIR"
+
+chmod 777 "$NETMHC_BUNDLE_TMPDIR"
+chmod 777 "$TMPDIR"
+
+ls "$NETMHC_BUNDLE_TMPDIR"
+ls "$TMPDIR"
+
+netMHCpan-4.0 -listMHC
free -m
env
-cd {work_dir}
--
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