From f135243c964c8342d801d640b0b4acd54b778f89 Mon Sep 17 00:00:00 2001
From: Timothy ODonnell <odonnt02@li03c03.chimera.hpc.mssm.edu>
Date: Mon, 22 Jul 2019 12:57:28 -0400
Subject: [PATCH] update
---
.../GENERATE.WITH_HPC_CLUSTER.sh | 3 +++
.../cluster_submit_script_header.mssm_hpc.lsf | 8 +++++++-
2 files changed, 10 insertions(+), 1 deletion(-)
diff --git a/downloads-generation/models_class1_pan_unselected/GENERATE.WITH_HPC_CLUSTER.sh b/downloads-generation/models_class1_pan_unselected/GENERATE.WITH_HPC_CLUSTER.sh
index 2e4dc910..9faf5e56 100755
--- a/downloads-generation/models_class1_pan_unselected/GENERATE.WITH_HPC_CLUSTER.sh
+++ b/downloads-generation/models_class1_pan_unselected/GENERATE.WITH_HPC_CLUSTER.sh
@@ -28,6 +28,9 @@ git status
cd $SCRATCH_DIR/$DOWNLOAD_NAME
+export OMP_NUM_THREADS=1
+export PYTHONUNBUFFERED=1
+
cp $SCRIPT_DIR/generate_hyperparameters.py .
python generate_hyperparameters.py > hyperparameters.yaml
diff --git a/downloads-generation/models_class1_pan_unselected/cluster_submit_script_header.mssm_hpc.lsf b/downloads-generation/models_class1_pan_unselected/cluster_submit_script_header.mssm_hpc.lsf
index 34556ac1..a5199e86 100644
--- a/downloads-generation/models_class1_pan_unselected/cluster_submit_script_header.mssm_hpc.lsf
+++ b/downloads-generation/models_class1_pan_unselected/cluster_submit_script_header.mssm_hpc.lsf
@@ -1,5 +1,5 @@
#!/bin/bash
-#BSUB -J mhcf-{work_item_num} # Job name
+#BSUB -J MHCf-{work_item_num} # Job name
#BSUB -P acc_nkcancer # allocation account or Unix group
#BSUB -q normal # queue
#BSUB -R span[hosts=1] # one node
@@ -16,6 +16,12 @@ export TMPDIR=/local/JOBS/mhcflurry-{work_item_num}
export PATH=$HOME/.conda/envs/tf-cpu/bin/:$PATH
export PYTHONUNBUFFERED=1
+# See https://www.tensorflow.org/guide/performance/overview
+export KMP_AFFINITY=granularity=fine,verbose,compact,1,0
+export KMP_SETTINGS=1
+export KMP_BLOCKTIME=0
+export OMP_NUM_THREADS=16
+
set -e
free -m
--
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