From f2858cff2b243a46ff33631a5dfbcacac52330d0 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Wed, 12 Jun 2019 08:58:51 -0400
Subject: [PATCH] fix generrate.sh
---
.../models_class1_pan/GENERATE.sh | 14 ++++++--------
.../generate_hyperparameters.py | 16 +++++++++-------
2 files changed, 15 insertions(+), 15 deletions(-)
diff --git a/downloads-generation/models_class1_pan/GENERATE.sh b/downloads-generation/models_class1_pan/GENERATE.sh
index 8724ed3f..ca880004 100755
--- a/downloads-generation/models_class1_pan/GENERATE.sh
+++ b/downloads-generation/models_class1_pan/GENERATE.sh
@@ -15,8 +15,8 @@ rm -rf "$SCRATCH_DIR/$DOWNLOAD_NAME"
mkdir "$SCRATCH_DIR/$DOWNLOAD_NAME"
# 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)
+exec > >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt")
+exec 2> >(tee -ia "$SCRATCH_DIR/$DOWNLOAD_NAME/LOG.txt" >&2)
# Log some environment info
date
@@ -35,7 +35,7 @@ echo "Detected GPUS: $GPUS"
PROCESSORS=$(getconf _NPROCESSORS_ONLN)
echo "Detected processors: $PROCESSORS"
-time mhcflurry-class1-train-pan-allele-models \
+mhcflurry-class1-train-pan-allele-models \
--data "$(mhcflurry-downloads path data_curated)/curated_training_data.with_mass_spec.csv.bz2" \
--allele-sequences "$(mhcflurry-downloads path allele_sequences)/allele_sequences.csv" \
--pretrain-data "$(mhcflurry-downloads path random_peptide_predictions)/predictions.csv.bz2" \
@@ -43,14 +43,12 @@ time mhcflurry-class1-train-pan-allele-models \
--ensemble-size 4 \
--hyperparameters hyperparameters.yaml \
--out-models-dir models-unselected \
-
-
- #--num-jobs $(expr $PROCESSORS \* 2) --gpus $GPUS --max-workers-per-gpu 2 --max-tasks-per-worker 50
+ --num-jobs 4 --gpus $GPUS --max-workers-per-gpu 1 --max-tasks-per-worker 1
cp $SCRIPT_ABSOLUTE_PATH .
bzip2 LOG.txt
tar -cjf "../${DOWNLOAD_NAME}.with_unselected.tar.bz2" *
echo "Created archive: $SCRATCH_DIR/${DOWNLOAD_NAME}.with_unselected.tar.bz2"
-ls * | grep -v models-unselected | xargs -I {} tar -cjf "../${DOWNLOAD_NAME}.tar.bz2" {}
-echo "Created archive: $SCRATCH_DIR/${DOWNLOAD_NAME}.tar.bz2"
\ No newline at end of file
+ls -d * | grep -v models-unselected | xargs -I {} tar -cjf "../${DOWNLOAD_NAME}.tar.bz2" {}
+echo "Created archive: $SCRATCH_DIR/${DOWNLOAD_NAME}.tar.bz2"
diff --git a/downloads-generation/models_class1_pan/generate_hyperparameters.py b/downloads-generation/models_class1_pan/generate_hyperparameters.py
index ea728dc3..72be989f 100644
--- a/downloads-generation/models_class1_pan/generate_hyperparameters.py
+++ b/downloads-generation/models_class1_pan/generate_hyperparameters.py
@@ -48,12 +48,14 @@ base_hyperparameters = {
}
grid = []
-for layer_sizes in [[512, 256], [1024, 512], [1024, 1024]]:
- for l1 in [0.0, 0.0001, 0.001, 0.01]:
- new = deepcopy(base_hyperparameters)
- new["layer_sizes"] = layer_sizes
- new["dense_layer_l1_regularization"] = l1
- if not grid or new not in grid:
- grid.append(new)
+for layer_sizes in [[512, 256], [512, 512],]:
+ for pretrain in [True, False]:
+ for l1 in [0.0, 0.0001, 0.001, 0.01]:
+ new = deepcopy(base_hyperparameters)
+ new["layer_sizes"] = layer_sizes
+ new["dense_layer_l1_regularization"] = l1
+ new["train_data"]["pretrain"] = pretrain
+ if not grid or new not in grid:
+ grid.append(new)
dump(grid, stdout)
--
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