From f472d4b71a24f43fea7add5ffe62b3ac0dddfa00 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Fri, 9 Feb 2018 17:31:32 -0500
Subject: [PATCH] update comments
---
mhcflurry/class1_affinity_predictor.py | 18 +++++++---
mhcflurry/class1_neural_network.py | 29 +++++++++------
.../train_allele_specific_models_command.py | 35 ++++++++++++-------
3 files changed, 56 insertions(+), 26 deletions(-)
diff --git a/mhcflurry/class1_affinity_predictor.py b/mhcflurry/class1_affinity_predictor.py
index 5cf8bf5f..aa41f0cf 100644
--- a/mhcflurry/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_predictor.py
@@ -400,7 +400,8 @@ class Class1AffinityPredictor(object):
inequalities=None,
models_dir_for_save=None,
verbose=0,
- progress_preamble=""):
+ progress_preamble="",
+ progress_print_interval=5.0):
"""
Fit one or more allele specific predictors for a single allele using a
single neural network architecture.
@@ -438,6 +439,9 @@ class Class1AffinityPredictor(object):
progress_preamble : string
Optional string of information to include in each progress update
+ progress_print_interval : float
+ How often (in seconds) to print progress. Set to None to disable.
+
Returns
-------
list of `Class1NeuralNetwork`
@@ -488,7 +492,8 @@ class Class1AffinityPredictor(object):
model_num=model_num + 1,
n_models=n_models,
architecture_num=architecture_num + 1,
- n_architectures=n_architectures))
+ n_architectures=n_architectures),
+ progress_print_interval=progress_print_interval)
if n_architectures > 1:
# We require val_loss (i.e. a validation set) if we have
@@ -532,7 +537,8 @@ class Class1AffinityPredictor(object):
inequalities,
models_dir_for_save=None,
verbose=1,
- progress_preamble=""):
+ progress_preamble="",
+ progress_print_interval=5.0):
"""
Fit one or more pan-allele predictors using a single neural network
architecture.
@@ -568,6 +574,9 @@ class Class1AffinityPredictor(object):
progress_preamble : string
Optional string of information to include in each progress update
+ progress_print_interval : float
+ How often (in seconds) to print progress. Set to None to disable.
+
Returns
-------
list of `Class1NeuralNetwork`
@@ -589,7 +598,8 @@ class Class1AffinityPredictor(object):
inequalities=inequalities,
allele_encoding=allele_encoding,
verbose=verbose,
- progress_preamble=progress_preamble)
+ progress_preamble=progress_preamble,
+ progress_print_interval=progress_print_interval)
model_name = self.model_name("pan-class1", i)
self.class1_pan_allele_models.append(model)
diff --git a/mhcflurry/class1_neural_network.py b/mhcflurry/class1_neural_network.py
index 6ce50ffc..4b9e7878 100644
--- a/mhcflurry/class1_neural_network.py
+++ b/mhcflurry/class1_neural_network.py
@@ -418,7 +418,8 @@ class Class1NeuralNetwork(object):
sample_weights=None,
shuffle_permutation=None,
verbose=1,
- progress_preamble=""):
+ progress_preamble="",
+ progress_print_interval=5.0):
"""
Fit the neural network.
@@ -454,6 +455,10 @@ class Class1NeuralNetwork(object):
progress_preamble : string
Optional string of information to include in each progress update
+
+ progress_print_interval : float
+ How often (in seconds) to print progress update. Set to None to
+ disable.
"""
self.fit_num_points = len(peptides)
@@ -673,7 +678,10 @@ class Class1NeuralNetwork(object):
self.loss_history[key].extend(value)
# Print progress no more often than once every few seconds.
- if not last_progress_print or time.time() - last_progress_print > 5:
+ if progress_print_interval is not None and (
+ not last_progress_print or (
+ time.time() - last_progress_print
+ > progress_print_interval)):
print((progress_preamble + " " +
"Epoch %3d / %3d: loss=%g. "
"Min val loss (%s) at epoch %s" % (
@@ -697,14 +705,15 @@ class Class1NeuralNetwork(object):
min_val_loss_iteration +
self.hyperparameters['patience'])
if i > threshold:
- print((progress_preamble + " " +
- "Stopping at epoch %3d / %3d: loss=%g. "
- "Min val loss (%s) at epoch %s" % (
- i,
- self.hyperparameters['max_epochs'],
- self.loss_history['loss'][-1],
- str(min_val_loss),
- min_val_loss_iteration)).strip())
+ if progress_print_interval is not None:
+ print((progress_preamble + " " +
+ "Stopping at epoch %3d / %3d: loss=%g. "
+ "Min val loss (%s) at epoch %s" % (
+ i,
+ self.hyperparameters['max_epochs'],
+ self.loss_history['loss'][-1],
+ str(min_val_loss),
+ min_val_loss_iteration)).strip())
break
self.fit_seconds = time.time() - start
diff --git a/mhcflurry/train_allele_specific_models_command.py b/mhcflurry/train_allele_specific_models_command.py
index 4b525127..9396230b 100644
--- a/mhcflurry/train_allele_specific_models_command.py
+++ b/mhcflurry/train_allele_specific_models_command.py
@@ -26,7 +26,7 @@ from .common import configure_logging, set_keras_backend
# parallel, we use this global variable as a place to store data. Data that is
# stored here before creating the thread pool will be inherited to the child
# processes upon fork() call, allowing us to share large data with the workers
-# efficiently.
+# via shared memory.
GLOBAL_DATA = {}
@@ -119,7 +119,11 @@ parser.add_argument(
help="Keras backend. If not specified will use system default.")
parser.add_argument(
"--gpus",
- type=int)
+ type=int,
+ metavar="N",
+ help="Number of GPUs to attempt to parallelize across. Requires running "
+ "in parallel.")
+
def run(argv=sys.argv[1:]):
global GLOBAL_DATA
@@ -174,28 +178,30 @@ def run(argv=sys.argv[1:]):
predictor = Class1AffinityPredictor()
if args.num_jobs[0] == 1:
- # Serial run
+ # Serial run.
print("Running in serial.")
worker_pool = None
if args.backend:
set_keras_backend(args.backend)
else:
+ # Parallel run.
env_queue = None
if args.gpus:
+ print("Attempting to round-robin assign each worker a GPU.")
+
+ # We assign each worker to a GPU using the CUDA_VISIBLE_DEVICES
+ # environment variable. To do this, we push environment variables
+ # onto a queue. Each worker reads a single item from the queue,
+ # which is a list of environment variables to set.
next_device = itertools.cycle([
- "%d" % num
- for num in range(args.gpus)
+ "%d" % num for num in range(args.gpus)
])
- queue_items = []
+ env_queue = Queue()
for num in range(args.num_jobs[0]):
- queue_items.append([
+ item = [
("CUDA_VISIBLE_DEVICES", next(next_device)),
- ])
-
- print("Attempting to round-robin assign each worker a GPU", queue_items)
- env_queue = Queue()
- for item in queue_items:
+ ]
env_queue.put(item)
worker_pool = Pool(
@@ -238,6 +244,7 @@ def run(argv=sys.argv[1:]):
'data': None, # subselect from GLOBAL_DATA["train_data"]
'hyperparameters': hyperparameters,
'verbose': args.verbosity,
+ 'progress_print_interval': None if worker_pool else 5.0,
'predictor': predictor if not worker_pool else None,
'save_to': args.out_models_dir if not worker_pool else None,
}
@@ -361,6 +368,7 @@ def train_model(
data,
hyperparameters,
verbose,
+ progress_print_interval,
predictor,
save_to):
@@ -395,6 +403,7 @@ def train_model(
if "measurement_inequality" in train_data.columns else None),
models_dir_for_save=save_to,
progress_preamble=progress_preamble,
+ progress_print_interval=progress_print_interval,
verbose=verbose)
if allele_num == 0 and model_group == 0:
@@ -427,6 +436,8 @@ def calibrate_percentile_ranks(allele, predictor, peptides=None):
def worker_init(env_queue=None):
global GLOBAL_DATA
+ # The env_queue provides a way for each worker to be configured with a
+ # specific set of environment variables. We use it to assign GPUs to workers.
if env_queue:
settings = env_queue.get()
print("Setting: ", settings)
--
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