Input pipeline optimization

Simplify the model to its most simplest form. If there are no performance gain per iterations, the application bottleneck is in the input pipeline in reading and preprocess the data.

If GPU utilization is below 80%, the application may be input pipeline bounded.

watch -n 2 nvidia-smi

Verify the CPU utilization as well as the file I/O for bottleneck.

Use CPU for data preprocessing

Use CPU for data preprocessing so we can focus training on GPU. Estimator already put data processing on the CPU.

with tf.device('/cpu:0'):
  data = load__images()

Dataset API

Use feed_dict to feed data for placeholder is not optimal., feed_dict={x: batch_xs, y_: batch_ys})

Use TensorFlow Dataset API for feed data to the deep net. Dataset API utilizes C++ multi-threading and has a much lower overhead than Python code.

Data Format

NHWC (N, Height, width, channel) is the TensorFlow default and NCHW is the optimal format to use for NVIDIA cuDNN. If TensorFlow is compiled with the Intel MKL optimizations, many operations will be optimized and support NCHW. Otherwise, some operations are not supported on CPU when using NCHW. On GPU, NCHW is faster. But on CPU, NHWC is sometimes faster.

With GPU supports:

bn = tf.contrib.layers.batch_norm(
          input_layer, fused=True, data_format='NCHW'

Fused batch norm

Fused Ops combine operations into a single kernel for improved performance. Batch normalization is expensive and therefore should take advantage of fused=True. (12-30% speedup)

bn = tf.layers.batch_normalization(
    input_layer, fused=True, data_format='NCHW')

Avoid large amount of small files

To reduce File I/O overhead, we can preprocess many small data files into larger (~100MB) TFRecord files.

import argparse
import cPickle
import os

import tarfile
from six.moves import xrange  # pylint: disable=redefined-builtin
import tensorflow as tf

CIFAR_FILENAME = 'cifar-10-python.tar.gz'
CIFAR_LOCAL_FOLDER = 'cifar-10-batches-py'

def download_and_extract(data_dir):
  # download CIFAR-10 if not already downloaded.
  tf.contrib.learn.datasets.base.maybe_download(CIFAR_FILENAME, data_dir,
                                                CIFAR_DOWNLOAD_URL), CIFAR_FILENAME),

def _int64_feature(value):
  return tf.train.Feature(int64_list=tf.train.Int64List(value=[value]))

def _bytes_feature(value):
  return tf.train.Feature(bytes_list=tf.train.BytesList(value=[str(value)]))

def _get_file_names():
  """Returns the file names expected to exist in the input_dir."""
  file_names = {}
  file_names['train'] = ['data_batch_%d' % i for i in xrange(1, 5)]
  file_names['validation'] = ['data_batch_5']
  file_names['eval'] = ['test_batch']
  return file_names

def read_pickle_from_file(filename):
  with tf.gfile.Open(filename, 'r') as f:
    data_dict = cPickle.load(f)
  return data_dict

def convert_to_tfrecord(input_files, output_file):
  """Converts a file to TFRecords."""
  print('Generating %s' % output_file)
  with tf.python_io.TFRecordWriter(output_file) as record_writer:
    for input_file in input_files:
      data_dict = read_pickle_from_file(input_file)
      data = data_dict['data']
      labels = data_dict['labels']
      num_entries_in_batch = len(labels)
      for i in range(num_entries_in_batch):
        example = tf.train.Example(features=tf.train.Features(
                'image': _bytes_feature(data[i].tobytes()),
                'label': _int64_feature(labels[i])

def main(data_dir):
  print('Download from {} and extract.'.format(CIFAR_DOWNLOAD_URL))
  file_names = _get_file_names()
  input_dir = os.path.join(data_dir, CIFAR_LOCAL_FOLDER)
  for mode, files in file_names.items():
    input_files = [os.path.join(input_dir, f) for f in files]
    output_file = os.path.join(data_dir, mode + '.tfrecords')
    except OSError:
    # Convert to tf.train.Example and write the to TFRecords.
    convert_to_tfrecord(input_files, output_file)

if __name__ == '__main__':
  parser = argparse.ArgumentParser()
      help='Directory to download and extract CIFAR-10 to.')

  args = parser.parse_args()

CPU optimization

Build from source

The installed package are not built or optimized for your local CPU. If the application is not GPU bounded, we may want to build the source from scratch to take advantage of the CPU optimization.


Set the inter_op_parallelism_threads equal to the number of physical CPUs and

os.environ["KMP_BLOCKTIME"] = str(FLAGS.kmp_blocktime)
os.environ["KMP_SETTINGS"] = str(FLAGS.kmp_settings)
os.environ["KMP_AFFINITY"]= FLAGS.kmp_affinity
if FLAGS.num_intra_threads > 0:
  os.environ["OMP_NUM_THREADS"]= str(FLAGS.num_intra_threads


Convert the GoogleNet into 8-bit precision for inference.

curl -o /tmp/inceptionv3.tgz
tar xzf /tmp/inceptionv3.tgz -C /tmp/
bazel build tensorflow/tools/graph_transforms:transform_graph
bazel-bin/tensorflow/tools/graph_transforms/transform_graph \
  --in_graph=/tmp/classify_image_graph_def.pb \
  --outputs="softmax" --out_graph=/tmp/quantized_graph.pb \
  --transforms='add_default_attributes strip_unused_nodes(type=float, shape="1,299,299,3")
    remove_nodes(op=Identity, op=CheckNumerics) fold_constants(ignore_errors=true)
    fold_batch_norms fold_old_batch_norms quantize_weights quantize_nodes
    strip_unused_nodes sort_by_execution_order'

Running the new quantized model:

# Note: You need to add the dependencies of the quantization operation to the
#       cc_binary in the BUILD file of the label_image program:
#     //tensorflow/contrib/quantization:cc_ops
#     //tensorflow/contrib/quantization/kernels:quantized_ops

bazel build tensorflow/examples/label_image:label_image
bazel-bin/tensorflow/examples/label_image/label_image \
--image=<input-image> \
--graph=/tmp/quantized_graph.pb \
--labels=/tmp/imagenet_synset_to_human_label_map.txt \
--input_width=299 \
--input_height=299 \
--input_mean=128 \
--input_std=128 \
--input_layer="Mul:0" \

Operations and tensors

TensorFlow API constructs new tf.Operation (node) and tf.Tensor (edge) objects and add them to a tf.Graph instance.

  • tf.constant(10.0) adds a tf.Operation to the default graph that produces the value 10.0, and returns a tf.Tensor that represents the value of the constant.
  • _tf.matmul(a, b) creates a tf.Operation that multiplies the values of tf.Tensor objects \(a\) and \(b\) and returns a tf.Tensor for the multiplication result.
  • v = tf.Variable(0) creates a tf.Operation that store a writeable tensor value that persists between calls. The tf.Variable object wraps this operation, and can be used as a tensor to read the current value.
  • tf.train.Optimizer.minimize will add operations and tensors that calculate gradients and return a tf.Operation that apply those gradient changes to a set of variables.

TensorFlow will create a new tf.Tensor each time when a tensor-like object (numpy.ndarray or list) is passed as parameters. It will run out of memory if the object is used multiple times in constructing nodes. To avoid this, call tf.convert_to_tensor on the tensor-like object once and use the returned tf.Tensor instead.