TensorFlow

TensorFlow is "an open-source software library for Machine Intelligence".

Installing TensorFlow

These instructions install TensorFlow in your home directory using Compute Canada's pre-built Python wheels. Custom Python wheels are stored in /cvmfs/soft.computecanada.ca/custom/python/wheelhouse/. To install a TensorFlow wheel we will use the pip command and install it into a Python virtual environment. The instructions below are for Python 3.6 but you can also install other Python versions by loading a different Python module.

Load modules required by TensorFlow.

[name@server ~]$ module load python/3.6

Create a new Python virtual environment.

[name@server ~]$ virtualenv tensorflow

Activate your newly created Python virtual environment.

[name@server ~]$ source tensorflow/bin/activate

Install TensorFlow in your newly created virtual environment using the command from either one of the two following subsections.

Do not install the tensorflow package (without the _cpu or _gpu suffixes) as it has compatibility issues with other libraries.

CPU-only

(tensorflow)_[name@server ~]$ pip install --no-index tensorflow_cpu

GPU

(tensorflow)_[name@server ~]$ pip install --no-index tensorflow_gpu

R package

To use TensorFlow in R, you will need to first follow the preceding instructions on creating a virtual environment and installing TensorFlow in it. Once this is done, following these instructions.

Load the required modules.

[name@server ~]$ module load gcc r

Activate your Python virtual environment.

[name@server ~]$ source tensorflow/bin/activate

Launch R.

(tensorflow)_[name@server ~]$ R

In R, install package devtools, then tensorflow:

install.packages('devtools', repos='https://cloud.r-project.org')
devtools::install_github('rstudio/tensorflow')

You are then good to go. Do not call install_tensorflow() in R, as TensorFlow has already been installed in your virtual environment with pip. To use the TensorFlow installed in your virtual environment, enter the following commands in R after the environment has been activated.

library(tensorflow)
use_virtualenv(Sys.getenv('VIRTUAL_ENV'))

Submitting a TensorFlow job with a GPU

Once you have the above setup completed you can submit a TensorFlow job.

[name@server ~]$ sbatch tensorflow-test.sh

The job submission script contains

File : tensorflow-test.sh

#!/bin/bash
#SBATCH --gres=gpu:1        # request GPU "generic resource"
#SBATCH --cpus-per-task=6   # maximum CPU cores per GPU request: 6 on Cedar, 16 on Graham.
#SBATCH --mem=32000M        # memory per node
#SBATCH --time=0-03:00      # time (DD-HH:MM)
#SBATCH --output=%N-%j.out  # %N for node name, %j for jobID

module load cuda cudnn 
source tensorflow/bin/activate
python ./tensorflow-test.py

while the Python script has the form

File : tensorflow-test.py

import tensorflow as tf
node1 = tf.constant(3.0, dtype=tf.float32)
node2 = tf.constant(4.0) # also tf.float32 implicitly
print(node1, node2)
sess = tf.Session()
print(sess.run([node1, node2]))

Once the job has completed (should take less than a minute) you should see an output file called something like cdr116-122907.out with contents similar to the following example.

File : cdr116-122907.out

2017-07-10 12:35:19.489458: I tensorflow/core/common_runtime/gpu/gpu_device.cc:940] Found device 0 with properties:
name: Tesla P100-PCIE-12GB
major: 6 minor: 0 memoryClockRate (GHz) 1.3285
pciBusID 0000:82:00.0
Total memory: 11.91GiB
Free memory: 11.63GiB
2017-07-10 12:35:19.491097: I tensorflow/core/common_runtime/gpu/gpu_device.cc:961] DMA: 0
2017-07-10 12:35:19.491156: I tensorflow/core/common_runtime/gpu/gpu_device.cc:971] 0:   Y
2017-07-10 12:35:19.520737: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1030] Creating TensorFlow device (/gpu:0) -> (device: 0, name: Tesla P100-PCIE-12GB, pci bus id: 0000:82:00.0)
Tensor("Const:0", shape=(), dtype=float32) Tensor("Const_1:0", shape=(), dtype=float32)
[3.0, 4.0]

TensorFlow can run on all GPU node types. Cedar's GPU large node type, which is equipped with 4 x P100-PCIE-16GB with GPUDirect P2P enabled between each pair, is highly recommended for large scale deep learning or machine learning research. See Using GPUs with SLURM for more information.

Contrib compatiblity matrix

Compute Canada compiles TensorFlow wheels for maximum performance and adds features that are not available in Google's TensorFlow releases. Some of these features are part of the TensorFlow contrib folder and therefore not officially supported by TensorFlow developers, nor by Compute Canada staff. We try to accommodate as many users as possible by activating these features, but we are unable to provide support.

We present here a compatibility matrix of the contrib features we have compiled for each TensorFlow version and whether the feature is compiled, functional or tested.

TensorFlow Version	GDR	VERBS	MPI
1.4.0	compiled, functional	compiled, untested	compiled, functional
1.5.0	compiled, not functional	compiled, untested	compiled, not functional
1.6.0	compiled, not functional	compiled, untested	compiled, not functional
1.7.0	compiled, functional	compiled, functional	compiled, not functional
1.8.0	compiled, untested	compiled, untested	compiled, untested

If a contrib feature is missing in the version you use and you would like Compute Canada staff to try to integrate it, contact Technical support. We will do our best to recompile TensorFlow with that feature activated.

Monitoring

It is possible to connect to the node running a job and execute processes. This can be used to monitor resources used by TensorFlow and to visualize the progress of the training. See Attaching to a running job for examples.

TensorBoard

TensorFlow comes with a suite of visualization tools called TensorBoard. TensorBoard operates by reading TensorFlow events and model files. To know how to create these files, read TensorBoard tutorial on summaries. The event files are created in a directory specified by the user referred to as logdir.

The following command will launch TensorBoard:

[name@server ~]$ tensorboard --logdir=path/to/logdir --host 0.0.0.0

Note, however, that TensorBoard requires too much processing power to be run on a login node. Users are strongly encouraged to execute it in parallel with their TensorFlow job. The following submit script gives an example. The source code of mnist_with_summaries.py is available here.

File : tensorboard.sh

#!/bin/bash
#SBATCH --gres=gpu:1        # request GPU "generic resource"
#SBATCH --cpus-per-task=6   # maximum CPU cores per GPU request: 6 on Cedar, 16 on Graham.
#SBATCH --mem=32000M        # memory per node
#SBATCH --time=01:00      # time (DD-HH:MM)

source tensorflow/bin/activate
tensorboard --logdir=/tmp/tensorflow/mnist/logs/mnist_with_summaries --host 0.0.0.0 &
python mnist_with_summaries.py

Once the job is running, to access TensorBoard with a web browser, you need to create a connection between your computer and the compute node running TensorFlow and TensorBoard. To do this you first need the hostname of the compute node running the Tensorboard server which can be retrieved as follows:

[name@server ~]$ squeue --job JOBID -o %N

To create that connection, use the following command:

[name@my_computer ~]$ ssh -N -f -L localhost:6006:computenode:6006 userid@cluster.computecanada.ca

Replace computenode with the node hostname you retrieved from the preceding step, userid by your Compute Canada username, cluster by the cluster hostname (i.e.: Cedar, Graham, etc.).

Once the connection is created, go to http://localhost:6006.

TensorFlow with Multi-GPUs

TensorFlow provides different methods of managing variables when training models on multiple GPUs. "Parameter Server" and "Replicated" are the most two common methods.

• In this section, TensorFlow Benchmarks code will be used as an example to explain the different methods. Users can reference the TensorFlow Benchmarks code to implement their own.

Parameter Server

Variables are stored on a parameter server that holds the master copy of the variable. In distributed training, the parameter servers are separate processes in the different devices. For each step, each tower gets a copy of the variables from the parameter server, and sends its gradients to the param server.

Parameters can be stored in CPU:

python tf_cnn_benchmarks.py --variable_update=parameter_server --local_parameter_device=cpu

or GPU:

python tf_cnn_benchmarks.py --variable_update=parameter_server --local_parameter_device=gpu

Replicated

With this method, each GPU has its own copy of the variables. To apply gradients, an all_reduce algorithm or or regular cross-device aggregation is used to replicate the combined gradients to all towers (depending on the all_reduce_spec parameter's setting).

All reduce method can be default:

python tf_cnn_benchmarks.py --variable_update=replicated

Xring --- use one global ring reduction for all tensors:

python tf_cnn_benchmarks.py --variable_update=replicated --all_reduce_spec=xring

Pscpu --- use CPU at worker 0 to reduce all tensors:

python tf_cnn_benchmarks.py --variable_update=replicated --all_reduce_spec=pscpu

NCCL --- use NCCL to locally reduce all tensors:

python tf_cnn_benchmarks.py --variable_update=replicated --all_reduce_spec=nccl

Different variable managing methods perform differently with different models. Users are highly recommended to test their own models with all methods on different types of GPU node.

Benchmarks

This section will give ResNet-50 and VGG-16 benchmarking results on both Graham and Cedar with single and multiple GPUs using different methods for managing variables. TensorFlow v1.5 (built with CUDA 9 and cuDNN 7) is used. The benchmark can be found on github at TensorFlow Benchmarks.

• ResNet-50

Batch size is 32 per GPU. Data parallelism is used. (Results in "images per second")

Node type	1 GPU	Number of GPUs	ps,cpu	ps, gpu	replicated	replicated, xring	replicated, pscpu	replicated, nccl
Graham GPU node	171.23	2	93.31	324.04	318.33	316.01	109.82	315.99
Cedar GPU Base	172.99	4	662.65	595.43	616.02	490.03	645.04	608.95
Cedar GPU Large	205.71	4	673.47	721.98	754.35	574.91	664.72	692.25

• VGG-16

Batch size is 32 per GPU. Data parallelism is used. (Results in "images per second")

Node type	1 GPU	Number of GPUs	ps,cpu	ps, gpu	replicated	replicated, xring	replicated, pscpu	replicated, nccl
Graham GPU node	115.89	2	91.29	194.46	194.43	203.83	132.19	219.72
Cedar GPU Base	114.77	4	232.85	280.69	274.41	341.29	330.04	388.53
Cedar GPU Large	137.16	4	175.20	379.80	336.72	417.46	225.37	490.52

Troubleshooting

scikit image

If you are using the scikit-image library, you may get the following error: OMP: Error #15: Initializing libiomp5.so, but found libiomp5.so already initialized.

This is because the tensorflow library tries to load a bundled version of OMP which conflicts with the system version. The workaround is as follows:

(tf_skimage_venv) name@server $ cd tf_skimage_venv
(tf_skimage_venv) name@server $ export LIBIOMP_PATH=$(strace python -c 'from skimage.transform import AffineTransform' 2>&1 | grep -v ENOENT | grep -ohP -e '(?<=")[^"]+libiomp5.so(?=")' | xargs realpath)
(tf_skimage_venv) name@server $ find -path '*_solib_local*' -name libiomp5.so -exec ln -sf $LIBIOMP_PATH {} \;

This will patch the tensorflow library installation to use the systemwide libiomp5.so.

libcupti.so

Some tracing features of Tensorflow require libcupti.so to be available, and might give the following error if they are not:

I tensorflow/stream_executor/dso_loader.cc:142] Couldn't open CUDA library libcupti.so.9.0. LD_LIBRARY_PATH: /usr/local/cuda-9.0/lib64

The solution is to run the following before executing your script:

[name@server ~]$ module load cuda/9.0.xxx
[name@server ~]$ export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CUDA_HOME/extras/CUPTI/lib64/

Where xxx is the appropriate CUDA version, which can be found using module av cuda

libiomp5.so invalid ELF header

Sometimes the libiomp5.so shared object file will be erroneously installed as a text file. This might result in errors like the following:

/home/username/venv/lib/python3.6/site-packages/tensorflow/python/../../_solib_local/_U@mkl_Ulinux_S_S_Cmkl_Ulibs_Ulinux___Uexternal_Smkl_Ulinux_Slib/libiomp5.so: invalid ELF header

The workaround for such errors is to access the directory mentioned in the error (i.e. [...]/_U@mkl_Ulinux_S_S_Cmkl_Ulibs_Ulinux___Uexternal_Smkl_Ulinux_Slib) and execute the following command:

[name@server ...Ulinux_Slib] $ ln -sf $(cat libiomp5.so) libiomp5.so

This will replace the text file with the correct symbolic link.

Message Passing Interface