TensorFlow is a common machine learning package primarily run in python: https://www.tensorflow.org/

Keras (https://keras.io/) is a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano.

Pro Tip: Keras is also available in any standard TensorFlow install

import tensorflow.contrib.keras as keras
# or
import tensorflow as tf
tf.keras

Several versions of TensorFlow exist on Talapas this article will cover the GPU version of TensorFlow available on all GPU nodes.

Step-by-step guide

We will start by launching and iterative GPU session from one of the talapas login nodes

$ srun --account=<your account> --pty --gres=gpu:1 --mem=4G --time=60 --partition=testgpu bash

Wait for your interactive session to start

Load the modules for tensorflow

$ module load cuda/9.0
$ module load python3

Check what GPU resources are available

$ nvidia-smi 
+-----------------------------------------------------------------------------+
| NVIDIA-SMI 390.46                 Driver Version: 390.46                    |
|-------------------------------+----------------------+----------------------+
| GPU  Name        Persistence-M| Bus-Id        Disp.A | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap|         Memory-Usage | GPU-Util  Compute M. |
|===============================+======================+======================|
|   0  Tesla K80           Off  | 00000000:04:00.0 Off |                  Off |
| N/A   35C    P0    60W / 149W |     97MiB / 12206MiB |      0%      Default |
+-------------------------------+----------------------+----------------------+

Shows that we have successfully reserved 1 Tesla K80

Launch python 3 (Note: the python command will give you the default python2 version on the system, use python3)

$ python3
>>from tensorflow.python.client import device_lib
>>print(device_lib.list_local_devices())

2018-09-19 11:11:34.399858: I tensorflow/core/platform/cpu_feature_guard.cc:140] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2018-09-19 11:11:34.524069: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1344] Found device 0 with properties: 
name: Tesla K80 major: 3 minor: 7 memoryClockRate(GHz): 0.8235
pciBusID: 0000:04:00.0
totalMemory: 11.92GiB freeMemory: 11.75GiB
2018-09-19 11:11:34.524110: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1423] Adding visible gpu devices: 0
2018-09-19 11:11:34.796876: I tensorflow/core/common_runtime/gpu/gpu_device.cc:911] Device interconnect StreamExecutor with strength 1 edge matrix:
2018-09-19 11:11:34.796918: I tensorflow/core/common_runtime/gpu/gpu_device.cc:917]      0 
2018-09-19 11:11:34.796926: I tensorflow/core/common_runtime/gpu/gpu_device.cc:930] 0:   N 
2018-09-19 11:11:34.797220: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1041] Created TensorFlow device (/device:GPU:0 with 11399 MB memory) -> physical GPU (device: 0, name: Tesla K80, pci bus id: 0000:04:00.0, compute capability: 3.7)
[name: "/device:CPU:0"
device_type: "CPU"
memory_limit: 268435456
locality {
}
incarnation: 13411014324454836610
, name: "/device:GPU:0"
device_type: "GPU"
memory_limit: 11953517364
locality {
  bus_id: 1
  links {
  }
}
incarnation: 133570401343557472
physical_device_desc: "device: 0, name: Tesla K80, pci bus id: 0000:04:00.0, compute capability: 3.7"
]

this also confirms you are correctly using the GPU version of tensorflow and have access to one cpu and one Tesla k-80 CTRL+D to exit

Lets try to fit a simple model. Copy the following text into a file called my_test.py using your favorite text editor (for example emacs)

my_test.py

#
import tensorflow as tf

(x_train,y_train),(x_test,y_test)=tf.keras.datasets.mnist.load_data()
#Note this will download the mnist dataset to ~/.kears/datasets the first time you run it


#Lets create a 2 hidden layer neural network
input=tf.keras.layers.Input(shape=(28,28))
network=tf.keras.layers.Flatten()(input)
network=tf.keras.layers.Dense(10)(network)
network=tf.keras.layers.LeakyReLU()(network)
network=tf.keras.layers.Dropout(0.2)(network)
network=tf.keras.layers.Dense(10)(network)
network=tf.keras.layers.LeakyReLU()(network)
output=tf.keras.layers.Dense(10,activation='softmax')(network)

my_model=tf.keras.models.Model(input,output)
my_model.summary()
my_model.compile(loss='sparse_categorical_crossentropy',optimizer='adam',metrics=['acc'])
my_model.fit(x_train,y_train,validation_data=(x_test,y_test),epochs=10)

This model is training to identify a hand written number from a 28x28 pixel image. We use two fully connected layers, and dropout (to prevent overfitting).

Example Data: https://en.wikipedia.org/wiki/MNIST_database

Lets run it

$ python3 my_test.py 

(60000, 28, 28)
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input_1 (InputLayer)         (None, 28, 28)            0         
_________________________________________________________________
flatten_1 (Flatten)          (None, 784)               0         
_________________________________________________________________
dense_1 (Dense)              (None, 10)                7850      
_________________________________________________________________
leaky_re_lu_1 (LeakyReLU)    (None, 10)                0         
_________________________________________________________________
dropout_1 (Dropout)          (None, 10)                0         
_________________________________________________________________
dense_2 (Dense)              (None, 10)                110       
_________________________________________________________________
leaky_re_lu_2 (LeakyReLU)    (None, 10)                0         
_________________________________________________________________
dense_3 (Dense)              (None, 10)                110       
=================================================================
Total params: 8,070
Trainable params: 8,070
Non-trainable params: 0
_________________________________________________________________
Train on 60000 samples, validate on 10000 samples
Epoch 1/10
2018-09-19 11:52:13.929548: I tensorflow/core/platform/cpu_feature_guard.cc:140] Your CPU supports instructions that this TensorFlow binary was not compiled to use: AVX2 FMA
2018-09-19 11:52:14.058190: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1344] Found device 0 with properties: 
name: Tesla K80 major: 3 minor: 7 memoryClockRate(GHz): 0.8235
pciBusID: 0000:04:00.0
totalMemory: 11.92GiB freeMemory: 11.75GiB
2018-09-19 11:52:14.058229: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1423] Adding visible gpu devices: 0
2018-09-19 11:52:14.335734: I tensorflow/core/common_runtime/gpu/gpu_device.cc:911] Device interconnect StreamExecutor with strength 1 edge matrix:
2018-09-19 11:52:14.335778: I tensorflow/core/common_runtime/gpu/gpu_device.cc:917]      0 
2018-09-19 11:52:14.335786: I tensorflow/core/common_runtime/gpu/gpu_device.cc:930] 0:   N 
2018-09-19 11:52:14.336087: I tensorflow/core/common_runtime/gpu/gpu_device.cc:1041] Created TensorFlow device (/job:localhost/replica:0/task:0/device:GPU:0 with 11399 MB memory) -> physical GPU (device: 0, name: Tesla K80, pci bus id: 0000:04:00.0, compute capability: 3.7)
60000/60000 [==============================] - 7s 123us/step - loss: 4.1213 - acc: 0.6669 - val_loss: 1.4595 - val_acc: 0.8431
Epoch 2/10
60000/60000 [==============================] - 7s 109us/step - loss: 1.3066 - acc: 0.7841 - val_loss: 0.4579 - val_acc: 0.8820
Epoch 3/10
60000/60000 [==============================] - 7s 109us/step - loss: 0.6586 - acc: 0.8106 - val_loss: 0.3734 - val_acc: 0.8948
Epoch 4/10
60000/60000 [==============================] - 6s 108us/step - loss: 0.5859 - acc: 0.8254 - val_loss: 0.3708 - val_acc: 0.8942
Epoch 5/10
60000/60000 [==============================] - 6s 107us/step - loss: 0.5356 - acc: 0.8412 - val_loss: 0.3513 - val_acc: 0.9021
Epoch 6/10
60000/60000 [==============================] - 6s 107us/step - loss: 0.5148 - acc: 0.8457 - val_loss: 0.3542 - val_acc: 0.9043
Epoch 7/10
60000/60000 [==============================] - 6s 107us/step - loss: 0.5036 - acc: 0.8484 - val_loss: 0.3397 - val_acc: 0.9064
Epoch 8/10
60000/60000 [==============================] - 6s 107us/step - loss: 0.4928 - acc: 0.8533 - val_loss: 0.3207 - val_acc: 0.9140
Epoch 9/10
60000/60000 [==============================] - 6s 107us/step - loss: 0.4837 - acc: 0.8549 - val_loss: 0.3309 - val_acc: 0.9085
Epoch 10/10
60000/60000 [==============================] - 6s 107us/step - loss: 0.4819 - acc: 0.8560 - val_loss: 0.3224 - val_acc: 0.9127s

Congratulations you've trained your first network on Talapas! Let's try one more time in batch mode.

Use CRTL+D to close your interactive session

Write a new submit script to run the same training code, by putting the following into a file named submit_gpu_test

submit_gpu_test

#!/bin/bash                                                                                             
#SBATCH --job-name=GPUMnistTest     ### Job Name                                                        
#SBATCH --partition=gpu       ### Quality of Service (like a queue in PBS)                              
#SBATCH --time=0-01:00:00     ### Wall clock time limit in Days-HH:MM:SS                                
#SBATCH --nodes=1             ### Node count required for the job                                       
#SBATCH --ntasks-per-node=1   ### Nuber of tasks to be launched per Node                                
#SBATCH --gres=gpu:1          ### General REServation of gpu:number of gpus                             
#SBATCH --account=<your account> 

module load cuda/9.0
module load python3
python3 my_test.py > my_test_output

Submit this job
```
sbatch submit_gpu_test
```
That's it wait for your job to finish, and you'll see the training log in ~\my_test_output

Using the Latest Tensorflow with Singularity

If you need the latest version of tensorflow for your code, it is possible to pull a pre-made docker image and run it with singularity.

For example in an interactive GPU session (see above):

Build your image from the online repository - this will create a tf-l.simg file that can be executed with singularities other commands. This will take some time, but only needs to be done once.
```
$ singularity build tf-l.simg docker://tensorflow/tensorflow:latest-gpu
```

Try an interactive shell - Note: --nv is required for gpu usage, and -B will just mount a local directory to /tmp in the virtual image.

$ singularity shell -B my_dir:/tmp --nv tf-l.simg

Singularity tf-l.simg:~> python
Python 2.7.12 (default, Dec  4 2017, 14:50:18) 
[GCC 5.4.0 20160609] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import tensorflow as tf
>>> tf.__version__
'1.11.0'
>>> import keras
>>> keras.__version__
'2.2.2'

That's it you now have a working tensorflow environment. For more information about running jobs in singularity on Talapas see Singularity.

Talapas Knowledge Base

How-to Use Tensorflow/Keras on Talapas

TensorFlow is a common machine learning package primarily run in python: https://www.tensorflow.org/

Keras (https://keras.io/) is a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano.

Several versions of TensorFlow exist on Talapas this article will cover the GPU version of TensorFlow available on all GPU nodes.

Step-by-step guide

Using the Latest Tensorflow with Singularity

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