Setup Keras+Theano Backend and GPU on Ubuntu 16.04

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Setup Keras+Theano Backend and GPU on Ubuntu 16.04

Using GPUs to process tensor operations is one of the main ways to speed up training of large, deep neural networks.

Here are a couple of pointers on how to get up and running with Keras and Theano on a clean 16.04 Ubuntu machine, running an Nvidia graphics card.


Install numpy and scipy with native BLAS linkage

$ sudo apt-get install libopenblas-dev liblapack-dev gfortran python-numpy python-scipy
  • create a new virtualenv using system packages:

    $ virtualenv --system-site-packages -p python2.7 venv2
    $ source venv2/bin/activate
  • install theano and keras

    (venv2) $ pip install Theano
    (venv2) $ pip install Keras
    (venv2) $ pip install Cython

Install NVIDIA driver

In order to use the toolkit, you must install the proprietary NVIDIA driver.

This can be done running the following two commands:

$ sudo apt-get install xserver-xorg-video-intel
$ sudo nvidia-installer --update

Install CUDA toolkit version 8.0

Version 8 is the most recent version (as of this writing) for ubuntu 16.04.

  • Go to this link: NVIDIA - CUDA Downloads and look a link for CUDA Toolkit 8.

  • Right now, at the time this post was being written, you must register as a developer to be able to download the most recent toolkit You don't need to register anymore. It looks like this:

    cuda toolkit 8 As of this post, click this link to access CUDA Toolkit 8

  • Once you've registered, you'll see the downloads page for CUDA Toolkit 8. Download the .run file:

    CUDA Toolkit 8 CUDA Toolkit 8

  • Before running the .run file, you must shut down X: $ sudo service lightdm stop

  • After shutting down X, hit Ctrl + Alt + F1 (or F2, F3 and so on) and log in again.

  • Go to the directory where the .run file was downloaded and run the following command to run the installer:

    $ sudo sh

Testing the installation

  • Build the sample files

    Go to your home directory, extract the sample CUDA files there and build them using make:

    $ cd ~/
    $ /usr/local/cuda-8.0/bin/ .
    $ cd NVIDIA_CUDA-8.0_Samples/
    $ make
  • Run one of the files you built, called deviceQuery

    (You should see output that resembles the one below)

    $ cd NVIDIA_CUDA-8.0_Samples/bin/x86_64/linux/release
    $ ./deviceQuery
    ./deviceQuery Starting...
    CUDA Device Query (Runtime API) version (CUDART static linking)
    Detected 1 CUDA Capable device(s)
    Device 0: "GeForce GT625M"
    CUDA Driver Version / Runtime Version          8.0 / 8.0
    deviceQuery, CUDA Driver = CUDART, CUDA Driver Version = 8.0, CUDA Runtime Version = 8.0, NumDevs = 1, Device0 = GeForce GT625M
    Result = PASS

    Good. This means your GPU was identified and can be used. Now let's get it working on Theano.

Testing Theano with GPU

  • Download this python script Theano Testing with GPU. I'll call it

  • Run it while in the same virtualenv you have used at the beginning of the tutorial, using these extra parameters:

    note the extra shell parameters you need before the python command

    $ THEANO_FLAGS=mode=FAST_RUN,device=gpu,floatX=float32 python
    Using gpu device 0: GeForce GT625M (CNMeM is disabled, cuDNN not available)
    [GpuElemwise{exp,no_inplace}(<CudaNdarrayType(float32, vector)>), HostFromGpu(GpuElemwise{exp,no_inplace}.0)]
    Looping 1000 times took 0.765961 seconds
    Result is [ 1.23178029  1.61879349  1.52278066 ...,  2.20771813  2.29967761
    Used the gpu

    Congratulations! You've successfully linked Keras (Theano Backend) to your GPU! The script took only 0.765 seconds to run!

  • Optional if you want to compare GPU performanace against a regular CPU, you just need to adjust one parameter to measure the time this script takes when run on a CPU:

    $ THEANO_FLAGS=mode=FAST_RUN,device=cpu,floatX=float32 python 
    [Elemwise{exp,no_inplace}(<TensorType(float32, vector)>)]
    Looping 1000 times took 37.526567 seconds
    Result is [ 1.23178029  1.61879337  1.52278066 ...,  2.20771813  2.29967761
    Used the cpu

    That took 37 seconds. Nearly 50 times as slow as the GPU version!

    You will probably experience even greater gains with a better GPU (mine isn't very good, by far)

Troubleshooting installation

Lots of things can and will go wrong during this installation. These are some commong issues you may find and how to work around them:

Failed to fetch file: /var/cuda-repo-8-local/Release

This may happen if you download and install the .deb file. The easiest way to circumvent this is to just use the .run file instead.

ERROR (theano.sandbox.cuda): nvcc compiler not found on $PATH. Check your nvcc installation and try again

Open file ~/.theanorc add edit the path to CUDA root:


root = /usr/local/cuda-8.0

ERROR (theano.sandbox.cuda) Failed to compile cannot open shared object file: No such file or directory

Add the following environment variables to /etc/environment and then reboot:


modprobe: ERROR: could not insert 'nvidia_uvm': Unknown symbol in module

If you get this error message, look at the output of dmesg to see if there's anything interesting. You may get a message telling you what's wrong. For instance:

[  226.629034] NVRM: API mismatch: the client has the version 361.77, but
               NVRM: this kernel module has the version 304.131.  Please
               NVRM: make sure that this kernel module and all NVIDIA driver
               NVRM: components have the same version.

In my case, this was due to my having an old 304 driver lying around. All I had to do was to purge the package (sudo apt-get purge nvidia-304*) and the error message went away.

ERROR (theano.sandbox.gpuarray): pygpu was configured but could not be imported

Install libgpuarray and pygpu, as per this link: Theano: Libgpuarray Installation

ERROR: Installation failed: using unsupported compiler

Add --override to the command where you execute the downloaded .run file, e.g.:

$ sudo sh --override

ERROR: error: ‘memcpy’ was not declared in this scope

This may happen when you try to compile the examples in the toolkit (see chapter 6 of the Guide for the Toolkit)

Open file NVIDIA_CUDA-8.0_Samples/6_Advanced/shfl_scan/MakeFile and add the following line to line 149:

... previous lines ommitted
144 else ifeq ($(TARGET_OS),android)
145     LDFLAGS += -pie
146     CCFLAGS += -fpie -fpic -fexceptions
147 endif
149 # custom added line below
152 ifneq ($(TARGET_ARCH),$(HOST_ARCH))
153     ifeq ($(TARGET_ARCH)-$(TARGET_OS),armv7l-linux)
154         ifneq ($(TARGET_FS),)
... next lines ommitted

Othe tips

Enabling the GPU when running jupyter notebook

Simply prefix the jupyter notebook command with the flags, e.g.

$ THEANO_FLAGS=mode=FAST_RUN,device=gpu,floatX=float32 jupyter notebook

See also

Dialogue & Discussion