Deep Learning software installation guide on fresh Ubuntu

Guide to building and installing CUDA, CuDNN, OpenCV, FFMPEG, Theano, Tensorflow, Keras, Lasagne, Torch and Caffe. It also includes common issues faced and recommended libraries and versions.

Table of Contents

Recently I assembled a machine with 4 GPU (Titan X), a clone of NVIDIA DevBox. There are few other blog posts which describe the hardware guide, so I will not go into the same detail. Please refer this. The actual list of parts I bought can be found at PCPart Picker.

However this blog post is about the software guide. Although, most of the researchers or grad students like me will have their own custom requirement I thought I should share my software installation guide, for someone who might be new and would benefit from some of these. I have had to do this process couple of times now, and I have learned from my mistakes.

NOTE 1: Docker : If getting maximum performance is not a requirement, I would suggest the reader to download Docker Images for Deep Learning packages freely available online, for e.g. Time required for all these standalone installation is justified only when these are going to be used over and again, for e.g in a research lab.

NOTE 2: Redundancy : Some of the commands can be combined to be done in a single line, especially installing libs from apt-get. But I prefer to run them one at a time, for more control and feedback on installation process.

NOTE 3: Python 2 : While most of the scientific community is moving on with Python 3, it seems Deep Learning communmmunty is happy with Python 2. Thus all instllations except where mentioned pertain to Python 2.7.

NOTE 4: Anaconda : Why not Anaconda ? I have done some previous installations with Anaconda, but it becomes messy with smaller libs, and also compiling OpenCV. More importantly, I do not need all the utils of Anaconda, and on this machine I would like to minimize the libs installed.

Upgrade the Ubuntu

Always, upgrade the ubuntu for security and sanity purposes !

  • sudo apt-get update # Fetches the list of available updates
  • sudo apt-get upgrade # Strictly upgrades the current packages
  • sudo apt-get dist-upgrade # Installs updates (new ones)

RAID 1

Partition and mount the harddrives

Since my configuration has two HDD of 3 TB, I have configured them as RAID 1, this provides data redundancy. You do not want to lose weeks worth of training due to HDD crash ! If you do not want RAID 1, then skip this step.

Mounting

  • df -aTh # shows list of all mounts
  • sudo mount /dev/md0 /media/hdd/ # (Manual) mount existing
  • blkid # shows uuid for drives to add to fstab Add the following line to /etc/fstab

    the RAID 1 mount of two hdd

    UUID=06ad59d9-3176-4c16-95e9-77356cc572d7 /media/hdd ext2 defaults 0 1

  • sudo mount -a # (Permanent) mount using fstab

Install Essentials, Extras, Git, Zsh

  • sudo apt-get install -y build-essential
  • sudo apt-get install -y ubuntu-restricted-extras
  • sudo apt-get install -y vim
  • sudo apt-get install -y git
  • sudo apt-get install -y git-core
  • `sudo apt-get install -y checkinstall # allows for easy install/uninstall of packages from source
  • sudo apt-get install -y zsh
  • sudo apt-get install -y tmux
  • sudo apt-get install -y CMake
  • sudo apt-get install -y libopenblas-dev
  • `sudo apt-get install -y libhdf5-dev
  • sudo apt-get install -y gcc-4.8 # because CUDA (7.0 & 7.5) works will less than 4.9.0
    • make soft link for gcc in /usr/bin
  • sudo apt-get install -y g++-4.8 # because CUDA (7.0 & 7.5) works will less than 4.9.0
    • make soft link for g++ in /usr/bin
  • sudo apt-get install -y apache2
    • sudo /etc/init.d/apache2 start ` # start the Apache Server

Python

Python and Libs

  • python get-pip.py # install pip
  • sudo apt-get install python-dev # pythonLibs
  • sudo apt-get install libblas-dev liblapack-dev libatlas-base-dev gfortran
  • sudo pip install cython git+https://github.com/scipy/scipy # Installs Cython and Scipy both (Cython is requirement for scipy)
  • sudo pip install -U scikit-learn # Requires numpy and scipy
  • Matplotlib better to install using APT, lot of system lib dependency
    • sudo apt-get install -y matplotlib

Highend computing

  • sudo pip install numpy
  • sudo pip install markupsafe
  • sudo pip install h5py
  • sudo pip install nltk
  • sudo pip install nose
  • Install leveldb # for efficient use with Caffe, and probably other libs
    • git clone git@github.com:google/leveldb.git
    • make
    • sudo mv out-shared/libleveldb.* /usr/local/lib/
    • sudo cp -R include/leveldb /usr/local/include
    • sudo ldconfig

Python3 and Ipython (Jupyter)

  • sudo apt-get install python3-pip # to install jupyter for python3, it needs pip3 and does not work using pip
  • sudo pip install jupyter
  • sudo pip3 install jupyter # I don’t know why it requires sepearate installation, especially when not done using Anaconda !

NVIDIA

Install NVIDIA Drivers

I would highly advice against installation using apt-get as it always installs one version older, and with NVIDIA every generation of driver brings performance boosts.

  • sudo service lightdm stop # stop the X server before running the installation NOTE! Could not sign kernels, make a note of this. It might lead to problems with some libraries later on
  • Download AMD 64 bit Linux drivers from NVIDIA website (manual download and transfer and execute the provided script or binary)

Install CUDA

  • sudo ./cuda_7.0.28_linux.run --override # for cuda 7.0
  • sudo ln -s /usr/bin/g++-4.8 /usr/local/cuda/bin/g++ # this might be omitted if a symbolic link has been made from /usr/bin/g++ like mentioned above
  • sudo ln -s /usr/bin/gcc-4.8 /usr/local/cuda/bin/gcc # this might be omitted if a symbolic link has been made from /usr/bin/gcc like mentioned above

Install CuDNN

CuDNN improves the performance of deep learning libraries. Unfornately, not all of them work with latest version. Google’s Tensorflow requires v2, Theano & Caffe works with v3, whereas latest version is 4. To get the library you will have to register at NVIDIA CuDNN

  • Download the archive folder
  • cd <extracted_directory>
  • export LD_LIBRARY_PATH=pwd:$LD_LIBRARY_PATH

Although not required, I find it useful to rather install both the version of CuDNN (2 and 3). Put the libs of v2 in CUDA 6.5 or CUDA 7.0 (for Tensorflow), and v3 in CUDA 7.5.

Image processing and Computer Vision

Install OpenCV

This is to install OpenCV 3.1 on Ubuntu 15.10. Thanks to the people at BVLC/Caffe, I did not have to tweak the settings, and pretty much their provided instructions worked.

  • sudo apt-get -y install libopencv-dev build-essential cmake git libgtk2.0-dev pkg-config python-dev python-numpy libdc1394-22 libdc1394-22-dev libjpeg-dev libpng12-dev libtiff5-dev libjasper-dev libavcodec-dev libavformat-dev libswscale-dev libxine2-dev libgstreamer0.10-dev libgstreamer-plugins-base0.10-dev libv4l-dev libtbb-dev libqt4-dev libfaac-dev libmp3lame-dev libopencore-amrnb-dev libopencore-amrwb-dev libtheora-dev libvorbis-dev libxvidcore-dev x264 v4l-utils unzip

  • Download OpenCV from http://opencv.org/downloads.html and unpack. Enter the unpacked directory. Execute:

  • mkdir build && cd build/ # If you have Oh-my-zsh then just take build

  • cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=/usr/local -D WITH_TBB=ON -D WITH_V4L=ON -D WITH_QT=ON -D WITH_OPENGL=ON ..

  • make -j12 # j 12 makes 12 parallel processes using all the cores to speed up the process, in a single core, the build might take couple of hours.

  • sudo checkinstall # to create the deb package, and install it.

FFMPEG

  • sudo apt-get install -y ffmpeg

ImageMagick

  • sudo apt-get install -y imagemagick

Install GPU Libraries

Theano

  • sudo pip install Theano
  • sudo apt-get install -y python-pycuda # also installs the dependencies, but it is best to have own installation of nvidia-cuda, to make sure the version is proper and to maintain multiple version installation

Tensorflow

  • sudo pip install --upgrade https://storage.googleapis.com/tensorflow/linux/gpu/tensorflow-0.6.0-cp27-none-linux_x86_64.whl

    Tensorflow (as of Jan 15, 2016), works on Cuda 7.0 and CuDNN v2 ), thus change /usr/local/cuda softlink

Keras

  • sudo pip install keras # Could it get any easier !! Thanks people developer of Keras !

Lasagne

  • sudo pip install https://github.com/Lasagne/Lasagne/archive/master.zip # Preferred way to install Lasagne !

Torch

  • curl -s https://raw.githubusercontent.com/torch/ezinstall/master/install-deps | bash
  • git clone https://github.com/torch/distro.git ~/torch --recursive
  • cd ~/torch; ./install.sh

Aditionally to load caffe models in torch,

  • luarocks install loadcaffe

Caffe

Note

  • Switch back to GCC 5 and G++ 5, because the prebuilt libraries of Ubuntu 15.10 are built on gcc 5, and thus compiling caffe in 4.8 will not link them. However, caffe will refuse to compile with gcc 5, with error from following file /usr/local/cuda/include/host_config.h Just comment out the line 115, which checks the version of GCC
  • Use the CMake instead of default make (checkout https://github.com/BVLC/caffe/pull/1667 )

Requirements

  • sudo apt-get install libprotobuf-dev libleveldb-dev libsnappy-dev libopencv-dev libhdf5-serial-dev protobuf-compiler
  • sudo apt-get install --no-install-recommends libboost-all-dev
  • sudo apt-get install libgflags-dev libgoogle-glog-dev liblmdb-dev
  • for req in $(cat python/requirements.txt); do pip install $req; done

Issues

  • Linking Error in Leveldb e.g

            Linking CXX executable caffe
        ../lib/libcaffe.so.1.0.0-rc3: undefined reference to `leveldb::Status::ToString[abi:cxx11]() const'
        ../lib/libcaffe.so.1.0.0-rc3: undefined reference to `leveldb::DB::Open(leveldb::Options const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, leveldb::DB**)'
        collect2: error: ld returned 1 exit status
        tools/CMakeFiles/caffe.bin.dir/build.make:122: recipe for target 'tools/caffe' failed
        make[2]: *** [tools/caffe] Error 1

    Solution, recompile Leveldb with GCC 5

    • sudo apt-get install libsnappy-dev
    • wget https://leveldb.googlecode.com/files/leveldb-1.9.0.tar.gz\ntar -xzf leveldb-1.9.0.tar.gz\ncd leveldb-1.9.0make
    • sudo mv libleveldb.* /usr/local/lib
    • cd include
    • sudo cp -R leveldb /usr/local/include
    • sudo ldconfiG

  • Linking Error in Protobuf e.g

            Linking CXX executable caffe
        CMakeFiles/caffe.bin.dir/caffe.cpp.o: In function `std::string* google::MakeCheckOpString<cudaError, cudaError>(cudaError const&, cudaError const&, char const*)':
        caffe.cpp:(.text._ZN6google17MakeCheckOpStringI9cudaErrorS1_EEPSsRKT_RKT0_PKc[_ZN6google17MakeCheckOpStringI9cudaErrorS1_EEPSsRKT_RKT0_PKc]+0x43): undefined reference to google::base::CheckOpMessageBuilder::NewString()'
        CMakeFiles/caffe.bin.dir/caffe.cpp.o: In function `std::string* google::MakeCheckOpString<unsigned long, int>(unsigned long const&, int const&, char const*)':
        caffe.cpp:(.text._ZN6google17MakeCheckOpStringImiEEPSsRKT_RKT0_PKc[_ZN6google17MakeCheckOpStringImiEEPSsRKT_RKT0_PKc]+0x43): undefined reference to `google::base::CheckOpMessageBuilder::NewString()'
        CMakeFiles/caffe.bin.dir/caffe.cpp.o: In function `main':
        caffe.cpp:(.text.startup+0x3e): undefined reference to `google::SetVersionString(std::string const&)'
        caffe.cpp:(.text.startup+0x6e): undefined reference to `google::SetUsageMessage(std::string const&)'
        ../lib/libcaffe.so.1.0.0-rc3: undefined reference to `google::protobuf::internal::WireFormatLite::WriteStringMaybeAliased(int, std::string const&, google::protobuf::io::CodedOutputStream*)

    Solution, change your current compiler to GCC Use gcc --version to make sure the correct version, and which gcc to check the softlinks to actual gcc

  • Relevant issues to checkout https://github.com/BVLC/caffe/issues/2690 and https://github.com/BVLC/caffe/issues/3046

  • In Ubuntu 15.10 when using GCC 5.2, compiling might fail as Protobuf was compiled with wrong flags. Add the following to Makefile CXXFLAGS += -D_GLIBCXX_USE_CXX11_ABI=0

  • Issues with Google Lib Protobuf (even after the ABI CXX11 fix)

    • cd /usr/local/lib
    • sudo mkdir libprotobuf_
    • mv libprotobuf* libprotobuf_
    • cd ~
    • apt-get source libprotobuf-dev
    • ll
    • cd protobuf-2.6.1
    • make
    • ./configure
    • make -j12
    • sudo make install

Installation

  • mkdir build
  • cd build
  • cmake .. # Make kept giving me issues, but CMake worked.
  • make all
  • make test
  • make runtest
  • make pycaffe # To be able to import caffe

To be updated with instructions for Nervana

Optional

Remove unnecessary Ubuntu folders

When working with only terminal via ssh, you do not need some of these folders //

  • rm -rf ~/Desktop
  • rm -rf ~/Public # Is not persistent, after restart Ubuntu recreates this directory
  • rm -rf ~/Pictures
  • rm -rf ~/Music
  • rm -rf ~/Videos
  • rm -rf ~/Downloads
  • rm -rf ~/Templates
  • rm -rf ~/Documents
  • rm -rf ~/examples.desktop

Customization

These are my personal customization which I do on every machine I use. You may find them useful. They increase visual appeal and efficiency of working on Linux Machine.

  • chsh -s which zsh # Change the shell to ZSH (which zsh should be inside backticks, but Github Markdown messes up the formatting)
  • sudo reboot now # Requires restart
  • git clone git@github.com:iamaaditya/dotfiles.git
  • ~/dotfiles/install.sh # Run the commands to make the shortcuts
  • git clone https://github.com/VundleVim/Vundle.vim.git ~/.vim/bundle/Vundle.vim # Install bundle

    Solarized Color for vim

  • cd ~/.vim/colors/
  • wget https://raw.githubusercontent.com/altercation/vim-colors-solarized/master/colors/solarized.vim

    Powerline & associated fonts

  • pip install powerline-status # Powerline
  • wget https://github.com/Lokaltog/powerline/raw/develop/font/PowerlineSymbols.otf https://github.com/Lokaltog/powerline/raw/develop/font/10-powerline-symbols.conf
  • mkdir -p ~/.fonts/ && mv PowerlineSymbols.otf ~/.fonts/
  • fc-cache -vf ~/.fonts
  • mkdir -p ~/.config/fontconfig/conf.d/ && mv 10-powerline-symbols.conf ~/.config/fontconfig/conf.d/ Note - if some aspects of powerline does not show up, check http://askubuntu.com/questions/283908/how-can-i-install-and-use-powerline-plugin

If you are curious on what this customization looks like, take a look at this screenshot. Here it shows Tmux session with multiple windows, and a multiple panes in the same window. Switching windows and panes in Tmux is very easy. Copy information across windows, sessions and servers is really at the tip of the finger. Also Solarized colors make it tolerable to use the screen for hours. screenshot

Written on January 15, 2016