TensorFlow Configuration and Optimization Notes

Notes for installing TensorFlow on linux, with GPU enabled.

Background

TensorFlow is the second-generation ML framework from Google. (See this comparison of deep learning software.) The current state-of-the art image recognition models (inception-v3) use this framework.

Prequisites

Assuming Fedora 24 with Nvidia 1060 installed, running nvidia as opposed to nouveau drivers. See Fedora 24 Notes, and RPM Fusion’s installation page for installing the Nvidia drivers. In sum,

dnf install -y xorg-x11-drv-nvidia akmod-nvidia "kernel-devel-uname-r == $(uname -r)"
dnf install xorg-x11-drv-nvidia-cuda
dnf install vulkan

After, install some devel packages.

dnf install -y vulkan-devel

Download the Nvidia GPU CUDA Toolkit. The version used for this install is 8.0.61, and the network install for Fedora x86_64 was used.

This version of CUDA Toolkit is not C++11/C++14/C++17 aware. So, be aware! One way around this is to mod like below, and use -std=gnu++98.

117c117,118
 5
---
> /* bkoz use -std=c++98 if necessary */
> #if __GNUC__ > 6

Next, compile top-of-tree OpenCV (aka 3.2) with CUDA enabled. To do so, use the following configure list, mod for paths on system:

cmake -DVERBOSE=1 -DCMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS} -std=gnu++98 -Wno-deprecated-gpu-targets" -D BUILD_EXAMPLES=1 -D BUILD_DOCS=1 -D WITH_OPENNI=1 -D WITH_CUDA=1 -D CUDA_FAST_MATH=1 -D WITH_CUBLAS=1 -D WITH_FFMPEG=1 -D WITH_EIGEN=1 -D ENABLE_FAST_MATH=1 -D ENABLE_SSE3=1 -D ENABLE_AVX=1 -D CMAKE_BUILD_TYPE=RELEASE -D ENABLE_PRECOMPILED_HEADERS=OFF  -D CMAKE_INSTALL_PREFIX=/home/bkoz/bin/H-opencv -D OPENCV_EXTRA_MODULES_PATH=/home/bkoz/src/opencv_contrib.git/modules /home/bkoz/src/opencv.git/

Admittedly, this abuse of CMAKE_CXX_FLAGS is not optimal. Maybe EXTRA_CXX_FLAGS?

Now, for Nvidia cuDNN. The version used for this install is 5.1

When that is done, use pip to install TensorFlow.

sudo pip install --upgrade pip;
sudo pip install tensorflow-gpu

This should output something like:

Collecting tensorflow-gpu
  Downloading tensorflow_gpu-0.12.1-cp27-cp27mu-manylinux1_x86_64.whl (89.7MB)
    100% |████████████████████████████████| 89.7MB 19kB/s 
Requirement already satisfied: mock>=2.0.0 in /usr/lib/python2.7/site-packages (from tensorflow-gpu)
Requirement already satisfied: six>=1.10.0 in /usr/lib/python2.7/site-packages (from tensorflow-gpu)
Requirement already satisfied: numpy>=1.11.0 in /usr/lib64/python2.7/site-packages (from tensorflow-gpu)
Collecting protobuf>=3.1.0 (from tensorflow-gpu)
  Downloading protobuf-3.2.0-cp27-cp27mu-manylinux1_x86_64.whl (5.6MB)
    100% |████████████████████████████████| 5.6MB 284kB/s 
Collecting wheel (from tensorflow-gpu)
  Downloading wheel-0.29.0-py2.py3-none-any.whl (66kB)
    100% |████████████████████████████████| 71kB 3.3MB/s 
Requirement already satisfied: pbr>=0.11 in /usr/lib/python2.7/site-packages (from mock>=2.0.0->tensorflow-gpu)
Requirement already satisfied: funcsigs>=1 in /usr/lib/python2.7/site-packages (from mock>=2.0.0->tensorflow-gpu)
Requirement already satisfied: setuptools in /usr/lib/python2.7/site-packages (from protobuf>=3.1.0->tensorflow-gpu)
Installing collected packages: protobuf, wheel, tensorflow-gpu
Successfully installed protobuf-3.2.0 tensorflow-gpu-0.12.1 wheel-0.29.0

After this has completed, add in Keras.

Optimization

For Nvidia GPUs, take a look at this interesting post from Netflix. In sum, add

NVreg_CheckPCIConfigSpace=0
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Postgres 9.4 to 9.5 database migration x Fedora 24

Fedora changed major versions of the postgresql database package, meaning that all user databases have to migrated from the 9.4.x series that used to be the default, to the 9.5.x series that is the current upstream stable package.

Fedora 24 -> 9.5.3
Fedora 23 -> 9.4.5
Fedora 22 -> 9.4.1

The general plan is to use the postgres tool pg_upgrade, ie take a empty database created with the new database, and populate it with the data from the old database.

So, the first step is to install both the current postgres package, and the previous version of the postgres package from the older Fedora release. For this purposes, the 9.4.x series.

Use the PostgreSQL Yum repository. From that index, select PostgreSQL 9.4 running on Fedora 24 – x86_64. The download file is: pgdg-fedora94-9.4-4.noarch.rpm.

rpm -ivh pgdg-fedora94-9.4-4.noarch.rpm

Refresh dnf cache and install postgres 9.4 package.

dnf list | grep postgresql;
dnf install postgresql94-server postgresql94-contrib;

This installs postgres version 9.4 into /usr/pgsql-9.4/bin/postgres.

Via the information page for the repository referenced above:

/usr/pgsql-9.4/bin/postgresql94-setup initdb
systemctl enable postgresql-9.4.service
systemctl start postgresql-9.4.service 

After this, finished with setup. Use this excellent blog post about upgrading, starting with item 3.

Fedora 24 Notes

Install:
San Francisco, California USA

Using x86_64 netinstall images as install media.

Update/Post-Install:

Use RPM Fusion Repositories.

Some basics

dnf install -y unrar tcsh gnome-tweak-tool livecd-tools ncftp lftp

Install KDE, Razor-qt, and MATE Desktops

	 	 
dnf install -y lightdm-gtk-greeter-settings mate-desktop mate-applets network-manager-applet caja mate-themes bluecurve-gtk-themes gnome-themes-legacy;
dnf groupinstall mate-desktop;  
dnf groupinstall kde-desktop;
dnf install -y gnome-themes;

Still a little sketchy, but optionally mate-compiz can be installed:

dnf groupinstall mate-compiz;

Install the basics for VLC

dnf install -y vlc vlc-core vlc-extras;
dnf install -y gaupol mediainfo

Install media xtra codecs.

dnf install -y ffmpeg ffmpeg-devel ffmpeg-compat-devel gstreamer-plugins-bad gstreamer-plugins-ugly gstreamer-plugins-good gstreamer-plugins-good-extras gstreamer-plugins-bad-free gstreamer-plugins-bad-free-extras gstreamer-plugins-bad-nonfree gstreamer-ffmpeg;
dnf install -y k3b-extras-freeworld;

Install negativo.
Use negativo17 repositories for HandBrake, volia.

dnf config-manager --add-repo=http://negativo17.org/repos/fedora-handbrake.repo;
dnf install -y HandBrake-gui HandBrake-cli;
dnf install -y makemkv mkvtoolnix mkvtoolnix-gui;
dnf install -y libdvdcss;

Use makemkv for Bluray.

Install some editors, utilities, and basics

dnf install -y abiword emacs tcsh

Install devel 1

dnf install -y openni openni-devel openni-doc  tbb tbb-devel tbb-doc eigen3-devel eigen3-doc openrdate simple-mtpfs emacs python-BeautifulSoup

Install devel 2

dnf groupinstall -y "Development Tools";
dnf install -y gcc-c++ libstdc++-devel libstdc++-docs boost boost-devel boost-doc valgrind gdb elfutils nemiver dwarves dejagnu emacs expect flex bison cmake git-svn mpfr-devel libmpc-devel lsb;
dnf debuginfo-install glibc;

Install database

dnf install -y glom libpqxx-devel libpqxx postgresql-devel

Install computer vision (hand-build clandmarks)

dnf install -y CImg-devel rapidxml-devel opencv opencv-devel

Install graphic

dnf install -y freetype-freeworld inkscape* ufraw ufraw-gimp 

Install technical documentation toolchain

dnf install -y pdfedit doxygen doxygen-latex graphviz  docbook5-style-xsl docbook5-schemas docbook2X docbook-style-xsl dblatex texinfo-tex dblatex docbook-utils-pdf  graphviz-python graphviz-R graphviz-graphs graphviz-doc R-core

Install sysadmin

sudo dnf install -y system-config-network system-config-samba system-config-services system-config-users system-config-firewall system-config-httpd