Bilder

# Preparing a Linux machine for Bilder

__If all you need is python and sphinx__ (e.g., for builds of documentation), then you need only

* CMake (probably present)

* Python (probably present)

* Python-dev or Python-devel (on Fedora)

* Latex as installed below

and then you can add the arguments,  -W python,cmake, and your installed Python and CMake will be used if your path is correct.

## Java

At least one package (Babel) needs Oracle's java, so we recommend installing it.

## GCC

It is often useful to get a newer gcc that has mmintrinsics, although this may break compatibility with all but very recent versions of [[ CUDAgccCompatibility | CUDA ]].

Below are the instructions for building gcc-6.4.0.

### Make sure 32bit glibc-devel is installed

~~~~~~

yum -y install glibc-devel.i686

dnf -y install glibc-devel.i686

zypper install glibc-devel-32bit  (SLES 11 SP3)

~~~~~~

### Get and unpack the source package

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export GCCVER=6.4.0

wget ftp://ftp.gnu.org/gnu/gcc/gcc-${GCCVER}/gcc-${GCCVER}.tar.xz

tar xf gcc-${GCCVER}.tar.bz2 && cd gcc-${GCCVER}

~~~~~~

### Patch as needed

If your system has glibc 2.26 or later, you will need to fix the source by making the changes specified in  https://gcc.gnu.org/git/?p=gcc.git;a=commit;h=72edc2c02f8b4768ad660f46a1c7e2400c0a8e06 and also

~~~~~~

for i in libgcc/config/*/linux-unwind.h; do

  if grep -q "struct ucontext" $i; then

    sed -i.bak 's/struct ucontext/ucontext_t/' $i

  fi

done

~~~~~~

### Build

Define CONTRIB_DIR to be your tarball installation directory, e.g.,

~~~~~~

export CONTRIB_DIR=/contrib

~~~~~~

Usually CONTRIB_DIR=/contrib, but if one does not have root access, one has to put this in a user area. If one does have root access, one should execute the following commands:

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mkdir /internal /contrib /volatile

chmod 775 /internal /contrib /volatile

~~~~~~

Unpack gcc, go into the gcc source directory, and build according to the instructions below.

**gcc:**

~~~~~~

./contrib/download_prerequisites

mkdir build && cd build

../configure --prefix=$CONTRIB_DIR/gcc-${GCCVER} --enable-languages=c,c++,fortran --with-pic

env LD_RUN_PATH=$CONTRIB_DIR/gcc-${GCCVER}/lib64 make -j 4

make install

# Alias as desired.

mkdir -p $CONTRIB_DIR/bin && cd $CONTRIB_DIR/bin

ln -s $CONTRIB_DIR/gcc-${GCCVER}/bin/{c,g}* .

~~~~~~

### Fix permissions

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chmod -R g+rwX $CONTRIB_DIR/gcc-${GCCVER}

chmod -R o+rX $CONTRIB_DIR/gcc-${GCCVER}

find $CONTRIB_DIR/gcc-${GCCVER} -type d -exec chmod g+rs '{}' \;

~~~~~~

## Java

Install Oracle's Java.

Once it is installed, you will need to modify your path to include /usr/java/default/bin before /usr/bin or use the alternatives package:

~~~~~~

for i in java jar javac; do

  alternatives --install /usr/bin/$i j$i /usr/java/jdk1.6.0_16/bin/$i 3

done

alternatives --config java # Pick 3

~~~~~~

On SLES , Install using the tar package from Oracle, then change into the installation directory

~~~~~~

for i in java jar javac; do

  /usr/sbin/update-alternatives --install /usr/bin/$i $i <installation directory>/bin/$i 3

done

~~~~~~

where <installation directory\> is the absolute path to where Java was just installed  

## Version control systems

Make sure git, mercurial, and subversion are all installed.

## LaTeX

Install the texlive-latex package. You may need to install other packages over time. For gui usage, see texworks: http://www.tug.org/texworks

If you cannot install in the system area, you can download

~~~~~~

wget http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz

tar xzf install-tl-unx.tar.gz

cd install-tl-20150411 (date might be different)

./install-tl -no-gui

~~~~~~

This is now interactive, so set

* Set scheme to basic

** To do this type 'S' and hit enter.

** Then enter 'd' to set the scheme to basic.

** Type 'R' and hit enter to return to the main configuration page.

* Set TEXDIR = $CONTRIB_DIR/texlive

** Start by typing 'D' and hit enter.

** Then enter '1' to change TEXDIR.

** Type $CONTRIB_DIR/texlive and hit return.

** To return to configuration type 'R' and return.

* Set page size to Letter size

** Type 'O' and hit enter.

** Enter 'P'

** Return to main menu by typing 'R' and enter. 

* Install

** Type 'I' and hit enter to install.

* Put your texlive in your PATH.

** Edit you bashrc (vim ~/.bashrc)

** Add "export PATH=$PATH:<$CONTRIB_DIR>/texlive/bin/x86_64-linux/" (enter the full CONTRIB_DIR value)

** Exit and save. Then source ~/.bashrc.

To ensure you are using the correct texlive installation type "which pdflatex" and make sure it 

the one in $CONTRIB_DIR/texlive/bin/x86_64-linux/. If it is not the correct pdflatex, you may

have to remove the system version (sudo yum remove texlive). 

and then

~~~~~~

    for i in breakurl capt-of cmap comment courier ec eepic environ epstopdf eqparbox \

fancybox fancyvrb framed footnote framed fricychap gensymb helvetic latexmk lineno mdwtools mmap \

mptopdf multirow newfloat overpic palatino parskip pdftex pifont revtex4 siunitx subfiles \

symbol tabulary threeparttable titlesec trimspaces txfonts units upquote url wrapfig \

xcite xcolor xypic zapfding; do

     tlmgr install $i

    done

~~~~~~

You may also want to install some of the fonts, avantgar bookman charter cmextra courier euro-ce eurosym marvosym mathpazo ncntrsbk pxfonts rsfs symbol times txfonts utopia wasy zapfchan zapfding.

## Additional packages

Other parts of the toolchain introduce other package requirements.  Below are the initial lists.

### Fedora

The following packages are needed for Fedora

~~~~~~

  bison

  glib2-devel

  libxml2-devel

  openssl-devel

  zlib-devel

  patch

~~~~~~

You may also need

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  libblas-devel

  lapack-devel

~~~~~~

For more recent versions of Fedora, you will need.

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  egl-wayland

  mesa-libEGL-devel

  redhat-rpm-config

~~~~~~

### Ubuntu

The following packages are needed for Ubuntu

~~~~~~

   ace-netsvcs

   bison

   flex

   gfortran

   graphviz

   graphviz-dev

   heirloom-mailx

   libblas-dev

   libfreetype6-dev

   libgl1-mesa-dev

   libglu1-mesa-dev

   liblapack-dev

   libntlm0

   libpng12-dev

   libxext-dev

   libxrender-dev

   libxtst-dev

   libzzip-dev

   mailutils

   python2.6

   python2.6-dev

   zlib-dev *

~~~~~~

* You will probably want a lightweight command line editor other than gedit, so "sudo apt-get install vim"  or "sudo apt-get install emacs" 

* zlib-dev doesn't exist on ubuntu 16.04 - use zlib1g-dev instead.

mailutils is necessary for configuring the system for jenkins. 

You'll be offered to choose:

* Internet site

* Internet with smarthost

* Satellite system

* Local only

Internet with smarthost is recommended.

The use of the following commands are helpful. To search for an available package dealing with a keyword, use:

~~~~~~

    $ sudo apt-cache search keyword

~~~~~~

To install a particular package, use:

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    $ sudo apt-get install libblah-dev

~~~~~~

Note: that development packages names typically end with "dev" not "devel" as in other flavors of linux.

### Suse Linux Enterprise Server (SLES)

The following packages are needed on SLES

~~~~~~

   bison

   blas-devel

   blas-devel-static

   libblas3

   flex

   freetype2-devel

   gcc

   gcc-32bit

   gcc-fortran

   git

   glibc-devel

   glibc-devel-32bit

   graphviz

   graphviz-devel

   gstreamer-0_10-devel

   gstreamer-0_10-plugins-base-devel

   libbz2-devel

   lapack-devel

   lapack-devel-static

   liblapack3

   libapr-util1 (needed to build subversion)

   libapr1      (needed to build subversion)

   libneon27    (needed to build subversion)

   libpng-devel

   libssh-devel

   libxml2-devel

   mailx

   mercurial

   Mesa-devel

   python-devel

   xorg-x11-devel

   xorg-x11-libXext-devel

   xorg-x11-libXrender-devel

   xorg-x11-libs

   zlib-devel

~~~~~~

To get blas-devel, blas-devel-static and lapack-devel, lapack-devel-static on SLES 11 SP3 , add the Science repository

~~~~~~

   zypper addrepo http://download.opensuse.org/repositories/science/SLE_11_SP3/science.repo

   zypper refresh

   zypper install blas-devel blas-devel-static lapack-devel lapack-devel-static

~~~~~~

## Qt Prerequisites

Qt-5 must be built with QtWebEngine, which particularly introduces requirements for other packages as noted at

* https://doc.qt.io/qt-5.10/qtwebengine-platform-notes.html

* https://wiki.qt.io/QtWebEngine/How_to_Try

* https://www.ics.com/blog/building-qtwebengine

* http://www.linuxfromscratch.org/blfs/view/svn/x/qtwebengine.html

Each of the above websites appears to have made assumptions about what is already installed, so as one encounters more workstations, one is likely to find yet another package missing.  This is our list so far.

### Fedora

~~~~~~

sudo yum install alsa-lib-devel cups-devel bison flex gperf

sudo yum install libcap-devel libgcrypt-devel libgcrypt libgudev1-devel libsndfile-devel libwebp-devel

sudo yum install libXcomposite-devel libXcursor-devel libXi-devel libXrandr-devel libxslt-devel libXtst-devel

sudo yum install mesa-libEGL-devel nss-devel opus-devel pciutils-devel pulseaudio-libs-devel re2c ruby systemd-devel

~~~~~~

## Vendor-specific version of graphics driver

If you are preparing a Linux machine for the VisIt Visualization package, the vendor-specific graphics driver for your graphics card should be installed.

By default, a generic graphics driver is installed.  On Fedora, the generic driver is "nouveau".

To determine if the nouveau driver is installed on your system, enter the command

~~~~~~

     lsmod | grep nouv

~~~~~~

You will need to download and install the appropriate driver from your graphics card vendor.  This generally uninstalls the nouveau drivers.

## NVIDIA CUDA Toolkit

If you have a compatible GPU and wish to compile with nvcc code, you must first install the CUDA Toolkit. The linux installation page is 

~~~~~~

     https://developer.nvidia.com/cuda-toolkit-70

~~~~~~

Download the applicable file. Your Linux distribution may or may not be natively supported for version 7.0. You may alternatively use version 7.5 if supported or an older version if necessary. As an example, we will include the steps known to work for Fedora 22. On Fedora 22, download the Fedora 21 Local RPM package. 

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     cd <location of download>

     sudo rpm -i cuda-repo-fedora21-7-0-local-7.0-28.x86_64.rpm   #<or whatever file you downloaded> 

     sudo dnf install cuda

~~~~~~

Different Linux distributions will have different package handlers (here we use dnf, ubuntu has apt-get, fedora < 22 uses yum). You should now have the directory /usr/local/cuda-7.0. Add /usr/local/cuda-7.0/bin to your path. To ensure you have gotten the necessary components, type:

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     which nvcc

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CUDA-8 does not work with Fedora 27.  A workaround is specified at https://xpra.org/trac/ticket/1600.

Looks like CUDA-9.1 works, but with only select versions of gcc, e.g., gcc-5.4.0 according to https://github.com/tensorflow/tensorflow/issues/10220.

The output should be /usr/local/cuda-7.0/bin/nvcc. This will allow bilder to build GPU c++ code.