Preparing a Linux machine for Bilder¶

Bilder on Linux¶

At least one package (Babel) needs Oracle's java, so we recommend installing it. It is often useful to get a newer gcc that has mmintrinsics.

GCC¶

Below are the instructions for building gcc-4.9.3.

Make sure 32bit glibc-devel is installed¶

yum -y install glibc-devel.i686
zypper install glibc-devel-32bit  (SLES 11 SP3)

Get the source packages¶

export GCCVER=4.9.3
wget ftp://ftp.gnu.org/gnu/gcc/gcc-${GCCVER}/gcc-${GCCVER}.tar.bz2

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:

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:

tar xjf gcc-${GCCVER}.tar.bz2 && cd gcc-${GCCVER}
./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¶

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 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 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.

Fedora¶

The following packages are needed for Fedora

   bison
   glib2-devel
   gstreamer-devel
   gstreamer-plugins-base-devel
   libxml2-devel
   openssl-devel
   zlib-devel
   patch

If you cannot install in the system area, bilder/extras/gstreamer.sh may
be modified to do what you need.

You may also need

   libblas-devel
   lapack-devel

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:

    $ 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

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.

     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:

     which nvcc

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