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John Cary, 02/22/2018 08:43 AM

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. This may break compatibility with some versions of CUDA .

Below are the instructions for building gcc-6.4.0. (As of this writing 6.4 is the latest compiler to work with CUDA-9.1, and gcc-5.3.1 will not build QT-5.10.0)

Make sure 32bit glibc-devel is installed¶

Do the applicable of

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¶

export GCCVER=6.4.0
wget ftp://ftp.gnu.org/gnu/gcc/gcc-${GCCVER}/gcc-${GCCVER}.tar.xz
tar xf gcc-${GCCVER}.tar.xz && cd gcc-${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:

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¶

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

tlmgr install breakurl capt-of cmap comment courier ec eepic environ epstopdf eqparbox \
fancybox fancyvrb framed footnote fricychap gensymb helvetic latexmk lineno mdwtools mmap \
mptopdf multirow needspace newfloat overpic palatino parskip pdftex pifont revtex4 siunitx subfiles \
symbol tabulary threeparttable titlesec trimspaces txfonts units upquote ur  varwidth wrapfig \
xcite xcolor xypic zapfding

You may also want to install some of the fonts,

tlmgr install  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 (cut and paste after dnf install) are needed for Fedora

bc bison glib2-devel lapack-devel libblas-devel libcurl-devel libxml2-devel openssl-devel patch redhat-lsb zlib-devel

For more recent versions of Fedora, you will need.

egl-wayland mesa-libEGL-devel redhat-rpm-config

Ubuntu¶

The following packages are needed for Ubuntu

   ace-netsvcs
   bc
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 (in cut/paste for zypper form) are needed on SLES

bc bison blas-devel blas-devel-static libblas3 flex freetype2-devel
gcc gcc-32bit gcc-fortran git glibc-devel glibc-devel-32bit
graphviz graphviz-devel libbz2-devel lapack-devel lapack-devel-static liblapack3 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

The following are needed to build subversion

libapr-util1 libapr1 libneon27

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

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 bison cups-devel dbus-devel flex fontconfig-devel gperf libicu-devel
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.

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.

IMPORTANT NOTE: CUDA versions only support particular GCC versions, and the latest GCC may not support your CUDA. See this wiki page for details

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Updated by John Cary over 6 years ago · 43 revisions

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