Preparing a Mac machine for Bilder¶

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

• XCode with command line tools
• Latex installed as noted below

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

Bilder on Darwin¶

Darwin comes with bash, so it is Bilder ready for the most part.

OS X Versions¶

Yosemite's XCode that supports C++ 11 by default.

El Capitan's clang compiler supports OpenMP.

Case insensitive file system¶

We have noted and filed bugs for CMake errors on OS X when using the case-sensitive file system. To fix we use the case-insensitive file system. There may be problems with various packages and the case-insensitive file system.

C and C++ compilers and Xcode command line tools¶

Install Xcode. To obtain version 6, visit https://developer.apple.com/xcode/download, then at the bottom third of the page, click on the "Additional Tools" link . Sign in with your Apple ID.

    sudo xcode-select --install

X11¶

X11 should not be needed, but if it is needed:

Install XQuartz X11.

Create a symbolic link so that the X11 headers can be found by the compiler:

    sudo ln -s /opt/X11/include/X11 /usr/local/include/X11

HomeBrew¶

One must select a non-OSX package manager for some additional packages. The candidates are HomeBrew, MacPorts, and Fink, with the HomeBrew being our recommendation at this time, as it is active, and it has the philosophy of not building extraneous stuff that is already present on OSX, which MacPorts tends to do, thus using up more disk space. HomeBrew also installs packages in their own subdirs with links to other places in /opt, thus making removal a matter removing a directory and then removing broken links in /opt/homebrew.

HomeBrew requires that one not have root privileges. So we make the directory into which we can write:

    sudo -s
    mkdir -p /opt/homebrew
    chgrp -R admin /opt
    chmod -R 775 /opt
    chmod -R 2775 /opt/homebrew
    exit

and then we work as nonroot:

    cd /opt
    curl -L https://github.com/Homebrew/brew/tarball/master | tar xz --strip 1 -C homebrew
    chmod -R a+rX /opt/homebrew
    find /opt/homebrew -type l -exec chmod -h a+r '{}' \;

and finally as root to pick up the paths by default:

    sudo -s
    echo "/opt/homebrew/bin" > /etc/paths.d/homebrew
    echo "/opt/homebrew/share/man" > /etc/manpaths.d/homebrew
    chmod a+r /etc/paths.d/homebrew /etc/manpaths.d/homebrew
    exit

Get the required packages...

    brew install gnupg libpng freetype gd ghostscript

Nice to have:

    brew install imagemagick

If permissions end up wrong, the commands

    chmod -R a+rX /opt/homebrew
    find /opt/homebrew -type l -exec chmod -h a+r '{}' \;

may help.

To get fortran and a more recent version of the gcc compiler

    brew install gcc49 --with-fortran

NOT REQUIRED: If your computer is a Jenkins Slave Only, then you will need svn 1.7 (skip otherwise)

If your Jenkins is set to use svn 1.7 (which means you'd need your local svn client to be 1.7 as well), then you can upgrade via HomeBrew as follows:

    # Only for Jenkins Slave!!
    brew install subversion17

In the process of building svn 1.7, you may find that subversion fails to build because scons is not installed properly. If that's the case, go to /opt/homebrew/opt/scons/bin and do the following:

    # Only for Jenkins Slave and SVN fails to build!!
    brew update
    brew doctor
    brew install subversion17

gfortran¶

Recommended Option: HomeBrew¶

Install gcc with HomeBrew as detailed above, using the --with-fortran option to the gcc install. If you have done that, then you can skip this section.

As of this writing, Bilder will look for gfortran-4.9 as a backup to gfortran.

Option 2: HPC¶

Install gfortran from SourceForge HPC. (Do not also install the other gcc compilers.)

As of March 29, 2015, the version is 4.9.0.

Install via

    $ tar xzf gfortran-4.9-bin.tar.gz -C /

Option 3: GNU¶

Install gfortran using the installer from http://gcc.gnu.org/wiki/GFortranBinaries.

As of March 29, 2015, the version is 4.9.0.

The binaries will end up being installed in /usr/local/bin

LaTeX¶

Those with sufficient hard drive space (3.4GB after install) may wish to download the full MacTeX package from http://www.tug.org/mactex/downloading.html. After installing, one can see the 'README ME FIRST.pdf' in /Applications/Tex. You will likely need to add /usr/texbin to your path:

    setenv PATH /usr/texbin:${PATH}  # For tcsh
    export PATH=/usr/texbin:${PATH}  # For bash

For those who like GUIs, the !TeXworks in /Applications/TeX/TeXworks should work fine.

For those with limited space, install BasicTeX from https://tug.org/mactex/morepackages.html. Add to your PATH:

    /usr/local/texlive/2016/bin/universal-darwin/

and run

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

and then used the autoupdate feature to get any additionally needed packages. Gives a 230 M installation. (As opposed to the usual 2GB installation.)

You many also need

    sudo chmod -R a+rX /usr/local/texlive/2016basic/texmf-dist/{tex,fonts}

as it seems that tlmgr does not get the permissions correct.

Disable spindump¶

for faster compilations via

    sudo launchctl unload -w /System/Library/LaunchDaemons/com.apple.spindump.plist

Git¶

If any repository package requires Git protocol, then for Lion and earlier you may need Git from http://git-scm.com/download/mac and add /usr/local/git/bin to your path.

Java¶

You will need to install java by invoking the executable in any way such as...

java -version

Follow the instructions in the dialog that takes you to the Oracle website and choose the latest version to download. (as of Nov 2015 this is 1.8)

HostName¶

For bilder to properly send emails the fully qualified hostname must set on the machine. To check this try...

     hostname -f

this should return machinename.domainname.com rather than just machinename. If it does not, then set the hostname of the machine by typing the following commands.

     sudo scutil --set ComputerName "newname"
     sudo scutil --set LocalHostName "newname"
     sudo scutil --set HostName "newname"
     dscacheutil -flushcache

Restart your Mac after this.

Power Saving Modes¶

For build machines that are not personal machines, disabling certain options will help in connectivity and responsiveness:

Under Spotlight
 - disabled the main HD. (multiple mdworkers taking up a lot of cpu.)

Under Energy Saver
 - Computer sleep: Set to never
 - Unchecked Put hard disks to sleep when possible
 - Unchecked Wake for network access

 
 
 
 
 
 
 
 
 
 

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DEPRECATED INSTRUCTIONS¶

Macports ###¶

This provides wget, freetype, and other utilities. Get macports from http://www.macports.org/install.php and install.

Note: Before proceeding with the installation of various macports packages noted below on Lion machines with Xcode 4.3, one needs to run

    sudo xcode-select -switch /Applications/Xcode.app

Otherwise, there will be an error installing zlib during the wget installation below.

After the macports installation, do

    sudo port install wget
    sudo port install ImageMagick +no_x11
    sudo port install f2c

XCode¶

Lion¶

On Lion, the command line compilers are not installed automatically. After installing Xcode, navigate to the
Preferences->Download dialog
and install the Command Line Tools. The dialog is..

!screenShotCommandLineTools.png!

or from the command line do

    sudo xcode-select --switch /Applications/Xcode.app/Contents/Developer/
    xcodebuild
      (hit agree)

You may subsequently need to build your first package with sudo in order to accept the Xcode licenses.

Mountain Lion ###¶

Same as Mavericks?

Mavericks¶

    sudo xcode-select --install

Java¶

(The below does not apply to yosemite.)

The cmake build may fail due to missing java headers linked to in /System/Library/Frameworks/JavaVM.framework/Headers. To fix:

    cd /System/Library/Frameworks/JavaVM.framework/Headers
    sudo mv jni.h jni.h.missing

Moving aside the system MPI (Snow Leopard and earlier)¶

The system MPI can interfere with the Bilder built MPI, so we recommend moving aside the system MPI:

    cd /usr/lib
    mkdir openmpi-save
    mv libopen-* libmpi* openmpi-save
    cd /usr/bin
    mkdir openmpi-save
    mv mpi* openmpi-save