Bilder

# Preparing a Mac machine for Bilder #

## Bilder on Darwin ##

It is recommended to have yosemite as compiles more efficiently and has an XCode that supports C++ 11 by default.

Darwin comes with bash, so it is Bilder ready for the most part. However, Darwin does not come with Fortran, so one needs to install it (see instructions below). A few other items are noted below.

## 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

~~~~~~

## gfortran ##

There are a number of options here.

### Homebrew gfortran ###

Install gcc with Homebrew as discussed below, using --with-fortran.

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

### HPC gfortran ###

Install gfortran from [SourceForge HPC](http://hpc.sourceforge.net).  (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 /

~~~~~~

### GNU Binaries ###

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

## X11 ##

Install [XQuartz X11](http://xquartz.macosforge.org/landing/).

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

~~~~~~

## Selecting and using a non-OSX package manager ##

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 ###

We follow the installation methodology of http://ascarter.net/2010/02/22/homebrew-for-os-x.html, in which

brew must be run by root and all files are owned by root.  Since sudo is then used, you may want the lines,

~~~~~~

    Defaults umask = 0002

    Defaults umask_override

~~~~~~

in /etc/sudoers (done with visudo). 

You may also want to check to make sure you do not have HomeBrew already installed with 'which brew' or checking in /usr/local/bin for a brew executable.  If you do have a copy installed, you might consider uninstalling it (see https://gist.github.com/mxcl/1173223 if installed in /usr/local) and starting a fresh install.

### Get HomeBrew and add it to your path ###

~~~~~~

    sudo -s

    mkdir -p /opt/homebrew

    chgrp -R admin /opt

    chmod -R 775 /opt

    chmod -R 2775 /opt/homebrew

    cd /opt

    curl -L http://github.com/mxcl/homebrew/tarball/master | tar xz --strip 1 -C homebrew

    chmod -R a+rX /opt/homebrew

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

    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 packages ###

Required packages...

~~~~~~

    sudo -s

    brew install libpng freetype gd

    brew install wget hg ghostscript

    exit

~~~~~~

Optional packages such as imagemagick can be installed the same way.

If permissions end up wrong, the commands

~~~~~~

    sudo chmod -R a+rX /opt/homebrew

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

~~~~~~

may help.

To get a more recent version of the gcc compiler

~~~~~~

    sudo brew tap homebrew/versions

    sudo brew install gcc49 --with-fortran

~~~~~~

### svn 1.7 (if needed for Jenkins) ###

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:

~~~~~~

    sudo 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:

~~~~~~

    brew update

    brew doctor

    brew install subversion17

~~~~~~

### 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

~~~~~~

## 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 /usr/local/texlive/2014basic/bin/universal-darwin/ to your path, run

~~~~~~

    sudo tlmgr update --self

    for i in breakurl cmap comment eepic epstopdf framed gensymb lineno mmap multirow overpic pdftex preprint revtex4 sectsty siunitx subfiles threeparttable titlesec units wrapfig xcite xypic courier helvetic palatino pifont symbol txfonts zapfding; do

      sudo tlmgr install $i

    done

~~~~~~

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 need also to do

~~~~~~

    sudo chmod -R a+rX /usr/local/texlive/2014basic/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.

## 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

~~~~~~

## Deprecated instructions for older OS ##

### 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

~~~~~~