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

With mojave, one must additionally

sudo installer -pkg /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg -target /

But https://apple.stackexchange.com/questions/337940/why-is-usr-include-missing-i-have-xcode-and-command-line-tools-installed-moja says it is better to use xcrun --show-sdk-path to figure this out.

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
git clone https://github.com/Homebrew/brew.git homebrew

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

These last too lines can be reused at anytime there is a permissions problem.

As root again execute these lines to pick up some paths in the defaults paths:

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

git large file support (for VisIt)

brew install git-lfs
git lfs install --force --skip-smudge

For Qt5:

brew install bison flex gperf libcapn

To get fortran, which comes with the gcc compiler:

brew install gcc@6

With versions older than gcc 6.5 (released Nov 2018) possibly needed for OSs older than Mojave, gfortran is not installed with gcc and you need to add the following argument "--with-fortran" to the above brew install command.

OPTIONAL:

If you receive an error regarding ruby version:

brew install ruby@2.3

may help.

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/2017/bin/universal-darwin/

and then install the packages noted at

LaTeX packages needed by Bilder

You may need to use sudo.

sudo tlmgr update --self
sudo tlmgr install <needed packages>

and then used the autoupdate feature to get any additionally needed packages. This minimal installation is 230 M instead of the usual 2GB.

Disable spindump¶

for faster compilations via

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

LLVM-Clang¶

LLVM-Clang (aka LlvmClang) is different from AppleClang. It has support for target attributes and openmp, and provides a build chain for high-performance computing. Check out the llvm-project of your chosen version.

We use homebrew to install this with

brew install llvm

Then link it into place using

cd /opt
rm -f llvmclang
ln -s /opt/homebrew/Cellar/llvm/8.0.1 llvmclang

NOT RECOMMENDED

You can also build from the llvm repo, but we have not worked out the configuration args.

cd /opt
git clone -b <Branch> https://github.com/llvm/llvm-project.git llvm-<Version>
# You can see the branches you can clone at https://github.com/llvm/llvm-project
# e.g.  git clone -b llvmorg-8.0.0 https://github.com/llvm/llvm-project.git llvm-8.0.0

To configure and build:

cd /opt/llvm-<Version>
mkdir build
cd build
cmake ../llvm -DLLVM_ENABLE_PROJECTS="clang;openmp;libcxx;libcxxabi" -DLLVM_ENABLE_RTTI:BOOL=ON -DLLVM_ENABLE_EH:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH="/opt/llvm-<Version>/install" -G "Unix Makefiles" -DCMAKE_BUILD_TYPE=Release
make # Add appropriate -j argument for the machine to build faster
          # with -j 8 on qamojavellvm the build and installation took a little under an hour
make install

Bilder will look in /opt/llvmclang/bin for llvm binaries (as well as $LLVM_DIR/bin, and your installation dir/bin, in case you need to keep multiple versions for different builds), so we set a link to the installation directory in the chosen version of llvm:

cd /opt
sudo ln -s llvm-<Version>/install llvmclang

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 "machinename"
sudo scutil --set LocalHostName "machinename"
sudo scutil --set HostName "machinename.domainname.com"
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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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

DEPRECATED INSTRUCTIONS¶

Other gfortran options (besides HomeBrew)¶

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

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.

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