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MUSCLE 2 Installation

MUSCLE 2 Installation

The recent bundle of MUSCLE can be downloaded from the Downloads section. The bundled package contains the source code, documentation and precompiled Java archives (jar). We maintain a list of clusters where MUSCLE is already deployed.

Dependencies

In order to use the MUSCLE, you need

a recent Java runtime, either Oracle-Java or Open-JDK;
a Ruby interpreter;
the CMake build system.

For the MUSCLE Transport Overlay, to communicate between different clusters, also Boost is needed.

Installation of dependencies on a Debian flavored Linux

Run

sudo apt-get install build-essential cmake ruby libboost-dev

to install all dependencies at once.

Installation of dependencies on Mac OS X

Most dependencies are installed when installing Xcode. In Xcode 4, the command-line tools are installed by opening Preferences -> Downloads and pressing Install for "Command-line tools". For Boost and CMake, download the packages on their website or use an installation manager like HomeBrew or MacPorts. With HomeBrew?, you can run

brew install boost cmake

Installation of dependencies on Scientific Linux 5.6

To install all dependencies in a single command, run

sudo yum install ruby gcc-c++ cmake jdk curl

Note: you may need to add the reference to the repository with extra packages. To do this create the file 'epel.repo' in the /etc/yum.repos.d directory. The content of the file may look as follows:

[epel]
name=Extra Packages for Enterprise Linux 5 - $basearch 
 
#baseurl=http://download.fedoraproject.org/pub/epel/5/$basearch
mirrorlist=http://mirrors.fedoraproject.org/mirrorlist?repo=epel-5&arch=$basearch
failovermethod=priority
enabled=1
gpgcheck=0

Remainder of the installation

If your ruby version is 1.8.x:

ruby --version

then it is necessary to install json with the following command

sudo gem install json

When the dependencies are in place, you are ready to build and install MUSCLE. Download the muscle bundle from Downloads section, or from the command-line. Then unzip the folder, go to the build directory inside and run the build.sh command.

curl -#O http://apps.man.poznan.pl/trac/muscle/downloads/MUSCLE-2.0.1-sources.zip
unzip MUSCLE-2.0.1-sources.zip
cd MUSCLE-2.0.1/build

sudo ./build.sh

This installs MUSCLE in /opt/muscle. For another location, add this as the first argument to build.sh.

The command

source /opt/muscle/etc/muscle.profile

should always be run before executing MUSCLE. It can help to put this command in ~/.bashrc so that it runs at login.

Finally, see if MUSCLE is working correctly:

muscle2 --version

Advanced building options

Although the build.sh script should be sufficient in more cases, sometimes it can not detect where certain libraries are located. This is often true for the MPI example and for compiling the MTO with Boost. The build settings can be modified by setting the following environment variables:

Variable	Setting	Example
`BOOST_INCLUDEDIR`	Location of Boost headers	`/opt/boost/include`
`BOOST_LIBRARYDIR`	Location of Boost libraries	`/opt/boost/lib`
`MPI_C_COMPILER`	Compiler used for the C MPI example	`/usr/bin/mpicc`
`MPI_C_FLAGS`	Flags to give the C MPI compiler	`-O3 -Wall`
`MPI_C_INCLUDE_PATH`	Location of include files for C MPI	`/usr/include`
`MPI_C_LIBRARIES`	All libraries needed to link with for C MPI (semicolon separated)	`/usr/lib/libmpi.so;/usr/lib/libm.so`

Possible build options can be evaluated by going to the build directory and running

cmake -L ..

Even more detailed build options are found with

cmake -LA ..

These options can be passed to cmake by setting the environment variable

export MUSCLE_CMAKE_OPTIONS="-DOPTION=VALUE -DOPTION2=VALUE2"

For example, to build the python extension:

export MUSCLE_CMAKE_OPTIONS="-DBUILD_PYTHON=ON"
sudo ./build.sh

And if the libraries can not be found

export MUSCLE_CMAKE_OPTIONS="-DBUILD_PYTHON=ON -DPYTHON_INCLUDE_DIR=/usr/include/python2.7 -DPYTHON_LIBRARY=/usr/lib/libpython2.7.so"
sudo ./build.sh