= MUSCLE 2 Installation =

The recent bundle of MUSCLE can be downloaded from the [[http://apps.man.poznan.pl/trac/muscle/downloads|Downloads section]]. The bundled package contains the source code, documentation and precompiled Java archives (jar). We maintain a [[Clusters|list of clusters]] where MUSCLE is already deployed.

The offered version of MUSCLE 2 in extends and improves the [[http://muscle.berlios.de/|package]] provided by Jan Hegewald. We can list here the following elements:
* improved installation procedure (some dependencies are already included in the bundle),
* added support for generation of OTF trace logs,
* updated API
* implemented Port Range traversing technique for cross-cluster execution.

== Dependencies ==

The core functionality of the MUSCLE is written in Java. To be able to integrate native code with the MUSCLE, there is also a native part which is written in C++. Bootstrapping and platform independent configuration is done with a flexible setup mechanism written in Ruby. 

In order to use the MUSCLE, you need a recent Java runtime, either [[http://www.java.com/en/download/index.jsp|Oracle-Java]] or [[http://openjdk.java.net/|Open-JDK]]. Java third-party dependencies are already provided in the bundle and do not need to be independently installed. 

For the command-line interface [[http://www.ruby-lang.org/|Ruby]] is needed.

To compile and install MUSCLE, use the [[http://www.cmake.org/|CMake]] package. For the MUSCLE Transport Overlay, to communicate between different clusters,[[http://www.boost.org/|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 Scientific Linux 5.6 ===

'''Note:''' Some part of the presented installation procedure requires to be invoked by root.

{{{
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
}}}

=== Installation of dependencies on Mac OS X ===

Most dependencies are installed when installing Xcode. In [[http://itunes.apple.com/us/app/xcode/id497799835?ls=1&mt=12|Xcode 4.4]], the command-line tools are installed by opening Preferences -> Downloads and pressing Install at the item "Command-line tools". For Boost and CMake, download the packages on their website or use an installation manager like [[http://mxcl.github.com/homebrew/|HomeBrew]] or [[http://www.macports.org/|MacPorts]].

=== 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 [[http://apps.man.poznan.pl/trac/muscle/downloads|Downloads section]], e.g.
{{{
curl -#O http://apps.man.poznan.pl/trac/muscle/downloads/muscle-2.0-RC1.zip
}}}

Extract the download, e.g.
{{{
$ unzip muscle-2.0-RC1.zip
}}}
Change your working directory to the the MUSCLE directory:
{{{
$ cd muscle-2.0-RC1/build
}}}
Invoke MUSCLE build script with installation; this installs MUSCLE in /opt/muscle. For another location, add this as the first argument.
{{{
sudo ./build.sh
}}}
See if MUSCLE is working correctly:
{{{
source /opt/muscle/etc/muscle.profile
muscle2 --version
}}}
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.

== Further reading ==
For more information how to use MUSCLE see the [[Documentation]] and [[Tutorials]] sections.

----

For MUSCLE version 1.x installation, see [[MUSCLE1 Installation]]