Changes between Initial Version and Version 1 of MUSCLE1 Installation

Timestamp:

09/24/12 11:40:04 (12 years ago)

Author:

jorisborgdorff

Comment:

--

MUSCLE1 Installation

@@ +1 @@
+= MUSCLE v1 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 in several places extends and improve 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,
+* 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]]. Main 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, the [[http://www.cmake.org/|CMake]] package. For the C++ library, [[http://www.boost.org/|Boost]] is needed.
+
+=== Installation of dependencies on a Debian flavored Linux ===
+
+Run
+{{{
+sudo apt-get install build-essentials cmake ruby ruby-dev libboost-dev libgemplugin-ruby
+}}}
+
+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.
+
+1. Check if a proper version of ruby is already installed in the system, otherwise install it:
+{{{
+#!div style="font-size: 90%"
+{{{#!sh
+ruby --version
+-bash: ruby: command not found
+
+yum install ruby
+...
+ruby --version
+ruby 1.8.5 (2006-08-25) [x86_64-linux]
+}}}
+}}}
+
+2. Ensure if you have a c++ compiler available on your system. If you have not, install this:
+{{{
+#!div style="font-size: 90%"
+{{{#!sh
+yum install gcc-c++
+}}}
+}}}
+
+3. Check if cmake is available, otherwise install cmake:
+{{{
+#!div style="font-size: 90%"
+{{{#!sh
+yum install cmake
+}}}
+}}}
+ '''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:
+ {{{
+ #!div style="font-size: 90%"
+ {{{#!sh
+ [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=$basearch
+ failovermethod=priority
+ enabled=1
+ gpgcheck=0
+ }}}
+ }}}
+
+4. Check if recent Java SE Runtime Environment (JRE) or Java SE Development Kit (JDK) are present in your system. As the precompiled MUSCLE package is already included at build/muscle.jar you may not need to compile the Java sources and JRE should be sufficient. Hovewer, if you want to recompile the Java part of the MUSCLE (recommended), a recent Java compiler is also required.  
+{{{
+#!div style="font-size: 90%"
+{{{#!sh
+yum install jdk
+}}}
+}}}
+
+=== Installation of dependencies on Mac OS X ===
+
+Most dependencies are installed when installing Xcode. In [[http://itunes.apple.com/us/app/xcode/id497799835?ls=1&mt=12|Xcode 4.3]], the command-line tools are installed by opening Preferences -> Downloads and pressing Install at the item "Command-line tools". For Boost and CMake, download the packages on their website or use an installation manager like [[http://mxcl.github.com/homebrew/|HomeBrew]] or [[http://www.macports.org/|MacPorts]].
+
+=== Remainder of the installation ===
+
+If your ruby version is 1.8.x, then it is necessary to install json with the following command
+{{{
+sudo gem install json
+}}}
+
+When the dependencies are in place, you are ready to build and install MUSCLE.  Download the muscle bundle from [[http://apps.man.poznan.pl/trac/muscle/downloads|Downloads section]], e.g.
+{{{
+#!div style="font-size: 90%"
+{{{#!sh
+wget http://apps.man.poznan.pl/trac/muscle/downloads/muscle-1.1.1.zip
+}}}
+}}}
+
+Extract the download, e.g.
+{{{
+#!div style="font-size: 90%"
+{{{#!sh
+$ unzip muscle-1.1.1.zip
+}}}
+}}}
+Change your working directory to the the MUSCLE directory:
+{{{
+#!div style="font-size: 90%"
+{{{#!sh
+$ cd muscle-1.1.1
+}}}
+}}}
+Invoke MUSCLE build script with  installation (we are installing muscle to the /opt/muscle directory which is default, type ./build.rb for more options):
+{{{
+#!div style="font-size: 90%"
+{{{#!sh
+$ ./build.rb install --prefix=/opt/muscle
+}}}
+}}}
+See if MUSCLE is working correctly:
+{{{
+#!div style="font-size: 90%"
+{{{#!sh
+$ /opt/muscle/bin/muscle --version
+}}}
+}}}
+
+== Sample execution ==
+There are some examples provided within the MUSCLE bundle. Example code for kernels can be found in the directories src/java/examples and src/cpp/examples. There are also prepared configurations for coupled examples CxA (MUSCLE simulations), which can be found in the src/cxa directory.
+
+=== Hello World ===
+
+==== Sender ====
+ At src/java/examples/simplejava/Sender we provide a minimalist kernel written in Java, which sends data (an array of double).
+
+==== Receiver ====
+ At src/java/examples/simplejava/ConsoleWriter we provide a simple kernel written in Java. It receives data (an array of double) and prints its content to the standard output.
+
+==== CxA (coupling schema) ====
+ The configuration src/cxa/SimpleExample.cxa.rb configures a minimal CxA which couples the src/java/examples/simplejava/Sender and src/java/examples/simplejava/ConsoleWriter kernels.
+
+==== Execution ====
+To run the simulation defined in src/cxa/SimpleExample.cxa.rb use the following command:
+{{{
+#!div style="font-size: 90%"
+{{{#!sh
+/opt/muscle/bin/muscle --cxa_file src/cxa/SimpleExample.cxa.rb --main plumber w r --autoquit
+}}}
+}}}
+
+== Further reading ==
+For more information how to use MUSCLE see doc/muscle_developers_guide.pdf included in the MUSCLE bundle.