= MUSCLE 2.0 =
[[PageOutline]]  
== Changelog ==
* removed JADE dependency
* support for standalone native kernels

== SVN access (developer version) ==
{{{
svn co https://apps.man.poznan.pl/svn/muscle/muscle/trunk
}}}
== Installation ==
The 2.0 version follows the stnadard CMake procedure. After downloading the source package go into the main dir and type:
{{{
mkdir build
cd build
cmake ..
make
make install
}}}

If needed it is also possible to configure some options for the installation. You can do this manually specifying the parameters using -D switch, eg. cmake .. -DMUSCLE_INSTALL_PREFIX=/somelocation, but the easiest way is to use ccmake or gmake programs. The following options may be particullarly important:
* MUSCLE_INSTALL_PREFIX - the default prefix for the installation (default: /opt/muscle)
* BUILD_API_DOC - determines if the API documentation should be build (default: No)
* BUILD_MTO - determines if the Muscle Transport Overlay should be build (default: Yes)
* BUILD_CPP - determines if the CPP part of the Muscle should be build (default: Yes)

=== Regression tests ===
After invoking the ''make install'' command, it is possible to make regression tests to check the consistency of the MUSCLE installation:
{{{
make test
}}}

== Current deployment ==

=== Local testbed - grass1  ===
{{{
module load muscle2/devel
}}}
**Limited resource. Only one node. Use PL-Grid sites instead!  **
=== PL-Grid sites ===
The PL-Grid e-infrastructure gives you access to reasonable computational power (> 230 Teraflops). You can use it both for production and test runs. If you want to debug/test your application interactively use `-I` option of the `qsub` command, e.g:
{{{
[reef] /home/plgrid/plgmamonski/reef > qsub -I -q plgrid-testing
qsub: waiting for job 6742856.ce.reef.man.poznan.pl to start
qsub: job 6742856.ce.reef.man.poznan.pl ready

[r399] /home/plgrid/plgmamonski/reef > 
[r399] /home/plgrid/plgmamonski/reef > module load muscle2/devel
 java/jdk1.6.0_23 load complete.
 intel/10.1 load complete.
 'openmpi/current' load complete.
}}}
**Do not run anything computational intensive at the frontend/ui machine as your account might be banned!**
==== Zeus (Cyfronet - Krakow) ====
Add the two following line to your `.bashrc`:
{{{
export QCG_SCRIPTS_DIR=/software/grid/plgrid/qcg-app-scripts/app-scripts/
. $QCG_SCRIPTS_DIR/common-mod.qcg
}}}
After next login you should be able to see the `muscle2` modules:
{{{
$module avail muscle2
---------------------/mnt/lustre/scratch/groups/plggmuscle/.qcg-modules ------
muscle2/devel
$module load muscle2
 java/current load complete.
 'openmpi/current' load complete.
$muscle2  --version
This is the Multiscale Coupling Library and Environment (MUSCLE) 2.0 
Revision: $Rev: 404 $ from $Date: 2012-06-28 15:34:05 +0200 (Thu, 28 Jun 2012) $: running in 64-bit mode
}}}
==== Reef (PSNC - Poznan) ====
Like Zeus, but set:
{{{
export QCG_SCRIPTS_DIR=/opt/exp_soft/plgrid/qcg-app-scripts/app-scripts/
. $QCG_SCRIPTS_DIR/common-mod.qcg
}}}
in your `~/.bashrc` file.
{{{!comment
==== Galera (TASK - Gdansk) ====
Like Zeus, but set:
{{
export QCG_SCRIPTS_DIR=/opt/exp_soft/plgrid/qcg-app-scripts/app-scripts/
. $QCG_SCRIPTS_DIR/common-mod.qcg
}}
in your `~/.bashrc` file.
}}}