MUSCLE 2.0

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.

Galera (TASK - Gdansk)

Like Zeus, but set:

export QCG_SCRIPTS_DIR=/software/grid/plgrid/qcg-app-scripts/app-scripts/
. $QCG_SCRIPTS_DIR/common-mod.qcg

in your ~/.bashrc file.