Currently submitting co-allocated MUSCLE application is only possible using the XML !JobProfile (compare [[QCG-SimpleClient]]). Beside the different job description format you have to suffix the `qcg-sub` command with the `QCG` keyword:
{{{
$ qcg-sub muscle.xml QCG
}}} 
== Example (Fusion - Transport Turbulence Equilibrium) ==
 * Install your application on every cluster you wish to use
 * register it on every cluster using [http://apps.man.poznan.pl/trac/qcg-computing/wiki/ComunityModules QCG Community Modules (QCE)] mechanism:
{{{
qcg-module-create -g plggmuscle Fusion/Turbulence
}}}
The module must bear the same name on every cluster. Inside the module you can set/prepend any environment variable, add dependencies to other modules, e.g.:
{{{
#%Module 1.0


proc ModulesHelp { } {
        puts stderr "\tName: Fusion/Turbulence"
        puts stderr "\tVersion: 0.1"
        puts stderr "\tMaintainer: plgmamonski"
}

module-whatis   "Fusion/Turbulence, 0.1"

#load all needed modules
module add muscle2

#sets TCL variable
set FUSION_KERNELS "/home/plgrid-groups/plggmuscle/fusionkernels"
#sets environment variable
setenv FUSION_KERNELS $FUSION_KERNELS
#add to the PATH native kernels
prepend-path PATH ${FUSION_KERNELS}/bin/

set curMod [module-info name]

if { [ module-info mode load ] } {
        puts stderr "$curMod load complete."
}

if { [ module-info mode remove ] } {
        puts stderr "$curMod unload complete."
}
}}}
You can set there two environment variables interpreted by the MUSCLE framework, namely: `MUSCLE_CLASSPATH` and `MUSCLE_LIBPATH`
which set the Java classpath and the path of dynamically loadable libraries respectively. Thanks to this mechanism you can use single abstract CxA that do not consist of any site-specific paths. Also you can load the module in the interactive QCG job, e.g:
{{{
bash-4.1$ module load Fusion/Turbulence
openmpi/openmpi-open64_4.5.2-1.4.5-2 load complete.
Fusion/Turbulence load complete.
bash-4.1$ muscle2 -ma -c $FUSION_KERNELS/cxa/testSimpleModelsB_shared.cxa.rb 
Running both MUSCLE2 Simulation Manager and the Simulation
=== Running MUSCLE2 Simulation Manager ===

}}}
* Prepare XML job description:
{{{
<qcgJob appId="MAPPER" xmlns:jxb="http://java.sun.com/xml/ns/jaxb" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <task persistent="true" taskId="task">
    <requirements>
      <topology>
        <processes masterGroup="true" processesId="init:transp:dupCorep:turb">
	  				<processesCount>
						<value>1</value>
					</processesCount>
          <candidateHosts>
            <hostName>inula.man.poznan.pl</hostName>
          </candidateHosts>
        </processes>
        <processes processesId="equil:dupEquil">
					<processesCount>
						<value>1</value>
					</processesCount>
          <candidateHosts>
            <hostName>zeus.cyfronet.pl</hostName>
          </candidateHosts>
        </processes>
      </topology>
    </requirements>
    <execution type="mapper">
      <executable>
        <application name="muscle2"/>
      </executable>
      <arguments>
        <value>FusionSimpleModels.cxa.rb</value>
        <value>--verbose</value>
      </arguments>
      <stdout>
        <directory>
          <location type="URL">gsiftp://qcg.man.poznan.pl/~/MAPPER/${JOB_ID}.output</location>
        </directory>
      </stdout>
      <stderr>
        <directory>
          <location type="URL">gsiftp://qcg.man.poznan.pl/~/MAPPER/${JOB_ID}.error</location>
        </directory>
      </stderr>
      <stageInOut>
        <file name="FusionSimpleModels.cxa.rb" type="in">
          <location type="URL">gsiftp://qcg.man.poznan.pl/~/MAPPER/FusionSimpleModels.cxa.rb</location>
        </file>
        <file name="fusion-preprocess.sh" type="in">
          <location type="URL">gsiftp://qcg.man.poznan.pl/~/MAPPER/fusion-preprocess.sh</location>
        </file>
        <file name="fusion-postprocess.sh" type="in">
          <location type="URL">gsiftp://qcg.man.poznan.pl/~/MAPPER/fusion-postprocess.sh</location>
        </file>
 
        <directory name="data" type="in">
          <location type="URL">gsiftp://qcg.man.poznan.pl/~/MAPPER/data</location>
        </directory>
        <directory name="out" type="out">
          <location type="URL">gsiftp://qcg.man.poznan.pl/~/MAPPER/${JOB_ID}.out</location>
        </directory>
 
      </stageInOut>
      <environment>
        <variable name="QCG_MODULES_LIST">Fusion/Turbulence</variable>
        <variable name="QCG_PREPROCESS">fusion-preprocess.sh</variable>
        <variable name="QCG_POSTPROCESS">fusion-postprocess.sh</variable>
      </environment>
    </execution>
    <executionTime>
      <executionDuration>P0Y0M0DT0H30M</executionDuration>
    </executionTime>
  </task>
</qcgJob>
}}}
 In the above example we:
   * run the simulation on the two clusters using advance reservations created  automatically by the QCG-Broker (in the co-allocation process) on two clusters: inula and zeus (`<candidateHosts>`),
   * we requested 30 minutes of maximum job walltime (`<executionDuration>`),
   * we specify the kernels to be run in the `processesId` attribute of the `<processes>` element (multiple kernels must be separated with a colon ":"),
   * we specify the number of processes to be allocated
   * we give the module name: `<variable name="QCG_MODULES_LIST">Fusion/Turbulence</variable>` that has to be loaded before starting MUSCLE
   * we specify pre and post process scripts. Example scripts:
{{{
$cat fusion-preprocess.sh 
#!/bin/bash
#copy all file from the data dir into current directory:
cp data/* .
$cat fusion-postprocess.sh 
#!/bin/bash
#copy all CPOs into the `out` directory
mkdir -p out
cp *.cpo out
}}}
   * provide staging directives
 * Example session:
{{{
#submit
qcg-sub fusion.xml QCG

https://elder7.man.poznan.pl:8443/qcg/services/
/C=PL/O=GRID/O=PSNC/CN=qcg-broker/qcg-broker.man.poznan.pl
UserDN = /C=PL/O=GRID/O=PSNC/CN=Mariusz Mamonski
ProxyLifetime = 23 Days 18 Hours 12 Minutes 0 Seconds
jobId = J1353272598993_MAPPER_0845

#get info
qcg-info J1353272598993_MAPPER_0845

https://elder7.man.poznan.pl:8443/qcg/services/
/C=PL/O=GRID/O=PSNC/CN=qcg-broker/qcg-broker.man.poznan.pl
UserDN = /C=PL/O=GRID/O=PSNC/CN=Mariusz Mamonski
ProxyLifetime = 23 Days 18 Hours 11 Minutes 50 Seconds

Note: 
TaskType: MAPPER
SubmissionTime: Sun Nov 18 22:03:20 CET 2012
FinishTime: 
ProxyLifetime: P23DT18H11M47S
Status: QUEUED
StatusDesc: 
ReservedTimeSlot: Sun Nov 18 22:04:00 CET 2012 - Sun Nov 18 22:35:00 CET 2012
StartTime: 

Allocation: 
HostName: inula.man.poznan.pl
ProcessesCount: 1
ProcessesGroupId: init:transp:dupCorep:turb
Status: UNCOMMITTED
StatusDescription: 
SubmissionTime: Sun Nov 18 22:03:24 CET 2012
FinishTime: 
LocalSubmissionTime: 
LocalStartTime: 
LocalFinishTime: 

}}}

#peek output
qcg-peek J1353272598993_MAPPER_0845
https://elder7.man.poznan.pl:8443/qcg/services/
/C=PL/O=GRID/O=PSNC/CN=qcg-broker/qcg-broker.man.poznan.pl
UserDN = /C=PL/O=GRID/O=PSNC/CN=Mariusz Mamonski
ProxyLifetime = 23 Days 18 Hours 9 Minutes 43 Seconds

openmpi/openmpi-open64_4.5.2-1.4.5-2 load complete.
Fusion/Turbulence load complete.
openmpi/openmpi-open64_4.5.2-1.4.5-2 load complete.
Running both MUSCLE2 Simulation Manager and the Simulation
=== Running MUSCLE2 Simulation Manager ===
Executing: java -server -Xms20m -Xmx100m -classpath /home/plgrid-groups/plggmuscle/2.0/devel-debug/share/muscle/java/muscle.jar:/home/plgrid-groups/plggmuscle/2.0/devel-debug/share/muscle/java/thirdparty/oncrpc.jar:/home/plgrid-groups/plggmuscle/2.0/devel-debug/share/muscle/java/thirdparty/platform.jar:/home/plgrid-groups/plggmuscle/2.0/devel-debug/share/muscle/java/thirdparty/JadeLeap.jar:/home/plgrid-groups/plggmuscle/2.0/devel-debug/share/muscle/java/thirdparty/jmml-util-0.1.jar:/home/plgrid-groups/plggmuscle/2.0/devel-debug/share/muscle/java/thirdparty/jna.jar:/home/plgrid-groups/plggmuscle/2.0/devel-debug/share/muscle/java/thirdparty/junit-4.10.jar:/home/plgrid-groups/plggmuscle/2.0/devel-debug/share/muscle/java/thirdparty/msgpack-0.6.6.jar:/home/plgrid-groups/plggmuscle/2.0/devel-debug/share/muscle/java/thirdparty/jsr-275-1.0-beta-2.jar:/home/plgrid-groups/plggmuscle/2.0/devel-debug/share/muscle/java/thirdparty/javassist-3.15.0-GA.jar:/home/plgrid-groups/plggmuscle/2.0/devel-debug/share/muscle/java/thirdparty/json_simple-1.1.jar:/home/plgrid-groups/plggmuscle/2.0/devel-debug/share/muscle/java/thirdparty/jcommander-1.17.jar -Dpl.psnc.muscle.socket.factory=muscle.net.CrossSocketFactory -Dpl.psnc.mapper.muscle.mto.address=192.168.11.102 -Dpl.psnc.map

#when the job is finished
[qcg] /home/plgrid/plgmamonski/reef/MAPPER > qcg-info J1353272598993_MAPPER_0845
https://elder7.man.poznan.pl:8443/qcg/services/
/C=PL/O=GRID/O=PSNC/CN=qcg-broker/qcg-broker.man.poznan.pl
UserDN = /C=PL/O=GRID/O=PSNC/CN=Mariusz Mamonski
ProxyLifetime = 23 Days 18 Hours 8 Minutes 57 Seconds

Note: 
TaskType: MAPPER
SubmissionTime: Sun Nov 18 22:03:20 CET 2012
FinishTime: Sun Nov 18 22:04:37 CET 2012
ProxyLifetime: P23DT18H8M54S
Status: FINISHED
StatusDesc: 
ReservedTimeSlot: Sun Nov 18 22:04:00 CET 2012 - Sun Nov 18 22:35:00 CET 2012
StartTime: Sun Nov 18 22:03:32 CET 2012

Allocation: 
HostName: inula.man.poznan.pl
ProcessesCount: 1
ProcessesGroupId: init:transp:dupCorep:turb
Status: FINISHED


#we can see the results:
 ls -l J1353272598993_MAPPER_0845.out/
total 60608
-rw-r--r-- 1 plgmamonski plgrid-users 2503411 Nov 18 22:04 bdseq_equilibrium_0000.cpo
-rw-r--r-- 1 plgmamonski plgrid-users 2503411 Nov 18 22:04 bdseq_equilibrium_0001.cpo
-rw-r--r-- 1 plgmamonski plgrid-users 2503411 Nov 18 22:04 bdseq_equilibrium_0002.cpo
-rw-r--r-- 1 plgmamonski plgrid-users 2503411 Nov 18 22:04 bdseq_equilibrium_0003.cpo
-rw-r--r-- 1 plgmamonski plgrid-users 2503411 Nov 18 22:04 bdseq_equilibrium_0004.cpo
...