= Use JUBE for messy-clams runs =

== Installation ==

 * on JURECA:
 {{{
module load JUBE
}}}

 * Download and installation on cluster workstation:
  * http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/JUBE/JUBE2/jube-installation_node.html
  * JUBE is installed in ''~/.local/bin''
  * add ''~/.local/bin'' to $PATH

==  Required files ==

  * Dummy makefile '''''${BASEDIR}/messy/mbm/clams/Makefile_jube'''''
  * Dummy MESSy script '''''${BASEDIR}/messy/util/xmessy_mmd.jube'''''
  * Dummy namelist directory '''''${BASEDIR}/messy/nml/MBM/clams_jube'''''
      (''dir_dummy_nml'' specified in ''namelistParam'' in JUBE script)
  * JUBE script, e.g. '''''${BASEDIR}/messy/util/xmessy_jube_clim.xml'''''

== JUBE script ==

 * Example for JUBE script: <<BR>>
   '''''messy-clams/messy/util/xmessy_jube_clim.xml'''''

 * Inside the script there is one parameterset for each clams namelist.
 
 * The namelist input is specified in these parametersets.

 * The dummy entries in the namelists ''${BASEDIR}/messy/nml/MBM/clams_jube/*.nml'' will be substituted with this input and copied to the namelist directory (NML_SETUP). <<BR>>
 '''Attention:''' Namelists in directory NML_SETUP will be overwritten if they already exist !
 
 * The specifications in the parametersets ''jobscriptParameter'' and ''xmessy_mmd'' are used to substitute the dummy entries in the messy script ''${BASEDIR}/messy/util/xmessy_mmd.jube''.

 * The messy-script ''xmessy_mmd.jube'' with substitutions is copied to the working directory (name: ''xmessy_mmd.$EXP_NAME'').

 
== Run JUBE script ==

 * copy JUBE script to working directory and change namelist data in the script

 * run JUBE script:
 {{{
jube run xmessy_jube_clim.xml [-t tag]
}}}

 * If the script is called with tag ''comp'', the basemodel ''clams'' is recompiled. <<BR>>
 '''Attention:''' The ''Makefile'' in subdirectory ''clams'' is replaced by the dummy makefile ''Makefile_jube'' with the current substitutions (parameterset ''makeParam'')


== JUBE commands ==

 {{{
jube run xmessy_jube_clim.xml [-t tags]

jube continue messy_bench
 
jube analyse messy_bench  [--id ID]
jube result messy_bench

jube info messy_bench [--id ID] [--step xxx]
jube log messy_bench [--id ID] [--command cmd]

jube help keyword

jube comment [-a] "..." messy_bench [-i ID]
jube comment -i ID -- "..." messy_bench
}}}

== Online documentation ==

https://apps.fz-juelich.de/jsc/jube/jube2/docu/index.html


== Run with Scalasca (on JURECA) ==

 {{{
module load Scalasca

jube run messy_clim.xml -t time scorep_comp scorep

scalasca -examine messy_bench/00000x/000003_exe/work/scorep_clams24_run
scalasca -examine -s messy_bench/00000x/000003_exe/work/scorep_clams24_run
}}}
   
-> scorep.score is created