## page was renamed from Juropatest/CompileExecute
== Compile and Execute CLaMS programs on JURECA/JUWELS ==

 * Load following modules
 {{{
module load Intel
module load ParaStationMPI
module load netCDF-Fortran
}}}

 * Add current directory to PATH in .bash_profile:
 {{{
PATH=.:$PATH
export PATH
}}}

 * For compilation of all CLaMS program, go to the clams directory and simply type
 {{{
make all 
}}}

 * For compilation of a specific program ''progname'' in package ''package-name'':
 {{{
cd clams-directory
make libs
cd package-name
make progname
}}}

 * It may be necessary to set the stack size to unlimited:
 {{{
ulimit -s unlimited
}}}
 Without unsetting this memory limit a memory fault can occur.

 * Create a batch script 
 {{{#!highlight ksh numbers=disable
#!/bin/ksh -x
#SBATCH --nodes=1
#SBATCH --ntasks=4
#SBATCH --ntasks-per-node=4
#SBATCH --output=mpi-out.%j
#SBATCH --error=mpi-err.%j
#SBATCH --time=00:05:00
#SBATCH --partition=batch
#SBATCH --account=icg1

srun ./traj_mpi
}}}

 * Submit job <<BR>>
 The job script is submitted using:
 {{{
sbatch <jobscript>
}}}
 On success, sbatch writes the job ID to standard out.

 * Other Slurm Commands
  * ''squeue  ''   <<BR>> 
  Show status of all jobs.
  * ''scancel <jobid>'' <<BR>>   
  Cancel a job.
  * ''scontrol show job <jobid> '' <<BR>> 
  Show detailed information about a pending, running or recently completed job.
  * ''scontrol update job <jobid> set ...'' <<BR>> 
  Update a pending job.
  * ''scontrol -h''	<<BR>> 
  Show detailed information about scontrol.
  * ''sacct -j <jobid>'' <<BR>>
  Query information about old jobs.
  * ''sprio''   <<BR>> 
  Show job priorities.
  * ''smap''	<<BR>> 
  Show distribution of jobs. For a graphical interface users are referred to '''llview'''.
  * '' sinfo'' <<BR>> 
  View information about nodes and partitions.

 * Interactive sessions:
   
  * allocate interactive session:
  {{{
salloc --partition=devel --nodes=2 --time=00:30:00
}}}

  * salloc will start a bash on the login node. Start program within the bash with:
  {{{
srun --nodes=2 --ntasks-per-node=8 progname
}}}

  * The interactive session is terminated by exiting the shell
  {{{
exit
}}}