Jureca/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

#!/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
The job script is submitted using:
```
sbatch <jobscript>
```
On success, sbatch writes the job ID to standard out.
Other Slurm Commands
- squeue
  Show status of all jobs.
- scancel <jobid>
  Cancel a job.
- scontrol show job <jobid>
  Show detailed information about a pending, running or recently completed job.
- scontrol update job <jobid> set ...
  Update a pending job.
- scontrol -h
  Show detailed information about scontrol.
- sacct -j <jobid>
  Query information about old jobs.
- sprio
  Show job priorities.
- smap
  Show distribution of jobs. For a graphical interface users are referred to llview.
- sinfo
  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
```