Compile and execute CLaMS programs on JUROPA

Compilation

All used libraries and module files are linked to:

/lustre/jhome47jicg11/jicg1108/clams_lib
/lustre/jhome47jicg11/jicg1108/clams_mod

The CLaMS makefiles are adjusted for compilation of CLaMS programs on JUROPA with the Intel compiler (mkincl/config/config.Linux_ifc).

The netCDF version 3.6.3 is used. For using netCDF 4 see Used Libraries (netCDF3/netCDF4).

The CLaMS programs can be compiled with:

{{{#highlight bash

gmake useComp=ifc [useMPI=true] progname

}}}

Create batch script

Write a batch script including the mpiexec command for the just compiled executable:

{{{#highlight bash

#!/bin/bash -x #MSUB -l nodes=<no of nodes>:ppn=<no of procs/node> #MSUB -l walltime=<hh:mm:ss> #MSUB -e <full path for error file> #MSUB -o <full path for output file>

cd $PBS_O_WORKDIR echo "workdir: $PBS_O_WORKDIR" NP=$(cat $PBS_NODEFILE | wc -l) # nodes*ppn echo "running on $NP cpus ..." mpiexec -np $NP <executable>

}}}

Job Limits

Batch jobs

max. number of nodes: 256 (default: 1)
max. wall-clock time: 12 hours (default: 30 min)

Interactive jobs:

max. number of nodes: 2 (default: 1)
max. wall-clock time: 30 min (default: 10 min)

Submit job

Submit the job with:

```
msub <jobscript>
```

On success msub returns the job ID of the submitted job.

Useful commands

checkjob -v <jobid>
get detailed information about a job
showq [r]
show status of all (running) jobs
canceljob <jobid>
cancel a job
mjobctl -q starttime <jobid>
show estimated starttime of specified job
mjobctl --help
show detailed information about this command

Interactive Session

Allocate interactive partition with X11 forwarding:
```
msub -I -X -l nodes=#:ppn=8
```
possible number of nodes: 1 or 2
Start your applications
Deallocate interactive partition with:
```
exit
```