Diff for "Jureca/CompileExecute"

Differences between revisions 4 and 18 (spanning 14 versions)

Compile and Execute CLaMS programs on JURECA

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
```

-  ⇤ ← Revision 4 as of 2015-09-16 09:52:07 → 
  Size: 1729
  Editor: NicoleThomas
  Comment:
+   ← Revision 18 as of 2022-10-07 08:38:08 → ⇥
  Size: 2268
  Editor: NicoleThomas
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 2:
-== Compile and Execute CLaMS programs on Juropatest ==
+== Compile and Execute CLaMS programs on JURECA ==
 Line 6:
-module load intel-para netCDF-Fortran/4.4.2
+module load Intel
module load ParaStationMPI
module load netCDF-Fortran
-Line 9:
+Line 11:
- * Add current directory to PATH in .profile:
+ * Add current directory to PATH in .bash_profile:
-Line 15:
+Line 17:
- * The libraries used by CLaMS are installed in directory /homec/jicg11/jicg1108
+ * For compilation of all CLaMS program, go to the clams directory and simply type
 {{{
make all 
}}}
-Line 17:
+Line 22:
- * The CLaMS programs can be compiled with:
+ * For compilation of a specific program ''progname'' in package ''package-name'':
-Line 19:
+Line 24:
-make [useMPI=true] progname
+cd clams-directory
make libs
cd package-name
make progname
-Line 29:
+Line 37:
- {{{
 #!/bin/bash -x
+ {{{#!highlight ksh numbers=disable
#!/bin/ksh -x
-Line 38:
+Line 46:
+#SBATCH --account=icg1
-Line 44:
+Line 53:
-   {{{
+ {{{
-Line 68:
+Line 77:
+ * 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
}}}