Diff for "Jureca/CompileExecute"

Differences between revisions 1 and 13 (spanning 12 versions)

Compile and Execute CLaMS programs on JURECA

Load following modules

module load intel-para
module load netCDF-Fortran

Add current directory to PATH in .bash_profile:
```
PATH=.:$PATH
export PATH
```
The libraries used by CLaMS are installed in directory /homec/jicg11/jicg1108
The CLaMS programs can be compiled with:
```
make [useMPI=true] 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

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 1 as of 2015-05-21 10:17:03 → 
  Size: 1520
  Editor: NicoleThomas
  Comment:
+   ← Revision 13 as of 2019-07-16 10:43:51 → ⇥
  Size: 2124
  Editor: NicoleThomas
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-== Compile and Execute CLaMS programs on Juropatest ==
+## page was renamed from Juropatest/CompileExecute
== Compile and Execute CLaMS programs on JURECA ==
 Line 6:
-module load intel-para netCDF-Fortran/4.4.2
+module load intel-para
module load netCDF-Fortran
-Line 9:
+Line 10:
- * Add current directory to PATH in .profile:
+ * Add current directory to PATH in .bash_profile:
-Line 22:
+Line 23:
+ * It may be necessary to set the stack size to unlimited:
 {{{
ulimit -s unlimited
}}}
 Without unsetting this memory limit a memory fault can occur.
-Line 23:
+Line 30:
- {{{
#!/bin/bash -x
+ {{{#!highlight ksh numbers=disable
#!/bin/ksh -x
-Line 38:
+Line 45:
-   {{{
+ {{{
-Line 62:
+Line 69:
+ * 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
}}}