Differences between revisions 2 and 8 (spanning 6 versions)

CLaMS on JUROPATEST

Access to Juropatest

The Juropatest system is available by two Login nodes:

ssh -X userid@juropatest1.fz-juelich.de
ssh -X userid@juropatest2.fz-juelich.de

Software on Juropatest

Access to installed software on JUROPATEST is organized through a hierarchy of modules.
Show what modules are compatible available to load right now (given the toolchain modules you have already loaded):
```
module avail
```

Load a specific version of a module

module load <modulename>/<moduleversion>

List what modules are currently loaded
```
module list
```

Unload a module

module unload <modulename>/<moduleversion>

Unload all modules
```
module purge
```
Find the location of a module within the module hierarchy
```
module spider <modulename>
```
Show how to load NetCDF:
```
module -r spider '.*netCDF.*'
```

Using NetCDF on Juropatest

Loading NetCDF Module

module load intel-para netCDF-Fortran/4.4.2
or
module load intel netCDF-Fortran/4.4.2

Compilerversions loaded by intel-para (21.05.2015):
- gcc-Version 4.9.2 (GCC)
- icc version 15.0.2 (gcc version 4.9.0 compatibility)
- ifort version 15.0.2
If the netcdf module is loaded, "ncdump" and "ncgen" can be used and compilation of programs using netcdf is possible (without specifying any library or include path).

Compile Fortran program with NetCDF:

ifort -o progname progname.f90 -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz

Compile and Execute CLaMS programs on Juropatest

Load following modules

module load intel-para netCDF-Fortran/4.4.2

Add current directory to PATH in .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
```

Create a batch script

#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.

Used Libraries

-  ⇤ ← Revision 2 as of 2015-01-13 11:31:12 → 
  Size: 2144
  Editor: NicoleThomas
  Comment:
+   ← Revision 8 as of 2015-05-21 10:14:53 → ⇥
  Size: 3518
  Editor: NicoleThomas
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 5:
+[[ /Access | Access to JUROPATEST ]]

[[ /CVS | CVS on JUROPATEST ]]

[[ /CompileExecute | Compile and execute CLaMS programs ]]

[[ /Libraries | Used Libraries ]]

[[ /Debug | Debugging ]]

[[ /Vampir | Using Vampir ]]

[[ /Scalasca | Using Scalasca ]]

[[ Netcdf4Utils | Netcdf4 Format]]
-Line 7:
+Line 24:
-The Juropatest system is available by two Login nodes:
+ The Juropatest system is available by two Login nodes:
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+Line 70:
-Line 57:
+Line 75:
-module load intel-para netCDF-Fortran/4.2
+module load intel-para netCDF-Fortran/4.4.2
-Line 59:
+Line 77:
-module load icc/2015.0.090 ifort/2015.0.090 psmpi/5.1.0-1 netCDF-Fortran/4.2
+module load intel netCDF-Fortran/4.4.2
-Line 62:
+Line 80:
- * Compilerversions loaded by intel-param (08.01.2015):
  * gcc-Version 4.4.7 20120313 (Red Hat 4.4.7-4) (GCC) 
  * icc version 15.0.0 (gcc version 4.4.7 compatibility)
  * ifort version 15.0.0
+ * Compilerversions loaded by intel-para (21.05.2015):
   * gcc-Version 4.9.2 (GCC) 
   * icc version 15.0.2 (gcc version 4.9.0 compatibility)
   * ifort version 15.0.2
-Line 75:
+Line 92:
-== Compile and Execute CLaMS programs on JUROPATEST ==
+== Compile and Execute CLaMS programs on Juropatest ==
-Line 79:
+Line 96:
-module load intel-para netCDF-Fortran/4.2
+module load intel-para netCDF-Fortran/4.4.2
-Line 95:
+Line 112:
+ * Create a batch script 
 {{{
#!/bin/bash -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 <<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.