Differences between revisions 9 and 11 (spanning 2 versions)

CLaMS on JUROPATEST

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

Used Libraries

-  ⇤ ← Revision 9 as of 2015-05-21 10:15:27 → 
  Size: 3338
  Editor: NicoleThomas
  Comment:
+   ← Revision 11 as of 2015-05-21 10:18:44 → ⇥
  Size: 1758
  Editor: NicoleThomas
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 11:
+[[ /Software | Software on JUROPATEST ]]

[[ /Netcdf | Using NetCDF ]]
-Line 12:
+Line 16:
-[[ /Debug | Debugging ]]

[[ /Vampir | Using Vampir ]]

[[ /Scalasca | Using Scalasca ]]

[[ Netcdf4Utils | Netcdf4 Format]]
-Line 85:
+Line 80:
-== 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 
 {{{
#!/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.