Differences between revisions 1 and 9 (spanning 8 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

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 1 as of 2015-01-13 09:41:40 → 
  Size: 181
  Editor: NicoleThomas
  Comment:
+   ← Revision 9 as of 2015-05-21 10:15:27 → ⇥
  Size: 3338
  Editor: NicoleThomas
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 5:
+[[ /Access | Access to JUROPATEST ]]

[[ /CVS | CVS on JUROPATEST ]]
-Line 8:
+Line 12:
+[[ /Debug | Debugging ]]

[[ /Vampir | Using Vampir ]]

[[ /Scalasca | Using Scalasca ]]

[[ Netcdf4Utils | Netcdf4 Format]]



== 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 
 {{{
#!/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.



[[ /Libraries | Used Libraries ]]