Elk FP-LAPW

Description

Elk FP-LAPW is an All-Electron Full-Potential Linearised Augmented-Plane Wave code for determining the properties of crystalline solids.

License

open-source under terms of the GNU General Public License version 3

Usage

Upcoming modulesystem change alert!

Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.

You can test the new version now by adding a line

source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules

to your script before loading a module. Then, you can list all versions of elk and load default version of elk as

module avail elk/ # list available modules
module load elk   # load (default) module

If you wish to keep up to the current system, it is still possible. Simply list all modules by

module avail elk

and choose explicit version you want to use.

1. Running the application -- Interactive mode:

• ask the scheduler for an interactive job having a desired number of nodes (nodes attribute) and a desired number of processors (ppn attribute) reserved

$ qsub -I -l nodes=X:ppn=Y -l mem=Zg

Note: Do not forget to apppropriately set the amount of requested memory (mem attribute) and/or another job requirements.

• load the application module

$ module add elk-2.2.9

• change the working directory to the one containing the ELK input file and run the computation
  • parallel computation on a single node (OpenMP):

$ cd $SCRATCHDIR/my_computation
$ elk >computation.log

• Note: Check the setting of the OMP_NUM_THREADS environment variable -- for such a computation, the variable should be set to the number of dedicated processors on a node (Y -- see above).

• distributed computation combined with parallel run (MPI + OpenMP):

$ cd $SCRATCHDIR/my_computation
$ mpirun -pernode elk >computation.log

• Note: Check the setting of the OMP_NUM_THREADS environment variable -- for such a computation, the variable should be set to the number of dedicated processors on a node (Y -- see above).

• distributed computation through multiple nodes (MPI only processes):

$ cd $SCRATCHDIR/my_computation
$ export OMP_NUM_THREADS=1
$ mpirun elk >computation.log

• Note: Check the setting of the OMP_NUM_THREADS environment variable -- for such a computation, the variable should be set to 1.

2. Running the application -- Batch mode:

• prepare the job description script -- use a general skeleton supplemented by the following lines:

...
# load the application module
module add elk-2.2.9

# change the working directory to the one containing the ELK input file and run the computation
cd $SCRATCHDIR/my_computation
elk >computation.log          # parallel computation on a single node
mpirun elk >computation.log   # distributed computation through multiple nodes (see other variants above)
...

• pass the job description file to the scheduler together with (at least) the requested number of nodes, processors and requested amount of memory

$ qsub -l nodes=X:ppn=Y -l mem=Zg mydescriptionscript.sh

Documentation

The documentation is available at producer's webpage (direct link to PDF manual).

Homepage

http://elk.sourceforge.net