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The main documentation is available via module help chem/siesta on the cluster. Most software modules for applications provide working example batch scripts.

Description Content
module load chem/siesta
License GNU General Public License (GPL).
Citing Publications
Links Homepage | Documentation
Graphical Interface No

1 Description

SIESTA (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is both a method and its computer program implementation, to perform electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.

1.1 Loading the module

See Software Modules documentation

1.2 Program Binaries

The binary siesta is main program of the SIESTA package.

Usage: siesta [options] [< infile] [> outfile]
Example: siesta RUN.fdf > RUN.out

For information about how to construct SIESTA input files, please see the documentation.

1.3 Hints for using SIESTA

1.3.1 Parallel Execution

It is usually more efficient to run several smaller jobs with reasonable speedup side by side. Check for a reasonable speedup by increasing the number of workers from 1, 2, 4, n cores. Do not forget to adjust the memory specification when changing the number of workers

1.3.2 Memory Management

It requires some experience to choose the perfect memory value. Monitoring a job interactively may help to estimate the memory consumption. Requesting 1GB more than the required amount is typically sufficient.

1.3.3 Runtime Specification

The wall-time limit is independent of the number of parallel workers. Selecting the best value requires some experience. In general, jobs with shorter wall times get higher priorities. It could help to run the job interactively for a small period of time to monitor its convergence. Furthermore, it may be advantageous to extrapolate the run time by looking at smaller test jobs.

2 Examples

As with all processes that require more than a few minutes to run, non-trivial compute jobs must be submitted to the cluster queuing system.

Example scripts are available in the directory $SIESTA_EXA_DIR:

$ module show chem/siesta                # show environment variables, which will be available after 'module load'
$ module load chem/siesta                # load module
$ ls $SIESTA_EXA_DIR                     # show content of directory $SIESTA_EXA_DIR
$ cat $SIESTA_EXA_DIR/README             # show examples README

Run a first simple example job on JUSTUS 2:

$ module load chem/siesta                          # load module
$ WORKSPACE=`ws_allocate siesta 3`                 # allocate workspace
$ cd $WORKSPACE                                    # change to workspace
$ cp -a $SIESTA_HOME/bwhpc-examples .              # copy example files to workspace
$ cd bwhpc-examples/h2o                            # change to test directory
$ sbatch bwhpc_siesta_h2o.sh                       # submit job
$ squeue                                           # obtain JOBID
$ scontrol show job <JOBID>                        # check state of job
$ ls                                               # when job finishes the results will be visible in this directory

3 Useful links