From bwHPC Wiki
Jump to: navigation, search
Description Content
module load chem/siesta
Availability BwForCluster_JUSTUS_2
License Free, open-source software, distributed under the GNU General Public License (GPL). More...
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.

2 Availability

SIESTA is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from the Cluster Information System (CIS).

In order to check which versions of SIESTA are installed on the compute cluster, run the following command:

$ module avail chem/siesta

3 License

SIESTA is free, open-source software released under the GNU General Public License (GPL). The SIESTA package in its entirety may be copied, modified or distributed according to the conditions described in its documentation.

4 Usage

4.1 Loading the module

You can load the default version of SIESTA with the following command:

$ module load chem/siesta

The module will try to load all modules it needs to function (e.g., compiler, mpi, ...). If loading the module fails, check if you have already loaded one of those modules, but not in the version required by SIESTA.

If you wish to load another (older) version of SIESTA, you can do so using

$ module load chem/siesta/<version>

with <version> specifying the desired version.

Please cite SIESTA in your publications according to the references.

4.2 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.

4.3 Hints for using SIESTA

4.3.1 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

4.3.2 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.

4.3.3 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.

5 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:

$ 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                       # 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

6 Useful links