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SIESTA

Description

SIESTA is an O(N) DFT code for electronic structure calculations and ab initio molecular dynamics simulations for molecules and solids. It uses norm-conserving pseudopotentials and linear combination of numerical atomic orbitals (LCAO) basis set.

How to Access SIESTA

NERSC uses modules to manage access to software. To use the default version of SIESTA, type:

% module load siesta

 

Access Restrictions

SIESTA is available at NERSC only to researchers at academic or public (non-defense) labs.

You must certify that this condition is met by using the siesta_register command. A NERSC consulting trouble ticket will be generated and you will be provided access in a timely manner.  The procedure for doing this is as follows:

  1. module load siesta
  2. siesta_register
  3. follow instructions
  4. wait for confirmation email from NERSC consultants


Using SIESTA on Hopper

There are two ways of running siesta on Hopper: submitting a batch job, or running interactively in an interactive batch session.

Sample Batch Script to Run SIESTA on Hopper

#PBS -N myjob
#PBS -q regular
#PBS -l mppwidth=16
#PBS -l walltime=8:00:00
#PBS -j oe
#PBS -V

cd $PBS_O_WORKDIR
module load siesta

aprun -n 16 siesta < test.fdf > test.out

Then submit the job script using the qsub command, e.g., assuming the job script name is test_siesta.pbs:

% qsub test_siesta.pbs

Sample Interactive Batch Script to Run SIESTA on Hopper

To request an interactive batch session, issue the command (e.g., requesting 16 PEs):

% qsub -I -V -q interactive -l mppwidth=16

When the batch session is returned to you, issue the following commands:

% cd $PBS_O_WORKDIR
% module load siesta
% aprun -n 16 siesta < test.fdf > test.out

Using SIESTA on Carver

Sample batch script to run siesta on Carver:

#PBS -N myjob
#PBS -q regular
#PBS -l nodes=2:ppn=8
#PBS -l walltime=8:00:00
#PBS -j oe
#PBS -V

cd $PBS_O_WORKDIR
module load siesta

mpirun -np 16 siesta < test.fdf > test.out

Documentation

The SIESTA code (Spanish Initiative for Electronic Simulations with Thousands of Atoms) is a  supported by the SIESTA Project at the Institute of Materials Science of Barcelona (ICMAB). 

Siesta Manuals

Compilation Instructions

Some advanced users may be interested in tweaking the SIESTA build parameters and building SIESTA themselves in their own directory. In order to aid in this process, and to provide a greater degree of transparency, the build instructions for the Abinit module are listed below. The following procedure was used to build SIESTA 3.1 on Hopper. In the main SIESTA source directory do:

% cd Obj

% sh ../Src/obj_setup.sh

% cp /usr/common/usg/siesta/3.1/arch.make .

% make

Availability

PackagePlatformCategoryVersionModuleInstall DateDate Made Default
SIESTA carver applications/ material sciences 3.0-b siesta/3.0-b 2010-04-06 2010-04-06
SIESTA carver applications/ material sciences 3.1 siesta/3.1 2012-03-07
SIESTA carver applications/ material sciences 3.2 siesta/3.2 2013-06-17
SIESTA edison applications/ material sciences 3.1 siesta/3.1 2013-05-07 2013-05-07
SIESTA hopper applications/ material sciences 3.0-rc2 siesta/3.0-rc2 2011-02-21 2011-03-10
SIESTA hopper applications/ material sciences 3.1 siesta/3.1 2012-03-27