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ALIs

Siesta: Electronic Structure and Molecular Dynamics

Introduction

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.

Please consult the Siesta Home page for further details and documentation.

Licensing and Versions

Leibniz Computing Centre makes use of the academic license for this package, Please note that you are required to obtain an academic license for individuals (see "Licenses" link on the SIESTA home page). Hence before using SIESTA on the LRZ HPC systems, please

1. contact LRZ HPC support via the service desk, giving your name and affiliation and user account(s).

2. take your licence agreement and attach an electronic copy (scan or email) to the incident filed at the service desk.

The following versions of SIESTA are available on the LRZ HPC systems:

• serial version 2.0s: Altix systems and all Opteron/EM64T based systems
• MPI parallel version 2.0p: SGI MPT (Altix 4700) and all Opteron/EM64T based systems
• MPI parallel version 3.0p: This is 3.0rc2, available for the Altix 4700 and all Opteron/EM64T based systems

Usage

After login to the system (choose one of the login nodes), please load the appropriate environment module via

module load siesta

(a non-default version can be loaded by explicitly specifying the version string). Subsequently, you can call parallel siesta via

mpiexec -n <num_procs>  $(which siesta)

For the serial version

siesta

is sufficient.

It is normally necessary to use SIESTA in batch mode; for this purpose example job scripts are provided below, which of course need modification for specific usage. Especially note that on the HLRB-II you need to use a PBS job script instead of the SGE ones provided for the cluster.

#!/bin/bash
#$-o $HOME/mydir/siesta.out -j y
#$-N siesta
#$-S /bin/bash
#$-l h_rt=24:00:00 
#$-pe mpi_8  16
# can also use parallel environments

# mpi_ice or uv instead
#$-M  wrzlprmft@mydomain
. /etc/profile
cd mydir
module load siesta

mpiexec -n $NSLOTS $(which siesta) 

#!/bin/bash
#$-o $HOME/mydir/siesta.out -j y
#$-N siesta
#$-S /bin/bash
#$-l h_rt=24:00:00 
#$-pe numa 16
#$-M  wrzlprmft@mydomain
. /etc/profile
cd mydir
module load siesta
mpirun -np $NSLOTS $(which siesta) 

#!/bin/bash
#PBS -o /home/hlrb2/group/user/mydir/siesta_job.out 
#PBS -j oe 
#PBS -N siesta_job
#PBS -S /bin/bash
#PBS -l walltime=24:00:00 
#PBS -l select=64:ncpus=1 
#PBS -M wrzlprmft@mydomain
#PBS -m abe
. /etc/profile.d/modules.sh
cd mydir
export OMP_NUM_THREADS=1
module load siesta

mpiexec -n 64 $(which siesta)

Documentation

Is available on the systems in PDF format. Please inspect the $SIESTA_DOC directory after loading the siesta environment module.