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Table of Contents

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SIESTA at a glance

Purpose:

ab

Ab initio electronic structure,

molecular dynamics

Molecular Dynamics
Latest version: 4.

0b2

1

Availability: all machines
Licence: mixed licence
Documentation: User's Guide

License: (tick) Free of use for academics users
                 Mixed
Website: https://departments.icmab.es/_ext-link

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Description

SIESTA is a program for ab initio electronic structure and molecular dynamics of solids and molecules.

SIESTA applies DFT hamiltonians (LDA, GGA) to strictly localized numerical basis sets and non-local pseudopotentials to obtain electronic structures. From these it can compute solid properties (band structure, DOS, k-space sampling, dielectric polarisation, phonons), perform Born-Oppenheimer molecular dynamics (NVT and NPT), and, in recent versions, Van der Waals potentials and ballistic electron transport properties (TranSIESTA).

A more detailed description can be found in this manifest.

Licence

SIESTA is provided free of charge to academic users only.

For more information please visit this page.

Available Versions

The currently available versions of SIESTA in our facilities are:

  • 2.0.2 (prades, pirineus)
  • 3.0-rc2 (pirineus)
  • TranSIESTA-3.0b (prades)
  • 3.1 (pirineus)
  • 3.2 (all machines)
  • 4.0b2 (pirineus, collserola)

To load a version, call it in a script via 

Code Block
languagetext
module load siesta/4.0b2

Benchmark

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SIESTA 3.2 benchmark at collserola: actual speed-up (green) and ideal speed-up (blue) vs. number of cores for the conjugated gradient optimisation of a hydrogen atom in solid silicon using the SIESTA methodology.

LSF example script (collserola)

Code Block
languagebash

SLURM Submit script example

For more information use the Job Script Generator.


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titlesiesta_example.slm
#!/bin/bash
## # IMPORTANT NOTICE: replace the email address # and the working directories with your own info ## # BSUB 
#SBATCH -J
gromacs
siesta_example
#
#SBATCH
BSUB 
-
o
e
gromacs.log # send standard output here # BSUB -e gromacs.err # send error output here # # Pick a queue # BSUB -q short # # Send an email notice once the job is finished # BSUB -N -u youremail@wherever # # Indicate the number of cores # BSUB -n 4 # # Pick the machine # BSUB -R collserola date # Set up the environment . /opt/modules/default/init/bash module load siesta/3.2-new # Run SIESTA with MPI mpijob siesta < input.inp > output.out date

LSF example script (pirineus)

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languagebash
#!/bin/bash ## # IMPORTANT NOTICE: replace the email address # and the working directories with your own info ## # BSUB -J gromacs # BSUB -o gromacs.log # send standard output here # BSUB -e gromacs.err # send error output here # # Pick a queue # BSUB -q short # # Send an email notice once the job is finished # BSUB -N -u youremail@wherever # # Indicate the number of cores # BSUB -n 4 # # BSUB -R collserola date # Set up the environment . /opt/modules/default/init/bash module load siesta/3.2 # Run SIESTA with MPI mpijob siesta < input.inp > output.out
siesta_example.%j.err
#SBATCH -o siesta_example.%j.out
#SBATCH -p std
#SBATCH -n 1
#SBATCH -t 0-02:00

module load apps/siesta/4.1

##
#  Modify the input and output files!
INPUT_FILE=siesta_example.inp
OUTPUT_FILE=siesta_example.out
 
##
#  You don't need to modify nothing more
cp -r ${SLURM_SUBMIT_DIR}/${INPUT_FILE} ${SCRATCH}
cd ${SCRATCH}
 
srun siesta < ${INPUT_FILE} > ${OUTPUT_FILE}
 
cp ./${OUTPUT_FILE} ${SLURM_SUBMIT_DIR}

Sbatch options:

The options shown in the example are detailed below. For more information and a more comprehensive list of available options, see the sbatch command page.

  • -J: Name for the job's allocation.
  • -e: Name of the stderr redirection filename.
  • -o: Name of the stdout redirection filename.
  • -p: Name of the partition (queue) where the job will be submitted.

  • -n: Number of tasks.

  • -c: Number of cores per task.
  • -t: Set the job's time limit. If the job don't finish before the time runs out, it will be killed.
date