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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.

 

Usage

 

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. Prior to invoking the program, the environment module siesta must be loaded.

Parallel processing (Linux Cluster)
Note that a run time limit of 24 hours is specified in the examples, and that at least 16 CPUs must be used on the Altix

Linux Cluster (SGE)

Linux Cluster (SLURM)

 
#!/bin/bash
#$-o $HOME/mydir/siesta.out -j y
#$-N siesta
#$-S /bin/bash
#$-l h_rt=24:00:00 
#$-pe mpi_8  16
#$-M  wrzlprmft@mydomain
. /etc/profile
cd mydir
module load siesta
mpiexec -n $NSLOTS $(which siesta) 

#!/bin/bash

#SBATCH -o /home/cluster/<group>/<user>/mydir/vasp.%j.out

#SBATCH -D /home/cluster/<group>/<user>/mydir

#SBATCH -J <job_name>

#SBATCH -M mpp1

# or use ice1 for the sgi ICE etc.

#SBATCH --ntasks=32

#SBATCH --mail-type=end

#SBATCH --mail-user=<email_address>@<domain>

#SBATCH --export=NONE

#SBATCH --get-user-env

#SBATCH --time=24:00:00

. /etc/profile.d/modules.sh
cd mydir
module load siesta
srun_ps $(which siesta)

Parallel processing (on SuperMUC, with LoadLeveler)
#!/bin/bash
#@ wall_clock_limit = 24:00:00
#  24 hours maximum run time
#@ job_type = parallel
#@ class = general
#@ network.MPI = sn_all,not_shared,us
#@ node = 2
#@ tasks_per_node = 40
#@ initialdir = $(home)/mydir
#@ output = job$(jobid).out
#@ error = job$(jobid).err
#@ notification=always
#@ notify_user=erika.mustermann@xyz.de
#@ queue

. /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.