Siesta

Versions Installed

Kay: 4.0.2/4.1.5

LXP:

Description

SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. SIESTA’s efficiency stems from the use of strictly localised basis sets and from the implementation of linear-scaling algorithms which can be applied to suitable systems. A very important feature of the code is that its accuracy and cost can be tuned in a wide range, from quick exploratory calculations to highly accurate simulations matching the quality of other approaches, such as plane-wave and all-electron methods.

The possibility of treating large systems with some first-principles electronic-structure methods has opened up new opportunities in many disciplines. The SIESTA program is distributed freely to academics and has become quite popular, being increasingly used by researchers in geosciences, biology, and engineering (apart from those in its natural habitat of materials physics and chemistry). Currently there are several thousand users all over the world, and the paper describing the method (J. Phys. Cond. Matt. 14, 2745 (2002)) has had more than 9000 citations.

License

Starting in the Spring of 2016, with the 4.0 version, SIESTA is released under the terms of the GPL open-source license. The source can be downloaded from here. Other versions of SIESTA are distributed to academics free of charge (please see the detailed conditions in the licence text), and can be installed by computer centres to be used only by academics. These are not open source versions. They cannot be redistributed. They can be accessed from here.

Benchmarks

N/A.

Additional Notes

To use siesta load the relevant environment module:

module load siesta/4.0.2

Further information can be obtained from Siesta: Home.

Siesta is a fully parallel application, below is an example of how to submit a job.

Job Submission Example

#!/bin/sh
# All the information about queues can be obtained using 'sinfo'
# PARTITION AVAIL  TIMELIMIT  
# DevQ         up    1:00:00   
# ProdQ*       up 3-00:00:00    
# LongQ        up 6-00:00:00    
# ShmemQ       up 3-00:00:00    
# PhiQ         up 1-00:00:00   
# GpuQ         up 2-00:00:00    

# Slurm flags
#SBATCH -p ProdQ
#SBATCH -N 1
#SBATCH -t 24:00:00
#SBATCH --job-name=SiestaJob

# Charge job to myproject 
#SBATCH -A MyProject

# Write stdout+stderr to file
#SBATCH -o output.txt

# Mail me on job start & end
#SBATCH --mail-user=myEmail@domain.ie
#SBATCH --mail-type=BEGIN,END

cd $SLURM_SUBMIT_DIR

module load siesta/4.0.2

mpirun -np 40 siesta < fe.fdf > fe.out

How to cite Siesta:

The SIESTA method for ab-initio order-N materials simulation J. M. Soler, E. Artacho,J. D. Gale, A. García, J. Junquera, P. Ordejón, and D. Sánchez-Portal, J. Phys.: Condens. Matt. 14, 2745-2779 (2002).

Version 4.1.5

This version is not MPI enabled but can use OMP threads. Thus it is restricted to a single node only. Below is an example of how to submit this version of siesta. You can change the number of OMP threads being used up to a maximum of 40.

#!/bin/sh
# All the information about queues can be obtained using 'sinfo'
# PARTITION AVAIL  TIMELIMIT  
# DevQ         up    1:00:00   
# ProdQ*       up 3-00:00:00    
# LongQ        up 6-00:00:00    
# ShmemQ       up 3-00:00:00    
# PhiQ         up 1-00:00:00   
# GpuQ         up 2-00:00:00    

# Slurm flags
#SBATCH -p ProdQ
#SBATCH -N 1
#SBATCH -t 24:00:00
#SBATCH --job-name=SiestaJob

# Charge job to myproject 
#SBATCH -A MyProject

# Write stdout+stderr to file
#SBATCH -o output.txt

# Mail me on job start & end
#SBATCH --mail-user=myEmail@domain.ie
#SBATCH --mail-type=BEGIN,END

cd $SLURM_SUBMIT_DIR

export OMP_PLACES=cores
export OMP_PROC_BIND=close
export OMP_NUM_THREADS=10

module load siesta/4.1.5

siesta < fe.fdf > fe.out