Over the past two weeks we have experienced Oakely login node crashes potentially caused by a Lustre bug.

SIESTA

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. More information can be found from here.

Availability & Restrictions

SIESTA is available on the Oakley cluster. A serial and a parallel build were created in order to meet users' computational needs.

VERSION GLENN OAKLEY
3.2-pl-4   X

The SIESTA program is distributed freely to academics. Use of SIESTA for academic purposes requires validation. To obtain validation, please complete and return the "Academic Agreement to Use SIESTA", located on the Academic Agreement Forms Page. Commercial users need to show proof of licence in order to use SIESTA at OSC.

Batch Usage

When you log into oakley.osc.edu, you are actually logged into a linux box referred to as the login node. To gain access to the 4000+ processors in the computing environment, you must submit your SIESTA job to the batch system for execution.

Assume that you have a test case in your work directory (where you submit your job, represented by $PBS_O_WORKDIR), with the input file 32_h2o.fdf. A batch script can be created and submitted for a serial or parallel run. The following are the sample batch scripts for running serial and parallel SIESTA jobs.

Sample Batch Script for Serial Jobs

#PBS -l walltime=0:30:00
#PBS -l nodes=1:ppn=12
#PBS -N siesta
#PBS -j oe
#
cd $PBS_O_WORKDIR
#
# Set up the package environment
module load siesta
#
# Execute the serial solver (nodes=1, ppn<=12)
siesta <32_h2o.fdf> output
exit

Sample Batch Script for Parallel Jobs

#PBS -l walltime=0:30:00
#PBS -l nodes=2:ppn=12
#PBS -N siesta
#PBS -j oe
#
cd $PBS_O_WORKDIR
#
# Set up the package environment
module swap intel/12.1.4.319 intel/13.1.3.192
module load siesta_par
#
# Execute the parallel solver (nodes>1, ppn=12)
mpiexec -np 24 siesta <32_h2o.fdf> output
exit

Further Reading

Online documentation is available at: http://departments.icmab.es/leem/siesta/Documentation/index.html.

Citations

1. “Self-consistent order-N density-functional calculations for very large systems”, P. Ordejón, E. Artacho and J. M. Soler, Phys. Rev. B (Rapid Comm.) 53, R10441-10443 (1996).

2. “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).


 

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