Difference between revisions of "SIESTA"
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== Description ==
== Description ==


''From the NERSC website:'' “SIESTA is an O (N) DFT code for electronic structure calculations and ab initio molecular dynamics simulations for molecules and solids. It uses norm-conserving pseudopotentials and linear combination of numerical atomic orbitals (LCAO) basis set.”
''From the NERSC website:'' '''SIESTA''' is an O (N) DFT code for electronic structure calculations and ab initio molecular dynamics simulations for molecules and solids. It uses norm-conserving pseudopotentials and linear combination of numerical atomic orbitals (LCAO) basis set.


*[http://www.nersc.gov/users/software/applications/materials-science/siesta/ SIESTA website on nersc.gov]
{{AppStandardHeader|3.1|siesta}}
 
== Version ==
 
*3.1
 
== Authorized Users ==
 
*<code>CIRCE</code> account holders
 
== Platforms ==
 
*<code>CIRCE</code> cluster


== Running SIESTA Jobs on CIRCE ==
== Running SIESTA Jobs on CIRCE ==


=== [[Modules]] ===
{{PleaseReadUserGuide}}
 
{{SLURMAppParams}}
Before running a job, you must first set up your environment properly. Below is the required module file.
 
*apps/siesta/3.1<br />See [[Modules]] for more information.


=== Submitting Jobs ===
=== Submitting Jobs ===
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If, for example, you have an SIESTA input file named input.in, you would set up a submit script like this:
If, for example, you have an SIESTA input file named input.in, you would set up a submit script like this:


The script below (for testing, name it “siesta-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue. For help on submitting jobs to the queue, see our [[SLURM Users|SLURM User’s Guide]]. Scripts are provided as examples only. Your SLURM executables, tools, and options will vary.
The script below (for testing, name it “siesta-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue.  


<pre style="white-space:pre-wrap; width:45%; border:1px solid lightgrey; background:#E0E0E0; color:black;">
<pre style="white-space:pre-wrap; width:45%; border:1px solid lightgrey; background:#E0E0E0; color:black;">
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*You can view the status of your job with the “squeue -u <username>” command
*You can view the status of your job with the “squeue -u <username>” command


=== Tutorials and Tests ===
{{Documentation}}
 
*SIESTA Home Page
The following contain input parameters for known SIESTA Examples:
**http://www.nersc.gov/users/software/applications/materials-science/siesta/  
 
*/apps/siesta/3.1/Tests
*/apps/siesta/3.1/Tutorials
*http://www.gromacs.org/Documentation/Tutorials
 
=== Additional Documentation ===
*SIESTA Manual
*SIESTA Manual
**/apps/siesta/3.1/Docs/siesta-3.1-manual.pdf
**/apps/siesta/3.1/Docs/siesta-3.1-manual.pdf
{{BKETOR}}
*SIESTA Tutorials
**/apps/siesta/3.1/Tutorials
**http://www.gromacs.org/Documentation/Tutorials
*SIESTA Known Tests
**/apps/siesta/3.1/Tests


{{MoreInformation}}
{{MoreInformation}}
{{ReportingBugs}}
{{ReportingBugs}}

Revision as of 18:25, 29 June 2016

SIESTA

Description

From the NERSC website: SIESTA is an O (N) DFT code for electronic structure calculations and ab initio molecular dynamics simulations for molecules and solids. It uses norm-conserving pseudopotentials and linear combination of numerical atomic orbitals (LCAO) basis set.

Version

  • 3.1

Authorized Users

  • CIRCE account holders
  • RRA account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • RRA cluster
  • SC cluster

Modules

SIESTA requires the following module file to run:

  • apps/siesta/3.1

Running SIESTA Jobs on CIRCE

The SIESTA user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Submitting Jobs

The SIESTA manual is essential to understanding the application and making the most of it. Please refer to the Additional Documentation section for a link to the guide.

If, for example, you have an SIESTA input file named input.in, you would set up a submit script like this:

The script below (for testing, name it “siesta-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue. 

#!/bin/bash
#
#SBATCH --comment=siesta-test
#SBATCH --ntasks=4
#SBATCH --job-name=siesta-test
#SBATCH --output=output.%j.siesta-test
#SBATCH --time=01:00:00

#### Slurm 4 processor SIESTA test to run for 1 hour.

module purge
module load apps/siesta/3.1

mpirun siesta < input.in

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job: 

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./siesta-test.sh
  • You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with SIESTA to the IT Help Desk: rc-help@usf.edu

Retrieved from "https://wiki.rc.usf.edu/index.php?title=SIESTA&oldid=673"