Siesta

Description
	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.
Site	Version (Latest: v2.0.1)	Notes
ngs.rl.ac.uk	v2.0.1	64 bit

License

Siesta is distributed freely for academics, under some conditions stated in the LICENSE. To use Siesta on the NGS you or your research group must already have signed a license agreement with Siesta. Therefore, before running Siesta on the NGS you should : 

• Obtain a license from the Siesta developers at Siesta License
• E-mail the NGS helpdesk with a copy of the license, the Siesta developers will send you, and requesting that are added to the Siesta registered users list.
• Your NGS id will then be added to the siesta group so that you can access the Siesta programs.

Users of this application should credit the code authors and the NGS accordingly and where applicable the specific site where the code is installed, when publishing work using NGS resources. 

Running Siesta on the NGS (General)

There a multiple ways in which jobs can be launched on the NGS. All the examples below us the example files to be found at

gsisftp://ngs.rl.ac.uk:2811/apps/siesta_mpi/examples

• Submission Using the UI/WMS

  To submit a Siesta job via the WMS, login to the UI and create a JDL file as below, replacing your NGS ID on the UI for ngsxxxx, then submit using:

  glite-wms-job-submit -o jobIDs -a siesta.jdl

  Type = "Job";
  JobType = "mpich";
  Executable = "/usr/ngs/SIESTA";
  Arguments = "md_nose.fdf par_md_nose5.out";
  CpuNumber = 4;
  StdOutput = "std.out";
  StdError = "std.err";
  Myproxyserver= "myproxy.ngs.ac.uk";
  InputSandbox = {"C.psf","md_nose.fdf","md_nose.pseudos","Mg.psf","O.psf"};
  InputSandboxBaseURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngs0055/siesta";
  OutputSandbox = {"std.err","par_md_nose5.out","std.out"};
  OutputSandboxBaseDestURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngs0055/siesta";
  Requirements = (
       member("NGS-UEE-SIESTA", other.GlueHostApplicationSoftwareRunTimeEnvironment)
  );
  ShallowRetryCount = -1;

• NGS Web Portal Submission

  After logging in to the NGS portal, select the "Siesta" template under the "Chemistry" category and make the amendments appropriate for your specific job. Read the description page of the template for further details.

• Submission Using Globus
  All the input files required to run Siesta should be in the working directory. The general input file 'name'.fdf , should be given as the FIRST argument and the output file name as the SECOND argument, as in the following example (the command should be in one line).:

  globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf \
  '&(executable=/usr/ngs/SIESTA_2_01)(jobType=mpi) \
  (count = 4)(arguments= md_nose.fdf par_md_nose5.out)'

  The input files can be copied to your home/working direcory from /apps/siesta_mpi/examples .

Compilation Information for ngs.rl.ac.uk 

If you need information on how this application was compiled please contact the NGS support centre.

Further Information 

• Siesta User's Manuals

• Siesta Home Page