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==Introduction==
 
==Introduction==
 
{{Software
 
{{Software
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==Version Selection==
 
==Version Selection==
  
The latest stable version of Siesta is 3.2 (patch) 4 and users are strongly encouraged to use it.
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The currently installed version (as of December, 2017) is version 4.0.  To see all available versions, run:
  
To load the siesta module, execute:
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module avail siesta
  
<pre>
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To load version 4.0, run:
module load siesta/3.2
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</pre>
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You can add this line to your startup script (.bashrc) to avoid executing it every time you log in.
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module load siesta/4.0
  
Both serial and mpi compiled executables are available, named siesta-serial and siesta-mpi respectively.
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This will put ''siesta'' and ''transiesta'' executable in your path so you can use them from the command line.
 
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Siesta 3.1 is still available, but will be removed soon.
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==Examples==
 
==Examples==
  
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You can see the examples included with version 4.0 by running:
  
To try the examples, first download the source code from Siesta website, using this [http://departments.icmab.es/leem/siesta/CodeAccess/Code/downloads.html link]
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ls $EBROOTSIESTA/Examples
  
To get the file directly to SHARCNET, just execute:
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To try the examples, copy them to your own space (in this example scratch directory):
  
  wget http://departments.icmab.es/leem/siesta/CodeAccess/Code/siesta-3.2-pl-5.tgz
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  cp -r $EBROOTSIESTA/Examples ~/scratch/
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cd ~/scratch/
  
then unpack the files with
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Then to try the SiH example:
  
  tar xvfz siesta-3.2-pl-5.tgz
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  cd Examples/SiH
  
There is a comprehensive set of examples in the tests directory. To try them, first log into a development node.  On orca, you can do this by doing:
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Copy the pseudopotential files:
  
  ssh orc-dev1
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  cp ../Vps/* .
  
On the development node it is possible to run short test programs without using sqsub. Next do:
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Create a file siesta_job.sh with the following content (replace ''def-someuser'' with your own account):
  
  cd siesta-3.2-pl-4/Tests
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  #!/bin/bash
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#SBATCH --account=def-someuser
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#SBATCH --ntasks=4               # number of MPI processes
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#SBATCH --mem-per-cpu=1024M      # memory; default unit is megabytes
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#SBATCH --time=0-00:05          # time (DD-HH:MM)
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module load siesta/4.0
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srun siesta < sih.fdf             
  
In that directory, edit the file
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Finally, submit the job (using 4 MPI processes in this example) with:
 
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test.mk
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so it has the line:
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SIESTA=siesta-serial
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Then to make sure you can find Siesta, execute:
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module load siesta
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Now you can cd into any of the directories in the tests directory and run :
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make
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This will copy the necessary pseudopotentials and then run the serial version of Siesta.
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If you want to run again, without using make, then just:
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cd work
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then run
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siesta-serial < ../FILE.fdf
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where you would replace FILE with the actual name of the .fdf file in the example you are trying.
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==Job Submission==
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Example of starting an mpi job (after module is loaded):
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<pre>
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sqsub -q mpi -r 40m -n 4 -o example.out -i example.fdf siesta-mpi
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</pre>
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Example of starting a serial job (after module is loaded):
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<pre>
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sqsub -q serial -r 40m -o example.out -i example.fdf siesta-serial
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</pre>
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==Example Job==
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sbatch siesta_job.sh
  
==General Notes==
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=General Notes=
  
 
<b>Note</b>: sometimes Siesta crashes when trying to generate xml output.  You can disable this output by adding
 
<b>Note</b>: sometimes Siesta crashes when trying to generate xml output.  You can disable this output by adding
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to your .fdf input file.
 
to your .fdf input file.
  
==References==
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=References=
  
 
o Siesta homepage<br>
 
o Siesta homepage<br>
http://www.icmab.es/siesta
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https://departments.icmab.es/leem/siesta/

Latest revision as of 09:40, 6 June 2019

This page is will be deleted pending it's creation on the CC wiki.

Introduction

SIESTA
Description: Linear-scaling DFT based on Numerical Atomic Orbitals
SHARCNET Package information: see SIESTA software page in web portal
Full list of SHARCNET supported software


SIESTA performs self-consistent DFT employing order-N techniques developed for tight-binding, founded on using Numerical Atomic Orbitals (NAOs) as a basis set.

Version Selection

The currently installed version (as of December, 2017) is version 4.0. To see all available versions, run:

module avail siesta

To load version 4.0, run:

module load siesta/4.0

This will put siesta and transiesta executable in your path so you can use them from the command line.

Examples

You can see the examples included with version 4.0 by running:

ls $EBROOTSIESTA/Examples

To try the examples, copy them to your own space (in this example scratch directory):

cp -r $EBROOTSIESTA/Examples ~/scratch/
cd ~/scratch/

Then to try the SiH example:

cd Examples/SiH

Copy the pseudopotential files:

cp ../Vps/* .

Create a file siesta_job.sh with the following content (replace def-someuser with your own account):

#!/bin/bash
#SBATCH --account=def-someuser
#SBATCH --ntasks=4               # number of MPI processes
#SBATCH --mem-per-cpu=1024M      # memory; default unit is megabytes
#SBATCH --time=0-00:05           # time (DD-HH:MM)
module load siesta/4.0
srun siesta < sih.fdf               

Finally, submit the job (using 4 MPI processes in this example) with:

sbatch siesta_job.sh

General Notes

Note: sometimes Siesta crashes when trying to generate xml output. You can disable this output by adding

WriteXML F

to your .fdf input file.

References

o Siesta homepage
https://departments.icmab.es/leem/siesta/