Siesta - Revision history

H Winkhardt: Redirected page to SIESTA

2021-11-05T14:51:02Z

Redirected page to SIESTA

← Older revision	Revision as of 16:51, 5 November 2021
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		#REDIRECT[[SIESTA]]

F Wagner: Blanked the page

2020-10-12T00:38:11Z

Blanked the page

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	{\| width=760px class="wikitable"
	\|-
	! Description !! Content
	\|-
	\| module load
	\| chem/siesta
	\|-
	\| Availability
	\| [[BwForCluster_JUSTUS_2]]
	\|-
	\| License
	\| Free, open-source software, distributed under the GNU General Public License (GPL). [[#License\|More...]]
	\|-
	\| Citing
	\| [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Publications/index.html Publications]
	\|-
	\| Links
	\| [https://departments.icmab.es/leem/siesta/ Homepage] \| [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Manuals/manuals.html Documentation]
	\|-
	\| Graphical Interface
	\| No
	\|}

	= 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.

	= Availability =

	SIESTA is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from the [https://www.bwhpc.de/software.html Cluster Information System (CIS)].

	In order to check which versions of SIESTA are installed on the compute cluster, run the following command:
	<pre>
	$ module avail chem/siesta
	</pre>

	= License =

	SIESTA is free, open-source software released under the GNU General Public License (GPL). The SIESTA package in its entirety may be copied, modified or distributed according to the conditions described in its [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Manuals/manuals.html documentation].

	= Usage =

	== Loading the module ==

	You can load the default version of SIESTA with the following command:
	<pre>
	$ module load chem/siesta
	</pre>

	The module will try to load all modules it needs to function (e.g., compiler, mpi, ...). If loading the module fails, check if you have already loaded one of those modules, but not in the version required by SIESTA.

	If you wish to load another (older) version of SIESTA, you can do so using
	<pre>
	$ module load chem/siesta/<version>
	</pre>
	with <version> specifying the desired version.

	Please cite SIESTA in your publications according to the [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Publications/index.html references].

	== Program Binaries ==

	The binary ''siesta'' is main program of the SIESTA package.
	<pre>
	Usage: siesta [options] [< infile] [> outfile]

	Example: siesta RUN.fdf > RUN.out
	</pre>

	For information about how to construct SIESTA input files, please see the [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Manuals/manuals.html documentation].

	== Hints for using SIESTA ==

	=== Parallel Execution ===

	It is usually more efficient to run several smaller jobs with reasonable speedup side by side. Check for a reasonable speedup by increasing the number of workers from 1, 2, 4, n cores. Do not forget to adjust the memory specification when changing the number of workers

	=== Memory Management ===

	It requires some experience to choose the perfect memory value. Monitoring a job interactively may help to estimate the memory consumption. Requesting 1GB more than the required amount is typically sufficient.

	=== Runtime Specification ===

	The wall-time limit is independent of the number of parallel workers. Selecting the best value requires some experience. In general, jobs with shorter wall times get higher priorities. It could help to run the job interactively for a small period of time to monitor its convergence. Furthermore, it may be advantageous to extrapolate the run time by looking at smaller test jobs.

	= Examples =

	As with all processes that require more than a few minutes to run, non-trivial compute jobs must be submitted to the cluster queuing system.

	Example scripts are available in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$SIESTA_EXA_DIR</span>:
	<pre>
	$ module show chem/siesta # show environment variables, which will be available after 'module load'
	$ module load chem/siesta # load module
	$ ls $SIESTA_EXA_DIR # show content of directory $SIESTA_EXA_DIR
	$ cat $SIESTA_EXA_DIR/README # show examples README
	</pre>

	Run a first simple example job:
	<pre>
	$ module load chem/siesta # load module
	$ WORKSPACE=`ws_allocate siesta 3` # allocate workspace
	$ cd $WORKSPACE # change to workspace
	$ cp -a $SIESTA_HOME/bwhpc-examples . # copy example files to workspace
	$ cd bwhpc-examples/h2o # change to test directory
	$ sbatch bwhpc_siesta_h2o.sh # submit job
	$ squeue # obtain JOBID
	$ scontrol show job <JOBID> # check state of job
	$ ls # when job finishes the results will be visible in this directory
	</pre>

	= Useful links =

	* [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Manuals/manuals.html Documentation (english)]
	* [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/list.html Mailing list (english)]
	* [https://en.wikipedia.org/wiki/SIESTA_(computer_program) Wikipedia article (english)]
	----
	[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]

F Wagner: /* Program Binaries */

2020-10-11T23:27:55Z

Program Binaries

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	</pre>		</pre>

	For information about how to construct input files, please see the [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Manuals/manuals.html documentation].		For information about how to construct SIESTA input files, please see the [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Manuals/manuals.html documentation].

	== Hints for using SIESTA ==		== Hints for using SIESTA ==

F Wagner: /* Loading the module */

2020-10-11T18:55:34Z

Loading the module

← Older revision		Revision as of 20:55, 11 October 2020
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	with <version> specifying the desired version.		with <version> specifying the desired version.

	Please cite SIESTA in your publications according to the [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/~~Manuals~~/~~manuals~~.html ~~documentation~~].		Please cite SIESTA in your publications according to the [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Publications/index.html references].

	== Program Binaries ==		== Program Binaries ==

F Wagner: /* Program Binaries */

2020-10-11T18:51:54Z

Program Binaries

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	</pre>		</pre>

	For information about how to construct input files see the [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Manuals/manuals.html ~~manual~~].		For information about how to construct input files, please see the [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Manuals/manuals.html documentation].

	== Hints for using SIESTA ==		== Hints for using SIESTA ==

F Wagner: /* Program Binaries */

2020-10-11T18:49:46Z

Program Binaries

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	</pre>		</pre>

	For information about how to construct input files see the https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Manuals/manuals.html manual.		For information about how to construct input files see the [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Manuals/manuals.html manual].

	== Hints for using SIESTA ==		== Hints for using SIESTA ==

F Wagner: /* Program Binaries */

2020-10-11T18:49:27Z

Program Binaries

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	</pre>		</pre>

	For information about how to construct input files see the ~~SIESTA~~ manual.		For information about how to construct input files see the https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Manuals/manuals.html manual.

	== Hints for using SIESTA ==		== Hints for using SIESTA ==

F Wagner: /* Program Binaries */

2020-10-11T18:48:42Z

Program Binaries

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	Example: siesta RUN.fdf > RUN.out		Example: siesta RUN.fdf > RUN.out
	</pre>		</pre>

			For information about how to construct input files see the SIESTA manual.

	== Hints for using SIESTA ==		== Hints for using SIESTA ==

F Wagner: /* Program Binaries */

2020-10-11T18:21:29Z

Program Binaries

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	The binary ''siesta'' is main program of the SIESTA package.		The binary ''siesta'' is main program of the SIESTA package.
	Standard usage:
	<pre>		<pre>
	Usage: siesta [options] [< infile] [> outfile]		Usage: siesta [options] [< infile] [> outfile]

F Wagner: /* Program Binaries */

2020-10-11T18:20:59Z

Program Binaries

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	The binary ''siesta'' is main program of the SIESTA package.		The binary ''siesta'' is main program of the SIESTA package.
	Standard usage:		Standard usage:
			<pre>

	Usage: R [options] [< infile] [> outfile]		Usage: siesta [options] [< infile] [> outfile]


	Example: siesta RUN.fdf > RUN.out		Example: siesta RUN.fdf > RUN.out
			</pre>

	== Hints for using SIESTA ==		== Hints for using SIESTA ==