Difference between revisions of "Namd"

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| Availability
  
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| Citing
 
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| [ Publications]
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| [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Publications/index.html Publications]
  
 
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| Links
  
| Links
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| [https://departments.icmab.es/leem/siesta/ Homepage] | [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Manuals/manuals.html Documentation]
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| [ Homepage] | [ Documentation]
 
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| Graphical Interface
  
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= Description =
  
= Description =
   
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'''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.
 +
'''NAMD''' (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 =
  
= 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)].
 +
NAMD 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:
 +
In order to check which versions of NAMD are installed on the compute cluster, run the following command:
 
<pre>
  
<pre>
−
$ module avail chem/siesta
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$ module avail chem/namd
 
</pre>
  
</pre>
   
 
= License =
  
= 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].
 +
NAMD is free, open-source software released under the GNU General Public License (GPL). The NAMD package in its entirety may be copied, modified or distributed according to the conditions described in its [ documentation].
   
 
= Usage =
  
= Usage =
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== Loading the module ==
  
== Loading the module ==
   
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You can load the default version of SIESTA with the following command:
 +
You can load the default version of NAMD with the following command:
 
<pre>
  
<pre>
−
$ module load chem/siesta
 +
$ module load chem/namd
 
</pre>
  
</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.
 +
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 NAMD.
   
−
If you wish to load another (older) version of SIESTA, you can do so using
 +
If you wish to load another (older) version of NAMD, you can do so using
 
<pre>
  
<pre>
−
$ module load chem/siesta/<version>
 +
$ module load chem/namd/<version>
 
</pre>
  
</pre>
 
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/Publications/index.html references].
 +
Please cite NAMD in your publications according to the [ references].
   
 
== Program Binaries ==
  
== Program Binaries ==
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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 input files, please see the [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Manuals/manuals.html documentation].
   
−
== Hints for using SIESTA ==
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== Hints for using NAMD ==
   
 
=== Parallel Execution ===
  
=== Parallel Execution ===
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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.
  
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">$SIESTA_EXA_DIR</span>:
 +
Example scripts are available in the directory <span style="background:#edeae2;margin:2px;padding:1px;border:1px dotted #808080">$NAMD_EXA_DIR</span>:
 
<pre>
  
<pre>
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$ module show chem/siesta # show environment variables, which will be available after 'module load'
 +
$ module show chem/namd # show environment variables, which will be available after 'module load'
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$ module load chem/siesta # load module
 +
$ module load chem/namd # load module
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$ ls $SIESTA_EXA_DIR # show content of directory $SIESTA_EXA_DIR
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$ ls $NAMD_EXA_DIR # show content of directory $NAMD_EXA_DIR
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$ cat $SIESTA_EXA_DIR/README # show examples README
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$ cat $NAMD_EXA_DIR/README # show examples README
 
</pre>
  
</pre>
   
 
Run a first simple example job:
  
Run a first simple example job:
 
<pre>
  
<pre>
−
$ module load chem/siesta # load module
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$ module load chem/namd # load module
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$ WORKSPACE=`ws_allocate siesta 3` # allocate workspace
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$ WORKSPACE=`ws_allocate namd 3` # allocate workspace
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$ cd $WORKSPACE # change to workspace
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$ cd $WORKSPACE # change to workspace
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$ cp -a $SIESTA_HOME/bwhpc-examples . # copy example files to workspace
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$ cp -a $NAMD_HOME/bwhpc-examples . # copy example files to workspace
 
$ cd bwhpc-examples/h2o # change to test directory
  
$ cd bwhpc-examples/h2o # change to test directory
 
$ sbatch bwhpc_siesta_h2o.sh # submit job
  
$ sbatch bwhpc_siesta_h2o.sh # submit job
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= Useful links =
  
= Useful links =
   
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* [https://departments.icmab.es/leem/SIESTA_MATERIAL/Docs/Manuals/manuals.html Documentation (english)]
 +
* [ Documentation (english)]
  +
* [ (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)]
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* [ Wikipedia article (english)]
 
----
  
----
 
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]
  
[[Category:Chemistry software]][[Category:BwForCluster_Chemistry]][[Category:BwForCluster_JUSTUS_2]]

Revision as of 23:27, 11 October 2020

Description Content
module load chem/namd
Availability BwForCluster_JUSTUS_2
License Free, open-source software, distributed under the GNU General Public License (GPL). More...
Citing [ Publications]
Links [ Homepage] | [ Documentation]
Graphical Interface No

1 Description

NAMD (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.

2 Availability

NAMD is available on selected bwHPC-Clusters. A complete list of versions currently installed on the bwHPC-Clusters can be obtained from the Cluster Information System (CIS).

In order to check which versions of NAMD are installed on the compute cluster, run the following command: 

$ module avail chem/namd

3 License

NAMD is free, open-source software released under the GNU General Public License (GPL). The NAMD package in its entirety may be copied, modified or distributed according to the conditions described in its [ documentation].

4 Usage

4.1 Loading the module

You can load the default version of NAMD with the following command: 

$ module load chem/namd

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 NAMD.

If you wish to load another (older) version of NAMD, you can do so using 

$ module load chem/namd/<version>

with <version> specifying the desired version.

Please cite NAMD in your publications according to the [ references].

4.2 Program Binaries

The binary siesta is main program of the SIESTA package. 

Usage: siesta [options] [< infile] [> outfile]
  
Example: siesta RUN.fdf > RUN.out

For information about how to construct input files, please see the documentation.

4.3 Hints for using NAMD

4.3.1 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

4.3.2 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.

4.3.3 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.

5 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 $NAMD_EXA_DIR: 

$ module show chem/namd                # show environment variables, which will be available after 'module load'
$ module load chem/namd                # load module
$ ls $NAMD_EXA_DIR                     # show content of directory $NAMD_EXA_DIR
$ cat $NAMD_EXA_DIR/README             # show examples README

Run a first simple example job: 

$ module load chem/namd                          # load module
$ WORKSPACE=`ws_allocate namd 3`                 # allocate workspace
$ cd $WORKSPACE                                  # change to workspace
$ cp -a $NAMD_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

6 Useful links

  • [ Documentation (english)]
  • [ (english)]
  • [ Wikipedia article (english)]
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