Smoldyn
| Description | Content |
|---|---|
| module load | chem/smoldyn |
| Availability | bwUniCluster |
| License | LGPL. See 'License'-Section in Download. |
| Citing | See 'Chapter 5 (Copyright and Citation)' in Documentation |
| Links | Homepage | Documentation |
| Graphical Interface | No |
Contents
1 Description
Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest individually to capture natural stochasticity and to yield nanometer-scale spatial resolution. It treats other molecules implicitly, enabling it to simulate hundreds of thousands of molecules over several minutes of real time. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes much as they would in a real biological system.
2 Versions and Availability
A list of versions currently available on all bwHPC-C5-Clusters can be obtained from the
Cluster Information System CIS
{{#widget:Iframe |url=https://cis-hpc.uni-konstanz.de/prod.cis/bwUniCluster/chem/smoldyn |width=99% |height=100 |border=0 }} On the command line interface of any bwHPC cluster, a list of the available Smoldyn versions using
$ module avail chem/smoldyn
3 Usage
3.1 Loading the module
You can load the default version of software name with the command
$ module load chem/smoldyn
The module will try to load modules it needs to function (e.g. compiler/intel). If loading the module fails, check if you have already loaded one of those modules, but not in the version needed for software name. If you wish to load a specific (older) version, you can do so using e.g.
$ module load chem/smoldyn/2.31
to load the version 2.31.
3.2 Program Binaries
Executing smoldyn:
smoldyn PARAMETER INPUT_FILE
The following parameters can used with the smoldyn command:
| normal: | parameters displayed and simulation run | |
| -o | suppress output: | text output files are not opened |
| -p | parameters only: | simulation is not run |
| -q | quiet: | parameters are not displayed |
| -t | text only: | no graphics are displayed |
| -V | version | display version number and quit |
| -v | verbose: | extra parameter information is displayed |
| -w | suppress warnings: | no warnings are shown |
3.3 Disk Usage
Scratch files are written to the current directory by default. Please change to a local directory before starting your calculations. For example:
$ mkdir -p /tmp/$USER/job_sub_dir $ cd /tmp/$USER/job_sub_dir
Multinode jobs are generally not possible except for parameter screening studies. An example who to conduct high throughput parameter studies with Smoldyn can be found in the example folder of the software module.
4 Examples
The software module contains smoldyn examples for the bwUniCluster:
$ module load chem/smoldyn $ mkdir ~/temp-smoldyn-examples/;cd ~/temp-smoldyn-examples/ $ cp -r $SMOLDYN_EXA_DIR/bwhpc-examples/* . $ msub bwunicluster_smoldyn.pbs
Results of the of the calculation can be found in the archive file that is written into the MOAB submit directory (~/temp-smoldyn-examples/)
5 Version-Specific Information
For information specific to a single version, see the information available via the module system with the command
$ module help chem/smoldyn
