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Smoldyn

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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

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

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