Tiger Team Projects

The following enumeration provides an overview of collaborations between members of the bwHPC-S5 team and scientists, i.e. tiger teams. To apply for support by a tiger team, click

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Tiger Team: tt-smoldyn

Pseudo-Parallelization of SMOLDYN

Researchers in the group of Prof. Dr. Ana J. García-Sáez are using high performance resources to simulate the time dependent spatial distribution of molecules and second messengers in biological cells. The simulations are conducted with the program Smoldyn that was especially developed for this kind of simulations. It is based on a theory of diffusion-limited chemical reaction rates that was derived by von Smoluchowski in 1917. The name “Smoldyn” is short for Smoluchowski dynamics, which comes from this theory (Smoldyn User’s Manual for Smoldyn version 2.31, 2013 Steve Andrews). A rudimentary parallelization based on threads is implemented into Smoldyn. However, it is not very well tested and usage is generally not recommended, as stated in the manual.

The key project objective of this Tiger Team is to provide a python script for high throughput parameters studies with Smoldyn on the bwUniCluster. Smoldyn has very powerful macro functionality for conducting parameter studies that allows users in combination with python scripts to change different parameters in a study automatically. Each simulation is then submitted as separate job to the queuing system of the cluster. This method allows the user to increase the number of calculations in an efficient way.

The project is successfully finished and the code developed by the Tiger Team is in use for production runs.

An example is attached to the bwHPC wiki article Smoldyn and can be started on the bwUniCluster by copying the files into a directory and execute.

Status: finished.