The software requirements for installing MesoRD are detailed in Chapter 2, Installation . MesoRD runs on several different operating systems. We have tested Linux/x86, Linux/x64, Mac OS X Snow Leopard™, Mac OS X Leopard™, Windows XP™, Windows Vista™ and Windows 7™. Our main platforms for development include Linux/x64, Mac OS X 10.6™, and Windows 7™.
Reaction-diffusion simulation in 3D is computationally demanding and MesoRD can therefore be a resource hog as far as CPU time, disk space and memory is concerned.
MesoRD will use whatever CPU time it is assigned.
MesoRD is multithreaded on a high level in the sense that the simulator and the visualiser run in separate threads. If the visualiser is enabled, MesoRD has the capability to significantly burden two cores on a multicore system. In addition to dual processors (or cores), a good 3D graphics card is necessary for smooth real-time visualisation while running large (>10000 subvolumes) simulations [2]. When running large simulations, we strongly recommend that the visualiser is turned off, since it will only slow things down.
How much disk space is needed depends on how often the system is checkpointed. Checkpoint files can become huge, especially if the system is big and checkpointing is done frequently. The size of the checkpoint files should scale linearly with the number of species and the number of sub volumes in the model. The number of sub volumes depends on the geometry specified and the spatial discretisation. If the sparse option (see the section called “ Sparse Output ”) is chosen in stochastic simulations the file sizes are dramatically decreased, since only data for non-empty subvolumes are stored.
Memory consumption should scale linearly with product of the number of subvolumes and the number of species. The deterministic simulation has been observed to require about 5 times more memory then the stochastic simulations. [3]