How to use StoSim

Quick How-To

  1. Place a file called stosim.conf and the code to run your simulation in a folder of your choice. In stosim.conf (copy the one from the basic example to start), set the name of your executable.
  2. Type stosim and hit Enter
  3. You should then see some output on the screen about what StoSim is doing and, if it went well, find results (the logfiles your executable wrote) in the “data” directory, in your folder (but if you like the plotting capabilities of StoSim you might never look there). Plots go in the “plots” directory.


There are several tutorials in this documentation which describe how to use StoSim in depth. Start with Setting up a basic simulation.

All commands at a glance


You can call StoSim like this:

$ stosim --help
usage: stosim [-h] [--folder PATH] [--simulations [NAME [NAME ...]]] [--run]
            [--check] [--resume] [--kill] [--list] [--more]
            [--plots [FIGURE [FIGURE ...]]] [--ttests] [-k] [-d]


This is a more detailled overview over the possible optional arguments:

-h, --help            show this help message and exit
--folder PATH         Path to simulation folder (this is where you keep your
                      stosim.conf), defaults to "."
--simulations [NAME [NAME ...]]
                      names of subsimulations (the filenames of their
                      configuration files, with or without the ".conf"
--run                 Only run, do not analyse.
--status              Check status of simulations.
--resume              Resume control of simulation scheduling.
--snapshot            Make a snapshot of current state (in the stosim-snapshots directory)
--kill                Kill simulations.
--list                List number of runs made so far, per configuration.
--more                Add more runs to current state of config and data.
--plots [FIGURE [FIGURE ...]]
                      Make plots (needs gnuplot and eps2pdf installed). Add
                      indices of figures as arguments if you only want to
                      generate specific ones.
--ttests              Run T-tests (needs Gnu R installed).
-k                    keep tmp analysis files.
-d                    delete old data without confirmation.


Each command line option can be shortened, as long as it’s recognisable from other short forms. So --p instead of --plots also works.´´


A very important use case: The results are not coming in as expected. A likely scenario is this: the plots can’t be created becuase your executable didn’t write data, most likely because there is a bug somewhere. Where to look for system output to start investigation?

You can inspect the output of all the simulation workers in this directory:


There will be one logfile per cpu (a “worker”) that was running jobs for you. Because StoSim uses fjd for scheduling workers and fjd uses the shared home directory for all its configs and logs, this even works when you told StoSim to use several computers (see Running simulations on remote computers for an example on that).