Benchmark Suite used for the RoadRunner 1.0 manuscript:
Brusselator & Piecewise SBML models, includes settings used.
How to Benchmark
Instructions to use rr-sbml-be
1: designed to take the same args as the COPASI test program. It reads sbml files and sbml test suite settings files from a specified location.
2: run it with no options, it spits out what it expects.
rr-sbml-benchmrk INPUT_DIRECTORY TESTNAME OUTPUTDIRECTORY SBMLLEVEL SBMLVERSION [steps override] [durration] [compiler]
To run it with the brusselator benchmark, assuming your brusselator test file directory is “/home/username/brusselator” and you want to write the output to “/home/username/output”, and you want to use sbml level 3, version 1, and you wanted to run the 00100 test, you would run:
rr-sbml-benchmark /home/username/brusselator/ 00100 /home/username/benchmark/ 3 1
Note, if you do not care about the output, you can just give “/dev/null” as the output dir and no out file will be produced.
To record time, simply run it with the time command, i.e.
time rr-sbml-benchmark /home/username/brusselator/ 00100 /home/username/benchmark/ 3 1_____________________________