libRoadRunner CLI

How to run the standalone roadrunner

The binary distribution comes with a standalone command line executable that can be used to quickly try out roadRunner. We will describe this executable here. The executable is called rr.exe and is found in the bin directory.

rr.exe 

libRoadRunner Standalone program. The rr executable can be used to test the integrity of the current build, but it is also a fully fledged SBML simulator.

Models

When you build and install RoadRunner, a folder with some test models is also provided. On a Linux build, this folder is typically placed in /usr/local/models.

The first test after building roadrunner library would be to run the rr application, using one of the models as input.

Run rr on Windows

To try out roadrunner you can run it in the Windows command prompt.

  1. Type cmd in the Start menu and press Enter.
  2. cd to the directory where you unzipped the downloaded files. For example, paste the following command and hit Enter.
cd %HOMEPATH%\Downloads\libroadrunner_win32\bin

Then paste the following to run roadrunner on the test model provided with the distribution, -m means run the following model

rr.exe -m ..\models\test_1.xml

To see the other options available you can run rr without any arguments.

rr.exe

Output will look like

rr.exe is a command line driven SBML simulator
USAGE for c:\Users\mgaldzic\Downloads\libroadrunner-1.0.0-win32\bin\rr.exe
-v<debug level>.......... Debug levels: Error, Warning, Info, Debug. Default: Info
-m<FileName>............. SBML Model File Name (with path)
-o<FileName>............. FileName for data output
-d<FilePath>............. Data output folder. If not given, data is output to current directory (implies -f is given)
-t<FilePath>............. Temporary data output folder. If not given, temp files are output to current directory
-p....................... Pause before exiting.
-c....................... Stop execution after compiling model
-u....................... Use users OS designated temporary folder
-s<#>.................... Set the start time for simulation. Default: 0
-e<#>.................... Set the end time for simulation. Default: 5
-z<#>.................... Set number of steps in the simulation. Default: 50
-l<List>................. Set selection list. Separate variables using ',' or space
-? ...................... Shows the help screen.

Systems Biology, UW 2013

Run rr on Linux or Mac OS X

To run rr using one of the models as input, type the following in a terminal;

rr -m/usr/models/test_1.xml

If the library is properly built, you should get simulated data back. You will also see some new files in the same directory as where you executed rr. These files, .h, .c and .so are on the fly generated sources and libs, representing the sbml model in your xml model file.

Typing rr in a terminal window will give you some more options for the application. For example rr -t<aFolder>, will write temporary files to specified folder.

To trace problems, -v<DebugLevel>, where DebugLevel is Debug, Debug1, Debug2 etc as a ‘string’, can be used to get more verbose feedback.

 

Other files in the bin directory

The roadrunner command line client, rr, is found in the bin directory where you unzipped the binary distribution.

bin/ -contains the executable command line client rr.exe
compilers/ - tcc is needed on Windows
include/ - header files
install_roadrunner.py - python installation on Windows
lib/ - all libraries
models/ - sample models
plugins/ - example plugins Demo and Add noise
rr_support/ - more headers
site-packages/ - SWIG Python bindings - installation copies this to system site-packages
testing/ - tests data, C, header, Test model and feedback model

bin/

bin/ directory has the standalone programs to run

rr-sbml-benchmark.exe - Run the benchmark tests
Specific Testing scripts
run_c_tests.bat
run_c_tests.sh
run_cpp_tests.bat
run_test_suite.exe
sbml_ts_tester.exe
cxx_api_tests.exe
llvm_testing.exe
Dependency libraries
conv.dll
libsbml.dll
libxml2.DLL
rrc_api.dll
rrplugins_c_api.dll
msvcp100.dll
msvcr100.dll
zlib1.dll