CPU Time with Python bindings

[Dilan Pathirana]

Hi,

I'm working on a tool to simulate PEtab problems (thereby also SBML) with COPASI using its Python bindings.

How can I access "CPU Time", to get the time taken for simulation? I've seen this done by writing a report definition to an XML file, then using CopasiSE to simulate. Is it possible to avoid this overhead and instead do everything with python-copasi?

Kind regards,

Dilan

[Frank Bergmann]

Hello Dilan, 

unfortunately the time variables are not directly exposed. I'll be sure to add that for a future version. For now it is a bit awkward to use, but possible. Here an example. 

     import COPASI

     

     dm = COPASI.CRootContainer.addDatamodel()

     cpu_time = dm.getObject(COPASI.CCommonName('CN=Root,Timer=CPU Time'))

     

     # calculate to update

     cpu_time.calculateValue()

     

     # print to access 

     start = float(cpu_time.printToString())

     

     # do something that takes a long time

     

     

     # calculate to update, then print to access the value

     cpu_time.calculateValue()

     end = float(cpu_time.printToString())

     

     # 

     print('that took {}'.format(end - start))

     

cheers

Frank

[Dilan Pathirana]

Hi Frank,

Thanks very much, that works well for me.

Kind regards,

Dilan