Execution of example simulation has multiple issues

[jonrkarr]

VCell now runs successfully in runBioSimulations with 5 example simulation runs. All runs terminate successfully. However, the results contain NaN for outputs of failed simulations (Euler with step size too high).

Example:

SED-ML file simulation.sedml in sbml-core/Vilar-PNAS-2002-minimal-circardian-clock.omex

• Report report_Euler_default
• Plot2D plot2d_Euler_default

Because the simulation failed, we would prefer to clearly communicate this to the user by labeled that simulation as FAILED.

Deeper investigation revealed multiple issues:

• [ ] Exit with non-zero exit code so that the HPC interpets this as a failure.
• [ ] Label the overall status in the log as failed
• [ ] Log should be consistent with outputs. It appears the status in the log may not be accurate.
  • [ ] Log indicates that multiple plots succeeded, but only 2 were produced
  • [ ] Same for reports
• [ ] Capture useful information about the failure in the output fields of the log. output field doesn't currently have instructive information.

[jonrkarr]

I'm also going to remove this COMBINE archive from the examples to reduce potential confusion as people would likely assume these are viable simulations.

[moraru]

Fixed