Speed of calculations

[rs028]

The model is noticeably slower (compared to version pre-1.0). Need to do

1. profiling to identify the bottlenecks and see how they can be eliminated.
2. Is it worth considering parallelization?

Known to affect model performance:

• time frequency and number of constraints.
• size of the mechanism.

Unclear if affect model performance:

• having species in the chemical mechanism that are not used (i.e. are always zero, see Size of the mechanism and speed of the simulation #436).
• type and implementation of the interpolation algorithm.
• LAPACK/BLAS support in CVODE.
• solver.parameters default values

[rs028]

Results from a rough evaluation of the problem.
Model running on HPC system (30 GB memory), no constraints, 24 hours simulation.

n. species	n. reactions	runtime
51	137	15 sec
2575	7779	10 min
5833	17224	5.5 days

Increasing the memory to 120 GB or decreasing the output frequency do not affect significantly the outcome.

[ZhuJFDU]

entire mechanism = low efficiency

[rs028]

Changing the solver type in solver.parameters may help with this issue. The default choice is spgmr + banded preconditioner. The other choices (spgmr or dense) may result in better performance.

Note: Could this be related to #436? When lots of species have zero concentration the matrix is sparse and the use of preconditioner makes it inefficient?