Running

CADET-Match is designed to be used through a command line interface. It is also possible to use CADET-Match using Jupyter notebooks but this is not recommended for normal usage. CADET-Match has automatic checkpointing and if matching is interrupted it will resume from the last step completed.

These commands can be run from the Windows command line or from any Linux command line. These commands can also be run through cluster control software.

python -m CADETMatch is the basis of all the commands and other options can be added as needed.

--json <path to json configuration file>

-n <int number of parallel processes to use> If -n is omitted one process will be created for each core on the machine.

--match Start parameter estimation or error modeling

--generate_map Find the maximum a posteriori for an MCMC run

The following options are for genering graphs. CADET-Match generates graphs automatically periodically but these commands can be used to generate graphs immediately. These commands should be safe to run while matching is proceeding but they may fail if the required data has not been generated yet.

--generate_corner Generate corner graphs for MCMC

--generate_graphs Generate progress graphs and 2D graphs

--generate_graphs_all Generate progress graphs, 2D graphs, and 3D graphs

--generate_graphs_autocorr Generate auto-correlation graphs

--generate_mcmc_plot_tube Generate MCMC plot tubes (probability plots of chromatograms based on MCMC posterior)

--generate_mcmc_mixing Generate MCMC mixing graphs

Starting a match

python -m CADETMatch --match --json <path to connfiguration file>

Generate graphs using 6 cores

python -m CADETMatch --generate_graphs --json <path to connfiguration file> -n 6

Running CADET-Match remotely

The most common way CADET-Match is used is by logging into a server with SSH and starting a matching session. These matches can take hours to days to complete and the following command allows CADET-Match to keep running once you logout.

nohup python -m CADETMatch --match --json <path to connfiguration file> &