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 ``
``-n `` 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
----------------
.. code-block:: bash
python -m CADETMatch --match --json
Generate graphs using 6 cores
-----------------------------
.. code-block:: bash
python -m CADETMatch --generate_graphs --json -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.
.. code-block:: bash
nohup python -m CADETMatch --match --json &
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