Building MOD Files¶
MOD (or NMOD) files are a way of extending the behavior of NEURON. See Using NMODL Files for more details.
When running neurodamus, these files need to be pre-compiled and available via the NRNMECH_LIB_PATH (for NEURON) and CORENEURONLIB (for coreneuron) environment variables.
Generally, there are 3 classes of MOD files considered within neurodamus; internal support, shared support and scientific. Both the support ones are bundled with the neurodamus install, so the user only needs to supply the scientific ones.
To make compiling the union of all these files easier, neurodamus supplies the neurodamus-compile-mods tool. This simplifies the creation of the compiled libraries, by allowing the user to provide only the scientific MOD files, and neurodamus-compile-mods will provide the supporting ones.
For instance:
neurodamus-compile-mods \
--input-dir some-mod-dir \
--with-internal-mods \
--output-type shell \
--output-dir output
Will compile the files within some-mod-dir along with the support MOD files since –with-internal-mods was specified. The compiled files will be put in the output directory.
Finally, the –output-type specifies what the tool will return on its STDOUT.
If shell is chosen, then environment variable setting is output:
EX:
NRNMECH_LIB_PATH=/path/to/libnrnmech.so
SPECIALS_PATH=/some/path/to/where/the/specials/are
Alternatively, json can be chosen, at which point a json object is printed.
If a SONATA circuit_config.json file exists, it can be examined, and if there are mechanisms_dir, they will also be included in the compilation.
neurodamus-compile-mods \
--circuit-config circuit_config.json \
[...]
If neurodamus-nrnivmodl is on the PATH, neurodamus-compile-mods will use that instead of nrnivmodl.
It is assumed that neurodamus-nrnivmodl provides the same interface as nrnivmodl, but adds any custom requirements for extra libraries (ie: libsonatareport.)
The tool can handle files with the same content, and ones with duplicate names. The former are deduplicated, so there aren’t symbol collisions, and the later ones are chosen by “latest wins”, in that ones that are later on the command line overwrite earlier ones.