Provides interface function for CoreNEURON mechanism library and NEURON. More...

Detailed Description

Provides interface function for CoreNEURON mechanism library and NEURON.

libcorenrnmech is a interface library provided to building standalone executable special-core. Also, it is used by NEURON to run CoreNEURON via dlopen to execute models via in-memory transfer.

Definition in file enginemech.cpp.

#include <cstdlib>
#include <coreneuron/engine.h>

Go to the source code of this file.

Namespaces
	coreneuron
	THIS FILE IS AUTO GENERATED DONT MODIFY IT.

Functions
void	coreneuron::modl_reg ()
	Mechanism registration function. More...

void	coreneuron::nrn_cleanup_ion_map ()
	Cleanup global ion map created during mechanism registration. More...

int	solve_core (int argc, char **argv)
	Initialize mechanisms and run simulation using CoreNEURON. More...

char *	prepare_args (int &argc, char *&argv, int use_mpi, const char mpi_lib, const char *nrn_arg)
	parse arguments from neuron and prepare new one for coreneuron More...

void	mk_mech_init (int argc, char **argv)
	initialize standard mechanisms from coreneuron More...

void	set_openmp_threads (int nthread)
	set openmp threads equal to neuron's pthread More...

int	corenrn_embedded_run (int nthread, int have_gaps, int use_mpi, int use_fast_imem, const char mpi_lib, const char nrn_arg)
	Run CoreNEURON in embedded mode with NEURON. More...

Variables
bool	coreneuron::nrn_have_gaps
	variables defined in coreneuron library More...

bool	coreneuron::nrn_use_fast_imem

bool	corenrn_embedded
	global variables from coreneuron library More...

int	corenrn_embedded_nthread

Function Documentation

◆ corenrn_embedded_run()

int corenrn_embedded_run	(	int	nthread,
		int	have_gaps,
		int	use_mpi,
		int	use_fast_imem,
		const char *	mpi_lib,
		const char *	nrn_arg
	)

Run CoreNEURON in embedded mode with NEURON.

Parameters

nthread	Number of Pthreads on NEURON side
have_gaps	True if gap junctions are used
use_mpi	True if MPI is used on NEURON side
use_fast_imem	True if fast imembrance calculation enabled
nrn_arg	Command line arguments passed by NEURON

Returns: 1 if embedded mode is used otherwise 0

Todo:: Change return type semantics

Definition at line 79 of file enginemech.cpp.

◆ mk_mech_init()

void mk_mech_init	(	int	argc,
		char **	argv
	)

initialize standard mechanisms from coreneuron

Definition at line 466 of file main1.cpp.

◆ prepare_args()

char* prepare_args	(	int &	argc,
		char **&	argv,
		int	use_mpi,
		const char *	mpi_lib,
		const char *	arg
	)

parse arguments from neuron and prepare new one for coreneuron

Definition at line 81 of file main1.cpp.

◆ set_openmp_threads()

void set_openmp_threads ( int nthread )

set openmp threads equal to neuron's pthread

If there are a number of mpi processes on this node as well, things can go very slowly as there are so many more threads than cores. Assume the NEURON users pc.nthread() is well chosen if OMP_NUM_THREADS is not set.

Definition at line 69 of file main1.cpp.

◆ solve_core()

int solve_core	(	int	argc,
		char **	argv
	)

Initialize mechanisms and run simulation using CoreNEURON.

This is mainly used to build nrniv-core executable

Definition at line 46 of file enginemech.cpp.

Variable Documentation

◆ corenrn_embedded

bool corenrn_embedded

global variables from coreneuron library

Definition at line 46 of file nrn_setup.cpp.

◆ corenrn_embedded_nthread

int corenrn_embedded_nthread

Definition at line 47 of file nrn_setup.cpp.