hnn_core.parallel_backends.MPIBackend#
- class hnn_core.parallel_backends.MPIBackend(n_procs: None | int = None, mpi_cmd: str = 'mpiexec', use_hwthreading_if_found: bool = True, sensible_default_cores: bool = True, override_hwthreading_option: None | bool = None, override_oversubscribe_option: None | bool = None)[source]#
The MPIBackend class.
- Parameters:
- n_procsNone | int
The number of MPI processes requested by the user. Defaults to ‘None’, in which case it will attempt to detect the number of cores (including hardware-threads) and start parallel simulation over all of them.
- mpi_cmdstr
The name of the mpi launcher executable. Will use ‘mpiexec’ (openmpi) by default.
- use_hwthreading_if_foundbool
Specifies whether the class should try to detect hardware-threading, and, if it is found, then both use MPI’s ‘–use-hwthread-cpus’ option and change the number of CPU cores used. Defaults to ‘True’. Note that this is passed to an option of the same name in
_determine_cores_hwthreading; see that function for more details.- sensible_default_coresbool
Whether to decrease the number of cores returned in a “reasonable manner”, such that it balances speed with the user experience. Specifically, this means that if the number of available cores is greater than some threshold (default 12), the threshold number of cores will be used instead of the total. If the number of cores is greater than 2 but less than the threshold (default 12), then the number of cores used will be subtracted by 1, so that there is a core left unused for the sake of the OS. Defaults to ‘True’. Note that this is passed to an option of the same name in
_determine_cores_hwthreading- override_hwthreading_optionNone | bool
Force use of MPI’s ‘–use-hwthread-cpus’ support if changed from its default value of ‘None’. By default, ‘–use-hwthread-cpus’ is only passed if the above argument ‘use_hwthreading_if_found’ is ‘True’ and if hardware-threading is detected. If this argument is set to ‘True’, then ‘–use-hwthread-cpus’ will always be used, regardless of hardware-threading detection. If ‘False’, then ‘–use-hwthread-cpus’ will never be used.
- override_oversubscribe_optionNone | bool
Force use of MPI’s ‘–oversubscribe’ support if changed from its default value of ‘None’. By default, ‘–oversubscribe’ is only passed if the user specifies a custom number of cores via ‘n_procs’ and if that number exceeds the number of detected available cores. If this argument is set to ‘True’, then ‘–oversubscribe’ will always be used. If ‘False’, then ‘–oversubscribe’ will never be used.
- Attributes:
- n_procsint
The number of processes MPI will actually use (spread over cores). If 1 is specified or mpi4py could not be loaded, the simulation will be run with the JoblibBackend
- mpi_cmdlist of str
The mpi command with number of procs and options to be passed to Popen
- expected_data_lengthint
Used to check consistency between data that was sent and what MPIBackend received.
- proc_queuethreading.Queue
A Queue object to hold process handles from Popen in a thread-safe way. There will be a valid process handle present the queue when a MPI simulation is running.
Methods
simulate(net, tstop, dt, n_trials[, postproc])Simulate the HNN model in parallel on all cores
Terminate running simulation on this MPIBackend
- simulate(net, tstop, dt, n_trials, postproc=False)[source]#
Simulate the HNN model in parallel on all cores
- Parameters:
- netNetwork object
The Network object specifying how cells are connected.
- tstopfloat
The simulation stop time (ms).
- dtfloat
The integration time step of h.CVode (ms)
- n_trialsint
Number of trials to simulate.
- postprocbool
If False, no postprocessing applied to the dipole
- Returns:
- dpllist of Dipole
The Dipole results from each simulation trial