Mechanism ABI

Code describing membrane mechanisms can be implemented in 3 ways:

  • custom C++/CUDA compiled into your Arbor program;

  • NMODL, compiled through Arbor’s modcc compiler;

  • custom code exposed through the Arbor Mechanism Application Binary Interface (ABI).

Here you will find the information needed to connect Arbor to mechanism implementations through the mechanism ABI. This ABI makes use of the C type calling convection, so any language that can expose itself through a C FFI can be used to implement mechanisms. The advantage of this method is that you can write and compile mechanisms in a multitude of languages, and store and distribute those mechanism libraries in compiled and optimized form. Any Arbor application can use them without compilation, of course assuming that both the mechanism and Arbor are compiled for the same target platform.

All functionality is offered via a single C header file in the Arbor include directory, mechanism_abi.h. The central datatypes here are arb_mechanism_type and arb_mechanism_interface, laying out the metadata and backend implementations respectively. A single arb_mechanism_type instance may be used by multiple arb_mechanism_interface instances.

Note

Note that mechanism_abi.h is heavily commented and is useful as documentation in its own right, also when writing mechanisms in other languages than C(++).

Metadata: arb_mechanism_type

This type collects all information independent of the backend.

struct arb_mechanism_type

This type collects all information independent of the backend.

Metadata:

unsigned long abi_version

mechanism was built using this ABI, should be ARB_MECH_ABI_VERSION

arb_mechanism_fingerprint fingerprint

unique ID, currently ignored

const char *name

(catalogue-level) unique name

arb_mechanism_kind kind

one of:

  • point

  • density

  • reversal_potential

bool is_linear

synapses only: if the state G is governed by dG/dt = f(v, G, M(t)), where: M(t) =Σ wᵢδᵢ(t) weighted incoming events, then f is linear in G and M.

If true, mechanisms must adhere to this contract.

Ignored for everything else.

bool has_post_events

implements post_event hook

Tables:

arb_field_info *globals
arb_size_type n_globals
arb_field_info *state_vars
arb_size_type n_state_vars
arb_field_info *parameters
arb_size_type n_parameters
arb_ion_info *ions
arb_size_type n_ions

Tables

All tables are given as an integer size and an array. There are two kinds of tables: arb_field_info and arb_ion_info. arb_field_info holds parameters, state variables, and global constants; arb_ion_info holds ion dependencies.

struct arb_field_info
const char *name

Field name, can be used from Arbor to query/set field values.

const char *unit

Physical units, just for introspection, not checked

arb_value_type default_value

values will be initialised to this value

arb_value_type range_low

valid range, lower bound, will be enforced

arb_value_type range_high

valid range, upper bound, will be enforced

struct arb_ion_info
const char *name

Ion name, eg Ca, K, …

bool write_int_concentration

writes Xi?

bool write_ext_concentration

writes Xo?

bool write_rev_potential

writes Er?

bool read_rev_potential

uses Er?

bool read_valence

Uses valence?

bool verify_valence

Checks valence?

int expected_valence

Expected value

Interlude: Parameter packs

In order to explain the interface type, we have to introduce the type arb_mechanism_ppack. This record is used to pass all information to and from the interface methods.

Objects of this type are always created and allocated by Arbor and passed fully formed to the interface. At this point:

  • Global data values are initialised

  • pointers in ion_state_view are set to their associated values in shared state on the Arbor side

  • pointers to state, parameters, globals, and constants are allocated and initialised to the given defaults.

  • SIMD only: arb_mechanism_ppack.index_constraints is set up.

struct arb_mechanism_ppack

Global data:

arb_index_type width

Number of CVs of this mechanism, size of arrays

arb_index_type n_detectors

Number of spike detectors

arb_index_type *vec_ci

[Array] Map CV to cell

arb_index_type *vec_di

[Array] Map

const arb_value_type *vec_t

[Array] time value

arb_value_type *vec_dt

[Array] time step

arb_value_type *vec_v

[Array] potential

arb_value_type *vec_i

[Array] current

arb_value_type *vec_g

[Array] conductance

arb_value_type *temperature_degC

[Array] Temperature in celsius

arb_value_type *diam_um

[Array] CV diameter

arb_value_type *time_since_spike

Times since last spike; one entry per cell and detector.

arb_index_type *node_index

Indices of CVs covered by this mechanism, size is width

arb_index_type *multiplicity

[Unused]

arb_value_type *weight

[Array] Weight

arb_size_type mechanism_id

Unique ID for this mechanism on this cell group

arb_deliverable_event_stream events

Events during the last period

arb_constraint_partition index_constraints

Index restrictions, not initialised for all backends.

User data:

arb_value_type **parameters

[Array] setable parameters

arb_value_type **state_vars

[Array] integrable state

arb_value_type *globals

global constant state

arb_ion_state *ion_states

[Array] views into shared state

Members tagged as [Array] represent one value per CV. To access the values belonging to your mechanism, a level of indirection via arb_mechanism_ppack.node_index is needed.

Example

Let’s assume mechanism hh is defined on two regions: R comprising CVs 0 and 1, R' with a single CV 9. Then node_index = [0, 1, 9] and width = 3. Arrays like vec_v will be of size 3 as well. To access the CVs’ diameters, one would write:

for (auto cv = 0; cv < ppack.width; ++cv) {
    auto idx = node_index[cv];
    auto d   = ppack_um[idx];
}

Warning

Note that values in arb_mechanism_ppack.diam_um cover _all_ CV’s regardless whether they are covered by the current mechanisms. Reading or writing to those values is considered undefined behaviour. The same holds for all other fields of arb_mechanism_ppack.

User Data

This section is derived from the tables passed in via the metadata struct, see above. One entry per relevant table entry is provided in the same order. So, if

arb_field_info globals[] = { arb_field_info { .name="A",
                                              .unit="lb ft / s",
                                              .default_value=42.0,
                                              .range_low=0,
                                              .range_high=123 },
                              arb_field_info { .name="B",
                                              .unit="kg m / s",
                                              .default_value=42.0,
                                              .range_low=0,
                                              .range_high=123 }};
arb_mechanism_type m = { .n_globals=2, .globals=globals };

the globals field of the corresponding parameter pack would have two entries, the first corresponding to A and initialised to 42.0 and the second for B set to 42.0.

The evolution of the state variables is left to the implementation via integrate_state, while globals and parameters are considered read-only. The ion states internal concentration Xi, external concentration Xo, trans-membrane current iX may also be read and written. Note that concurrent updates by multiple mechanisms might occur in any order and each mechanism will only observe the initial values at the time step boundary. All contribution by mechanisms are summed up into a final value. Further note that accessing these values without declaring this via a relevant arb_ion_info in the arb_mechanism_type is undefined behaviour. Parameter packs are specific to a backend.

Implementation: arb_mechanism_interface

The interface methods will be called with allocated and initialised arb_mechanism_ppack data. The actual layout is unspecified, but all pointers are allocated and set by Arbor. This means that your code must read/write to these locations in memory, and that you cannot change the pointer to point to another slice of memory allocated by your code.

typedef void (*arb_mechanism_method)(arb_mechanism_ppack*);

This is the type of all interface methods. These are collected in the record below with some metadata about the backend.

struct arb_mechanism_interface
arb_backend_kind backend

one of

  • cpu

  • gpu

arb_size_type partition_width

granularity for this backed, eg SIMD lanes

Interface methods:

arb_mechanism_method init_mechanism
  • called once during instantiation,

  • setup initial state, corresponds to NMODL’s INITIAL block,

  • will receive an allocated and initialised ppack object

arb_mechanism_method compute_currents
  • compute ionic currents and set them through pointers in ion_state, currents live in current_density

  • called during each integration time step - at the start for reversal potential mechanisms, before current reset - after event deliver for anything else

arb_mechanism_method apply_events

This method is expected to consume a set of arb_deliverable_event and apply effects to internal state, found in arb_mechanism_ppack.events which is of type arb_deliverable_event_stream.

These structures are set up correctly externally, but are only valid during this call. The data is read-only for arb_mechanism_interface.apply_events.

  • called during each integration time step, right after resetting currents

  • corresponding to NET_RECEIVE

arb_mechanism_method advance_state
  • called during each integration time step, after solving Hines matrices

  • perform integration on state variables

  • state variables live in state_vars, with a layout described above

arb_mechanism_method write_ions
  • update ionic concentrations via the pointers in ion_state

  • called during each integration time step, after state integration

arb_mechanism_method post_event
struct arb_deliverable_event
arb_size_type mech_id

mechanism type identifier (per cell group).

arb_size_type mech_index

instance of the mechanism

arb_float_type weight

connection weight

struct arb_deliverable_event_stream
arb_size_type n_streams

number of streams

const arb_deliverable_event *events

array of event data items

const arb_index_type *begin

array of offsets to beginning of marked events

const arb_index_type *end

array of offsets to end of marked events

SIMDization

If a mechanism interface processes arrays in SIMD bundles, it needs to set arb_mechanism_interface.partition_width to that bundle’s width in units of arb_value_type. The library will set up arb_mechanism_ppack.index_constraints in the parameter pack. This structure describes which bundles can be loaded/stored as a contiguous block, which ones must be gathered/scattered, which are to be broadcast from a constant, and so on. The reason for this is the indirection via arb_mechanism_ppack.node_index mentioned before. Please refer to the documentation of our SIMD interface layer for more information.

Making A Loadable Mechanism

Mechanisms interface with Arbor by providing three functions, one returning the metadata portion, and one for each implemented backend (currently two). The latter may return a NULL pointer, indicating that this backend is not supported. The naming scheme is shown in the example below

arb_mechanism_type make_arb_default_catalogue_pas();
arb_mechanism_interface* make_arb_default_catalogue_pas_interface_multicore();
arb_mechanism_interface* make_arb_default_catalogue_pas_interface_gpu();