From 6beb1ce0a066f771249697b0af4b0080cd2d2ea7 Mon Sep 17 00:00:00 2001
From: Ben Cumming <louncharf@gmail.com>
Date: Fri, 21 Apr 2017 15:01:45 +0200
Subject: [PATCH] Virtualize cell_group (#236)
Virtualization of the `cell_group` interface is necessary for support of other (i.e. non-multicompartment) cell models, including e.g. Poisson spike generators.
* Make `cell_group` an abstract base class; the previous `cell_group` class that is parameterized by the back-end FVM implementation is renamed `mc_cell_group` ('mc' stands for 'multi-compartment') and derives from the abstract `cell_group`.
* Remove template parameter `Cell` from `model` type: a `model` can in principle now manage multiple types of concrete objects derived from `cell_group`.
* Extend `model` constructor to take a hint about which back-end to use when constructing cell groups: `use_multicore` or `prefer_gpu`. This is a placeholder for a more sophisticated implementation once we have the requirements for a richer "ecosystem" of cell types.
* Simplified some generic types to remove template dependencies between front and back ends:
* Define a global `using time_type=float` in `common_types.hpp`.
* Define a concrete `sampler_function` type alias for the `std::function<...>` type used for samplers.
* Use a `null` back-end fallback for GPU if support is not there at compile time.
---
.ycm_extra_conf.py | 4 +-
miniapp/miniapp.cpp | 18 +-
src/backends.hpp | 22 ++
src/backends/fvm.hpp | 37 +++
src/backends/gpu/fvm.hpp | 4 +
src/backends/multicore/fvm.hpp | 4 +
src/cell_group.hpp | 272 ++----------------
src/fvm_multicell.hpp | 1 -
src/mc_cell_group.hpp | 272 ++++++++++++++++++
src/memory/allocator.hpp | 10 +-
src/memory/gpu.hpp | 2 +-
src/memory/host_coordinator.hpp | 6 +-
src/memory/memory.hpp | 4 +-
src/memory/wrappers.hpp | 6 +-
src/model.hpp | 74 +++--
src/sampler_function.hpp | 14 +
src/simple_sampler.hpp | 20 +-
src/util/config.hpp | 2 +-
tests/performance/io/disk_io.cpp | 2 -
tests/unit/CMakeLists.txt | 5 +-
tests/unit/test_backend.cpp | 23 ++
tests/unit/test_fvm_multi.cpp | 3 +-
..._cell_group.cpp => test_mc_cell_group.cpp} | 23 +-
...st_cell_group.cu => test_mc_cell_group.cu} | 5 +-
tests/unit/test_probe.cpp | 1 +
tests/validation/convergence_test.hpp | 2 +-
tests/validation/validate_ball_and_stick.cpp | 12 +-
tests/validation/validate_ball_and_stick.cu | 12 +-
tests/validation/validate_ball_and_stick.hpp | 40 ++-
tests/validation/validate_kinetic.cpp | 6 +-
tests/validation/validate_kinetic.cu | 6 +-
tests/validation/validate_kinetic.hpp | 23 +-
tests/validation/validate_soma.cpp | 5 +-
tests/validation/validate_soma.cu | 4 +-
tests/validation/validate_soma.hpp | 7 +-
tests/validation/validate_synapses.cpp | 6 +-
tests/validation/validate_synapses.cu | 6 +-
tests/validation/validate_synapses.hpp | 6 +-
38 files changed, 560 insertions(+), 409 deletions(-)
create mode 100644 src/backends.hpp
create mode 100644 src/mc_cell_group.hpp
create mode 100644 src/sampler_function.hpp
create mode 100644 tests/unit/test_backend.cpp
rename tests/unit/{test_cell_group.cpp => test_mc_cell_group.cpp} (76%)
rename tests/unit/{test_cell_group.cu => test_mc_cell_group.cu} (86%)
diff --git a/.ycm_extra_conf.py b/.ycm_extra_conf.py
index 035b3ed1..a48a781b 100644
--- a/.ycm_extra_conf.py
+++ b/.ycm_extra_conf.py
@@ -36,7 +36,7 @@ import ycm_core
# CHANGE THIS LIST OF FLAGS. YES, THIS IS THE DROID YOU HAVE BEEN LOOKING FOR.
flags = [
'-DNDEBUG',
- '-DNMC_HAVE_TBB',
+ '-DNMC_HAVE_CTHREAD',
'-std=c++11',
'-x',
'c++',
@@ -54,7 +54,7 @@ flags = [
'modcc',
'-I',
'/cm/shared/apps/cuda/8.0.44/include',
- '-DNMC_HAVE_CUDA'
+ '-DNMC_HAVE_GPU'
]
# Set this to the absolute path to the folder (NOT the file!) containing the
diff --git a/miniapp/miniapp.cpp b/miniapp/miniapp.cpp
index c9fb6b7c..474c57f3 100644
--- a/miniapp/miniapp.cpp
+++ b/miniapp/miniapp.cpp
@@ -17,10 +17,10 @@
#include <profiling/profiler.hpp>
#include <profiling/meter_manager.hpp>
#include <threading/threading.hpp>
+#include <util/config.hpp>
#include <util/debug.hpp>
#include <util/ioutil.hpp>
#include <util/nop.hpp>
-#include <util/optional.hpp>
#include "io.hpp"
#include "miniapp_recipes.hpp"
@@ -29,12 +29,6 @@
using namespace nest::mc;
using global_policy = communication::global_policy;
-#ifdef NMC_HAVE_CUDA
-using lowered_cell = fvm::fvm_multicell<gpu::backend>;
-#else
-using lowered_cell = fvm::fvm_multicell<multicore::backend>;
-#endif
-using model_type = model<lowered_cell>;
using sample_trace_type = sample_trace<time_type, double>;
using file_export_type = io::exporter_spike_file<global_policy>;
void banner();
@@ -101,7 +95,9 @@ int main(int argc, char** argv) {
options.file_extension, options.over_write);
};
- model_type m(*recipe, util::partition_view(group_divisions));
+ model m(*recipe,
+ util::partition_view(group_divisions),
+ config::has_cuda? backend_policy::prefer_gpu: backend_policy::use_multicore);
if (options.report_compartments) {
report_compartment_stats(*recipe);
}
@@ -202,11 +198,7 @@ void banner() {
std::cout << " starting miniapp\n";
std::cout << " - " << threading::description() << " threading support\n";
std::cout << " - communication policy: " << std::to_string(global_policy::kind()) << " (" << global_policy::size() << ")\n";
-#ifdef NMC_HAVE_CUDA
- std::cout << " - gpu support: on\n";
-#else
- std::cout << " - gpu support: off\n";
-#endif
+ std::cout << " - gpu support: " << (config::has_cuda? "on": "off") << "\n";
std::cout << "====================\n";
}
diff --git a/src/backends.hpp b/src/backends.hpp
new file mode 100644
index 00000000..0941d592
--- /dev/null
+++ b/src/backends.hpp
@@ -0,0 +1,22 @@
+#pragma once
+
+#include <string>
+#include <backends/fvm.hpp>
+
+namespace nest {
+namespace mc {
+
+enum class backend_policy {
+ use_multicore, // use multicore backend for all computation
+ prefer_gpu // use gpu back end when supported by cell_group type
+};
+
+inline std::string to_string(backend_policy p) {
+ if (p==backend_policy::use_multicore) {
+ return "use_multicore";
+ }
+ return "prefer_gpu";
+}
+
+} // namespace mc
+} // namespace nest
diff --git a/src/backends/fvm.hpp b/src/backends/fvm.hpp
index a8124da0..adb9838b 100644
--- a/src/backends/fvm.hpp
+++ b/src/backends/fvm.hpp
@@ -2,6 +2,43 @@
#include <backends/multicore/fvm.hpp>
+namespace nest {
+namespace mc {
+
+// A null back end used as a placeholder for back ends that are not supported
+// on the target platform.
+struct null_backend: public multicore::backend {
+ static bool is_supported() {
+ return false;
+ }
+
+ static mechanism make_mechanism(
+ const std::string&, view, view, const std::vector<value_type>&, const std::vector<size_type>&)
+ {
+ throw std::runtime_error("attempt to use an unsupported back end");
+ }
+
+ static bool has_mechanism(const std::string& name) {
+ return false;
+ }
+
+ static std::string name() {
+ return "null";
+ }
+};
+
+} // namespace mc
+} // namespace nest
+
+// FIXME: This include is where cuda-specific code leaks into the main application.
+// e.g.: CUDA kernels, functions marked __host__ __device__, etc.
+// Hence why it is guarded with NMC_HAVE_CUDA, and not, NMC_HAVE_GPU, like elsewhere in
+// the code. When we implement separate compilation of CUDA, this should be guarded with
+// NMC_HAVE_GPU, and the NMC_HAVE_CUDA flag depricated.
#ifdef NMC_HAVE_CUDA
#include <backends/gpu/fvm.hpp>
+#else
+namespace nest { namespace mc { namespace gpu {
+ using backend = null_backend;
+}}} // namespace nest::mc::gpu
#endif
diff --git a/src/backends/gpu/fvm.hpp b/src/backends/gpu/fvm.hpp
index 80a8de85..1d932a07 100644
--- a/src/backends/gpu/fvm.hpp
+++ b/src/backends/gpu/fvm.hpp
@@ -17,6 +17,10 @@ namespace mc {
namespace gpu {
struct backend {
+ static bool is_supported() {
+ return true;
+ }
+
/// define the real and index types
using value_type = double;
using size_type = nest::mc::cell_lid_type;
diff --git a/src/backends/multicore/fvm.hpp b/src/backends/multicore/fvm.hpp
index d04928cf..08e919de 100644
--- a/src/backends/multicore/fvm.hpp
+++ b/src/backends/multicore/fvm.hpp
@@ -18,6 +18,10 @@ namespace mc {
namespace multicore {
struct backend {
+ static bool is_supported() {
+ return true;
+ }
+
/// define the real and index types
using value_type = double;
using size_type = nest::mc::cell_lid_type;
diff --git a/src/cell_group.hpp b/src/cell_group.hpp
index f6e4a500..e6153024 100644
--- a/src/cell_group.hpp
+++ b/src/cell_group.hpp
@@ -1,272 +1,38 @@
#pragma once
-#include <cstdint>
-#include <functional>
-#include <iterator>
+#include <memory>
#include <vector>
-#include <algorithms.hpp>
-#include <cell.hpp>
#include <common_types.hpp>
#include <event_binner.hpp>
#include <event_queue.hpp>
+#include <sampler_function.hpp>
#include <spike.hpp>
-#include <util/debug.hpp>
-#include <util/partition.hpp>
-#include <util/range.hpp>
-
-#include <profiling/profiler.hpp>
+#include <util/optional.hpp>
+#include <util/make_unique.hpp>
namespace nest {
namespace mc {
-template <typename LoweredCell>
class cell_group {
public:
- using lowered_cell_type = LoweredCell;
- using value_type = typename lowered_cell_type::value_type;
- using size_type = typename lowered_cell_type::value_type;
- using source_id_type = cell_member_type;
-
- using sampler_function = std::function<util::optional<time_type>(time_type, double)>;
-
- cell_group() = default;
-
- template <typename Cells>
- cell_group(cell_gid_type first_gid, const Cells& cells):
- gid_base_{first_gid}
- {
- // Create lookup structure for probe and target ids.
- build_handle_partitions(cells);
- std::size_t n_probes = probe_handle_divisions_.back();
- std::size_t n_targets = target_handle_divisions_.back();
- std::size_t n_detectors = algorithms::sum(util::transform_view(
- cells, [](const cell& c) { return c.detectors().size(); }));
-
- // Allocate space to store handles.
- target_handles_.resize(n_targets);
- probe_handles_.resize(n_probes);
-
- lowered_.initialize(cells, target_handles_, probe_handles_);
-
- // Create a list of the global identifiers for the spike sources
- auto source_gid = cell_gid_type{gid_base_};
- for (const auto& cell: cells) {
- for (cell_lid_type lid=0u; lid<cell.detectors().size(); ++lid) {
- spike_sources_.push_back(source_id_type{source_gid, lid});
- }
- ++source_gid;
- }
- EXPECTS(spike_sources_.size()==n_detectors);
- }
-
- void reset() {
- spikes_.clear();
- events_.clear();
- reset_samplers();
- binner_.reset();
- lowered_.reset();
- }
-
- void set_binning_policy(binning_kind policy, time_type bin_interval) {
- binner_ = event_binner(policy, bin_interval);
- }
-
- void advance(time_type tfinal, time_type dt) {
- EXPECTS(lowered_.state_synchronized());
-
- // Bin pending events and enqueue on lowered state.
- time_type ev_min_time = lowered_.max_time(); // (but we're synchronized here)
- while (auto ev = events_.pop_if_before(tfinal)) {
- auto handle = get_target_handle(ev->target);
- auto binned_ev_time = binner_.bin(ev->target.gid, ev->time, ev_min_time);
- lowered_.add_event(binned_ev_time, handle, ev->weight);
- }
-
- lowered_.setup_integration(tfinal, dt);
-
- std::vector<sample_event> requeue_sample_events;
- while (!lowered_.integration_complete()) {
- // Take any pending samples.
- // TODO: Placeholder: this will be replaced by a backend polling implementation.
-
- PE("sampling");
- time_type cell_max_time = lowered_.max_time();
-
- requeue_sample_events.clear();
- while (auto m = sample_events_.pop_if_before(cell_max_time)) {
- auto& s = samplers_[m->sampler_index];
- EXPECTS((bool)s.sampler);
-
- time_type cell_time = lowered_.time(s.cell_gid-gid_base_);
- if (cell_time<m->time) {
- // This cell hasn't reached this sample time yet.
- requeue_sample_events.push_back(*m);
- }
- else {
- auto next = s.sampler(cell_time, lowered_.probe(s.handle));
- if (next) {
- m->time = std::max(*next, cell_time);
- requeue_sample_events.push_back(*m);
- }
- }
- }
- for (auto& ev: requeue_sample_events) {
- sample_events_.push(std::move(ev));
- }
- PL();
-
- // Ask lowered_ cell to integrate 'one step', delivering any
- // events accordingly.
- // TODO: Placeholder: with backend polling for samplers, we will
- // request that the lowered cell perform the integration all the
- // way to tfinal.
-
- lowered_.step_integration();
-
- if (util::is_debug_mode() && !lowered_.is_physical_solution()) {
- std::cerr << "warning: solution out of bounds for cell "
- << gid_base_ << " at (max) t " << lowered_.max_time() << " ms\n";
- }
- }
-
- // Copy out spike voltage threshold crossings from the back end, then
- // generate spikes with global spike source ids. The threshold crossings
- // record the local spike source index, which must be converted to a
- // global index for spike communication.
- PE("events");
- for (auto c: lowered_.get_spikes()) {
- spikes_.push_back({spike_sources_[c.index], time_type(c.time)});
- }
- // Now that the spikes have been generated, clear the old crossings
- // to get ready to record spikes from the next integration period.
- lowered_.clear_spikes();
- PL();
- }
-
- void enqueue_events(const std::vector<postsynaptic_spike_event>& events) {
- for (auto& e: events) {
- events_.push(e);
- }
- }
-
- const std::vector<spike>& spikes() const {
- return spikes_;
- }
-
- void clear_spikes() {
- spikes_.clear();
- }
-
- const std::vector<source_id_type>& spike_sources() const {
- return spike_sources_;
- }
-
- void add_sampler(cell_member_type probe_id, sampler_function s, time_type start_time = 0) {
- auto handle = get_probe_handle(probe_id);
-
- using size_type = sample_event::size_type;
- auto sampler_index = size_type(samplers_.size());
- samplers_.push_back({handle, probe_id.gid, s});
- sampler_start_times_.push_back(start_time);
- sample_events_.push({sampler_index, start_time});
- }
-
-private:
-
- // gid of first cell in group.
- cell_gid_type gid_base_;
-
- // The lowered cell state (e.g. FVM) of the cell.
- lowered_cell_type lowered_;
-
- // Spike detectors attached to the cell.
- std::vector<source_id_type> spike_sources_;
-
- // Spikes that are generated.
- std::vector<spike> spikes_;
-
- // Event time binning manager.
- event_binner binner_;
-
- // Pending events to be delivered.
- event_queue<postsynaptic_spike_event> events_;
-
- // Pending samples to be taken.
- event_queue<sample_event> sample_events_;
- std::vector<time_type> sampler_start_times_;
-
- // Handles for accessing lowered cell.
- using target_handle = typename lowered_cell_type::target_handle;
- std::vector<target_handle> target_handles_;
-
- using probe_handle = typename lowered_cell_type::probe_handle;
- std::vector<probe_handle> probe_handles_;
-
- struct sampler_entry {
- typename lowered_cell_type::probe_handle handle;
- cell_gid_type cell_gid;
- sampler_function sampler;
- };
-
- // Collection of samplers to be run against probes in this group.
- std::vector<sampler_entry> samplers_;
-
- // Lookup table for probe ids -> local probe handle indices.
- std::vector<std::size_t> probe_handle_divisions_;
-
- // Lookup table for target ids -> local target handle indices.
- std::vector<std::size_t> target_handle_divisions_;
-
- // Build handle index lookup tables.
- template <typename Cells>
- void build_handle_partitions(const Cells& cells) {
- auto probe_counts =
- util::transform_view(cells, [](const cell& c) { return c.probes().size(); });
- auto target_counts =
- util::transform_view(cells, [](const cell& c) { return c.synapses().size(); });
-
- make_partition(probe_handle_divisions_, probe_counts);
- make_partition(target_handle_divisions_, target_counts);
- }
-
- // Use handle partition to get index from id.
- template <typename Divisions>
- std::size_t handle_partition_lookup(const Divisions& divisions, cell_member_type id) const {
- // NB: without any assertion checking, this would just be:
- // return divisions[id.gid-gid_base_]+id.index;
-
- EXPECTS(id.gid>=gid_base_);
-
- auto handle_partition = util::partition_view(divisions);
- EXPECTS(id.gid-gid_base_<handle_partition.size());
-
- auto ival = handle_partition[id.gid-gid_base_];
- std::size_t i = ival.first + id.index;
- EXPECTS(i<ival.second);
-
- return i;
- }
-
- // Get probe handle from probe id.
- probe_handle get_probe_handle(cell_member_type probe_id) const {
- return probe_handles_[handle_partition_lookup(probe_handle_divisions_, probe_id)];
- }
+ virtual ~cell_group() = default;
+
+ virtual void reset() = 0;
+ virtual void set_binning_policy(binning_kind policy, time_type bin_interval) = 0;
+ virtual void advance(time_type tfinal, time_type dt) = 0;
+ virtual void enqueue_events(const std::vector<postsynaptic_spike_event>& events) = 0;
+ virtual const std::vector<spike>& spikes() const = 0;
+ virtual void clear_spikes() = 0;
+ virtual void add_sampler(cell_member_type probe_id, sampler_function s, time_type start_time = 0) = 0;
+};
- // Get target handle from target id.
- target_handle get_target_handle(cell_member_type target_id) const {
- return target_handles_[handle_partition_lookup(target_handle_divisions_, target_id)];
- }
+using cell_group_ptr = std::unique_ptr<cell_group>;
- void reset_samplers() {
- // clear all pending sample events and reset to start at time 0
- sample_events_.clear();
- using size_type = sample_event::size_type;
- for(size_type i=0; i<samplers_.size(); ++i) {
- sample_events_.push({i, sampler_start_times_[i]});
- }
- }
-};
+template <typename T, typename... Args>
+cell_group_ptr make_cell_group(Args&&... args) {
+ return cell_group_ptr(new T(std::forward<Args>(args)...));
+}
} // namespace mc
} // namespace nest
diff --git a/src/fvm_multicell.hpp b/src/fvm_multicell.hpp
index 78cb8428..ba2cb5c3 100644
--- a/src/fvm_multicell.hpp
+++ b/src/fvm_multicell.hpp
@@ -8,7 +8,6 @@
#include <vector>
#include <algorithms.hpp>
-#include <backends/fvm.hpp>
#include <cell.hpp>
#include <compartment.hpp>
#include <event_queue.hpp>
diff --git a/src/mc_cell_group.hpp b/src/mc_cell_group.hpp
new file mode 100644
index 00000000..ec3cbc72
--- /dev/null
+++ b/src/mc_cell_group.hpp
@@ -0,0 +1,272 @@
+#pragma once
+
+#include <cstdint>
+#include <functional>
+#include <iterator>
+#include <vector>
+
+#include <algorithms.hpp>
+#include <cell_group.hpp>
+#include <cell.hpp>
+#include <common_types.hpp>
+#include <event_binner.hpp>
+#include <event_queue.hpp>
+#include <sampler_function.hpp>
+#include <spike.hpp>
+#include <util/debug.hpp>
+#include <util/partition.hpp>
+#include <util/range.hpp>
+
+#include <profiling/profiler.hpp>
+
+namespace nest {
+namespace mc {
+
+template <typename LoweredCell>
+class mc_cell_group: public cell_group {
+public:
+ using lowered_cell_type = LoweredCell;
+ using value_type = typename lowered_cell_type::value_type;
+ using size_type = typename lowered_cell_type::value_type;
+ using source_id_type = cell_member_type;
+
+ mc_cell_group() = default;
+
+ template <typename Cells>
+ mc_cell_group(cell_gid_type first_gid, const Cells& cells):
+ gid_base_{first_gid}
+ {
+ // Create lookup structure for probe and target ids.
+ build_handle_partitions(cells);
+ std::size_t n_probes = probe_handle_divisions_.back();
+ std::size_t n_targets = target_handle_divisions_.back();
+ std::size_t n_detectors = algorithms::sum(util::transform_view(
+ cells, [](const cell& c) { return c.detectors().size(); }));
+
+ // Allocate space to store handles.
+ target_handles_.resize(n_targets);
+ probe_handles_.resize(n_probes);
+
+ lowered_.initialize(cells, target_handles_, probe_handles_);
+
+ // Create a list of the global identifiers for the spike sources
+ auto source_gid = cell_gid_type{gid_base_};
+ for (const auto& cell: cells) {
+ for (cell_lid_type lid=0u; lid<cell.detectors().size(); ++lid) {
+ spike_sources_.push_back(source_id_type{source_gid, lid});
+ }
+ ++source_gid;
+ }
+ EXPECTS(spike_sources_.size()==n_detectors);
+ }
+
+ void reset() override {
+ spikes_.clear();
+ events_.clear();
+ reset_samplers();
+ binner_.reset();
+ lowered_.reset();
+ }
+
+ void set_binning_policy(binning_kind policy, time_type bin_interval) override {
+ binner_ = event_binner(policy, bin_interval);
+ }
+
+ void advance(time_type tfinal, time_type dt) override {
+ EXPECTS(lowered_.state_synchronized());
+
+ // Bin pending events and enqueue on lowered state.
+ time_type ev_min_time = lowered_.max_time(); // (but we're synchronized here)
+ while (auto ev = events_.pop_if_before(tfinal)) {
+ auto handle = get_target_handle(ev->target);
+ auto binned_ev_time = binner_.bin(ev->target.gid, ev->time, ev_min_time);
+ lowered_.add_event(binned_ev_time, handle, ev->weight);
+ }
+
+ lowered_.setup_integration(tfinal, dt);
+
+ std::vector<sample_event> requeue_sample_events;
+ while (!lowered_.integration_complete()) {
+ // Take any pending samples.
+ // TODO: Placeholder: this will be replaced by a backend polling implementation.
+
+ PE("sampling");
+ time_type cell_max_time = lowered_.max_time();
+
+ requeue_sample_events.clear();
+ while (auto m = sample_events_.pop_if_before(cell_max_time)) {
+ auto& s = samplers_[m->sampler_index];
+ EXPECTS((bool)s.sampler);
+
+ time_type cell_time = lowered_.time(s.cell_gid-gid_base_);
+ if (cell_time<m->time) {
+ // This cell hasn't reached this sample time yet.
+ requeue_sample_events.push_back(*m);
+ }
+ else {
+ auto next = s.sampler(cell_time, lowered_.probe(s.handle));
+ if (next) {
+ m->time = std::max(*next, cell_time);
+ requeue_sample_events.push_back(*m);
+ }
+ }
+ }
+ for (auto& ev: requeue_sample_events) {
+ sample_events_.push(std::move(ev));
+ }
+ PL();
+
+ // Ask lowered_ cell to integrate 'one step', delivering any
+ // events accordingly.
+ // TODO: Placeholder: with backend polling for samplers, we will
+ // request that the lowered cell perform the integration all the
+ // way to tfinal.
+
+ lowered_.step_integration();
+
+ if (util::is_debug_mode() && !lowered_.is_physical_solution()) {
+ std::cerr << "warning: solution out of bounds for cell "
+ << gid_base_ << " at (max) t " << lowered_.max_time() << " ms\n";
+ }
+ }
+
+ // Copy out spike voltage threshold crossings from the back end, then
+ // generate spikes with global spike source ids. The threshold crossings
+ // record the local spike source index, which must be converted to a
+ // global index for spike communication.
+ PE("events");
+ for (auto c: lowered_.get_spikes()) {
+ spikes_.push_back({spike_sources_[c.index], time_type(c.time)});
+ }
+ // Now that the spikes have been generated, clear the old crossings
+ // to get ready to record spikes from the next integration period.
+ lowered_.clear_spikes();
+ PL();
+ }
+
+ void enqueue_events(const std::vector<postsynaptic_spike_event>& events) override {
+ for (auto& e: events) {
+ events_.push(e);
+ }
+ }
+
+ const std::vector<spike>& spikes() const override {
+ return spikes_;
+ }
+
+ void clear_spikes() override {
+ spikes_.clear();
+ }
+
+ const std::vector<source_id_type>& spike_sources() const {
+ return spike_sources_;
+ }
+
+ void add_sampler(cell_member_type probe_id, sampler_function s, time_type start_time) override {
+ auto handle = get_probe_handle(probe_id);
+
+ using size_type = sample_event::size_type;
+ auto sampler_index = size_type(samplers_.size());
+ samplers_.push_back({handle, probe_id.gid, s});
+ sampler_start_times_.push_back(start_time);
+ sample_events_.push({sampler_index, start_time});
+ }
+
+private:
+
+ // gid of first cell in group.
+ cell_gid_type gid_base_;
+
+ // The lowered cell state (e.g. FVM) of the cell.
+ lowered_cell_type lowered_;
+
+ // Spike detectors attached to the cell.
+ std::vector<source_id_type> spike_sources_;
+
+ // Spikes that are generated.
+ std::vector<spike> spikes_;
+
+ // Event time binning manager.
+ event_binner binner_;
+
+ // Pending events to be delivered.
+ event_queue<postsynaptic_spike_event> events_;
+
+ // Pending samples to be taken.
+ event_queue<sample_event> sample_events_;
+ std::vector<time_type> sampler_start_times_;
+
+ // Handles for accessing lowered cell.
+ using target_handle = typename lowered_cell_type::target_handle;
+ std::vector<target_handle> target_handles_;
+
+ using probe_handle = typename lowered_cell_type::probe_handle;
+ std::vector<probe_handle> probe_handles_;
+
+ struct sampler_entry {
+ typename lowered_cell_type::probe_handle handle;
+ cell_gid_type cell_gid;
+ sampler_function sampler;
+ };
+
+ // Collection of samplers to be run against probes in this group.
+ std::vector<sampler_entry> samplers_;
+
+ // Lookup table for probe ids -> local probe handle indices.
+ std::vector<std::size_t> probe_handle_divisions_;
+
+ // Lookup table for target ids -> local target handle indices.
+ std::vector<std::size_t> target_handle_divisions_;
+
+ // Build handle index lookup tables.
+ template <typename Cells>
+ void build_handle_partitions(const Cells& cells) {
+ auto probe_counts =
+ util::transform_view(cells, [](const cell& c) { return c.probes().size(); });
+ auto target_counts =
+ util::transform_view(cells, [](const cell& c) { return c.synapses().size(); });
+
+ make_partition(probe_handle_divisions_, probe_counts);
+ make_partition(target_handle_divisions_, target_counts);
+ }
+
+ // Use handle partition to get index from id.
+ template <typename Divisions>
+ std::size_t handle_partition_lookup(const Divisions& divisions, cell_member_type id) const {
+ // NB: without any assertion checking, this would just be:
+ // return divisions[id.gid-gid_base_]+id.index;
+
+ EXPECTS(id.gid>=gid_base_);
+
+ auto handle_partition = util::partition_view(divisions);
+ EXPECTS(id.gid-gid_base_<handle_partition.size());
+
+ auto ival = handle_partition[id.gid-gid_base_];
+ std::size_t i = ival.first + id.index;
+ EXPECTS(i<ival.second);
+
+ return i;
+ }
+
+ // Get probe handle from probe id.
+ probe_handle get_probe_handle(cell_member_type probe_id) const {
+ return probe_handles_[handle_partition_lookup(probe_handle_divisions_, probe_id)];
+ }
+
+ // Get target handle from target id.
+ target_handle get_target_handle(cell_member_type target_id) const {
+ return target_handles_[handle_partition_lookup(target_handle_divisions_, target_id)];
+ }
+
+ void reset_samplers() {
+ // clear all pending sample events and reset to start at time 0
+ sample_events_.clear();
+ using size_type = sample_event::size_type;
+ for(size_type i=0; i<samplers_.size(); ++i) {
+ sample_events_.push({i, sampler_start_times_[i]});
+ }
+ }
+};
+
+} // namespace mc
+} // namespace nest
diff --git a/src/memory/allocator.hpp b/src/memory/allocator.hpp
index 3755e293..9add1a67 100644
--- a/src/memory/allocator.hpp
+++ b/src/memory/allocator.hpp
@@ -2,7 +2,7 @@
#include <limits>
-#ifdef NMC_HAVE_CUDA
+#ifdef NMC_HAVE_GPU
#include <cuda.h>
#include <cuda_runtime.h>
#endif
@@ -138,7 +138,7 @@ namespace impl {
}
#endif
-#ifdef NMC_HAVE_CUDA
+#ifdef NMC_HAVE_GPU
namespace cuda {
template <size_type Alignment>
class pinned_policy {
@@ -243,7 +243,7 @@ namespace impl {
}
};
} // namespace cuda
-#endif // #ifdef NMC_HAVE_CUDA
+#endif // #ifdef NMC_HAVE_GPU
} // namespace impl
template<typename T, typename Policy >
@@ -318,7 +318,7 @@ namespace util {
}
};
-#ifdef NMC_HAVE_CUDA
+#ifdef NMC_HAVE_GPU
template <size_t Alignment>
struct type_printer<impl::cuda::pinned_policy<Alignment>>{
static std::string print() {
@@ -357,7 +357,7 @@ template <class T, size_t alignment=(512/8)>
using hbw_allocator = allocator<T, impl::knl::hbw_policy<alignment>>;
#endif
-#ifdef NMC_HAVE_CUDA
+#ifdef NMC_HAVE_GPU
// For pinned and allocation set the default alignment to correspond to
// the alignment of 1024 bytes, because pinned memory is allocated at
// page boundaries. It is allocated at page boundaries (typically 4k),
diff --git a/src/memory/gpu.hpp b/src/memory/gpu.hpp
index 8e950d56..c5955eac 100644
--- a/src/memory/gpu.hpp
+++ b/src/memory/gpu.hpp
@@ -1,6 +1,6 @@
#pragma once
-#ifdef NMC_HAVE_CUDA
+#ifdef NMC_HAVE_GPU
#include <string>
#include <cstdint>
diff --git a/src/memory/host_coordinator.hpp b/src/memory/host_coordinator.hpp
index e9cb0698..1f45b336 100644
--- a/src/memory/host_coordinator.hpp
+++ b/src/memory/host_coordinator.hpp
@@ -11,7 +11,7 @@
#include "allocator.hpp"
#include "util.hpp"
-#ifdef NMC_HAVE_CUDA
+#ifdef NMC_HAVE_GPU
#include "gpu.hpp"
#endif
@@ -23,7 +23,7 @@ namespace memory {
template <typename T, class Allocator>
class host_coordinator;
-#ifdef NMC_HAVE_CUDA
+#ifdef NMC_HAVE_GPU
template <typename T, class Allocator>
class device_coordinator;
#endif
@@ -124,7 +124,7 @@ public:
std::copy(from.begin(), from.end(), to.begin());
}
-#ifdef NMC_HAVE_CUDA
+#ifdef NMC_HAVE_GPU
// copy memory from device to host
template <class Alloc>
void copy(
diff --git a/src/memory/memory.hpp b/src/memory/memory.hpp
index e5261958..50bbdf14 100644
--- a/src/memory/memory.hpp
+++ b/src/memory/memory.hpp
@@ -6,7 +6,7 @@
#include "definitions.hpp"
#include "host_coordinator.hpp"
-#ifdef NMC_HAVE_CUDA
+#ifdef NMC_HAVE_GPU
#include "device_coordinator.hpp"
#endif
@@ -29,7 +29,7 @@ std::ostream& operator<< (std::ostream& o, host_view<T> const& v) {
return o;
}
-#ifdef NMC_HAVE_CUDA
+#ifdef NMC_HAVE_GPU
// specialization for pinned vectors. Use a host_coordinator, because memory is
// in the host memory space, and all of the helpers (copy, set, etc) are the
// same with and without page locked memory
diff --git a/src/memory/wrappers.hpp b/src/memory/wrappers.hpp
index ab463a23..50393017 100644
--- a/src/memory/wrappers.hpp
+++ b/src/memory/wrappers.hpp
@@ -5,7 +5,7 @@
#include <memory/memory.hpp>
-#ifdef NMC_HAVE_CUDA
+#ifdef NMC_HAVE_GPU
#include <cuda.h>
#include <cuda_runtime.h>
#endif
@@ -96,7 +96,7 @@ namespace util {
return is_on_host<typename std::decay<T>::type>::value;
}
- #ifdef NMC_HAVE_CUDA
+ #ifdef NMC_HAVE_GPU
template <typename T>
struct is_on_gpu : std::false_type {};
@@ -132,7 +132,7 @@ auto on_host(const C& c) -> decltype(make_const_view(c)) {
return make_const_view(c);
}
-#ifdef NMC_HAVE_CUDA
+#ifdef NMC_HAVE_GPU
template <
typename C,
typename = typename std::enable_if<util::is_on_gpu_v<C>()>::type
diff --git a/src/model.hpp b/src/model.hpp
index 837ddc8d..91d0cd4e 100644
--- a/src/model.hpp
+++ b/src/model.hpp
@@ -5,29 +5,36 @@
#include <cstdlib>
+#include <backends.hpp>
+#include <fvm_multicell.hpp>
+
#include <common_types.hpp>
#include <cell.hpp>
#include <cell_group.hpp>
#include <communication/communicator.hpp>
#include <communication/global_policy.hpp>
+#include <mc_cell_group.hpp>
#include <profiling/profiler.hpp>
#include <recipe.hpp>
+#include <sampler_function.hpp>
#include <thread_private_spike_store.hpp>
+#include <threading/threading.hpp>
+#include <trace_sampler.hpp>
#include <util/nop.hpp>
#include <util/partition.hpp>
#include <util/range.hpp>
-#include "trace_sampler.hpp"
-
namespace nest {
namespace mc {
-// FIXME: this is going to go
-template <typename Cell>
+using gpu_lowered_cell =
+ mc_cell_group<fvm::fvm_multicell<gpu::backend>>;
+
+using multicore_lowered_cell =
+ mc_cell_group<fvm::fvm_multicell<multicore::backend>>;
+
class model {
public:
- // FIXME: this is an intermediate step to remove the template parameter from model
- using cell_group_type = cell_group<Cell>; // FIXME
using communicator_type = communication::communicator<communication::global_policy>;
using spike_export_function = std::function<void(const std::vector<spike>&)>;
@@ -37,15 +44,19 @@ public:
};
template <typename Iter>
- model(const recipe& rec, const util::partition_range<Iter>& groups):
- cell_group_divisions_(groups.divisions().begin(), groups.divisions().end())
+ model( const recipe& rec,
+ const util::partition_range<Iter>& groups,
+ backend_policy policy):
+ cell_group_divisions_(groups.divisions().begin(), groups.divisions().end()),
+ backend_policy_(policy)
{
// set up communicator based on partition
- communicator_ = communicator_type{gid_partition()};
+ communicator_ = communicator_type(gid_partition());
// generate the cell groups in parallel, with one task per cell group
- cell_groups_ = std::vector<cell_group_type>{gid_partition().size()};
- threading::parallel_vector<probe_record> probes;
+ cell_groups_.resize(gid_partition().size());
+ // thread safe vector for constructing the list of probes in parallel
+ threading::parallel_vector<probe_record> probe_tmp;
threading::parallel_for::apply(0, cell_groups_.size(),
[&](cell_gid_type i) {
@@ -61,16 +72,21 @@ public:
cell_lid_type j = 0;
for (const auto& probe: cells[i].probes()) {
cell_member_type probe_id{gid, j++};
- probes.push_back({probe_id, probe});
+ probe_tmp.push_back({probe_id, probe});
}
}
- cell_groups_[i] = cell_group_type(gids.first, cells);
+ if (backend_policy_==backend_policy::use_multicore) {
+ cell_groups_[i] = make_cell_group<multicore_lowered_cell>(gids.first, cells);
+ }
+ else {
+ cell_groups_[i] = make_cell_group<gpu_lowered_cell>(gids.first, cells);
+ }
PL(2);
});
- // insert probes
- probes_.assign(probes.begin(), probes.end());
+ // store probes
+ probes_.assign(probe_tmp.begin(), probe_tmp.end());
// generate the network connections
for (cell_gid_type i: util::make_span(gid_partition().bounds())) {
@@ -89,14 +105,14 @@ public:
}
// one cell per group:
- model(const recipe& rec):
- model(rec, util::partition_view(util::make_span(0, rec.num_cells()+1)))
+ model(const recipe& rec, backend_policy policy):
+ model(rec, util::partition_view(util::make_span(0, rec.num_cells()+1)), policy)
{}
void reset() {
t_ = 0.;
for (auto& group: cell_groups_) {
- group.reset();
+ group->reset();
}
communicator_.reset();
@@ -132,14 +148,14 @@ public:
auto &group = cell_groups_[i];
PE("stepping","events");
- group.enqueue_events(current_events()[i]);
+ group->enqueue_events(current_events()[i]);
PL();
- group.advance(tuntil, dt);
+ group->advance(tuntil, dt);
PE("events");
- current_spikes().insert(group.spikes());
- group.clear_spikes();
+ current_spikes().insert(group->spikes());
+ group->clear_spikes();
PL(2);
});
};
@@ -207,14 +223,13 @@ public:
current_spikes().get().push_back({source, tspike});
}
- template <typename F>
- void attach_sampler(cell_member_type probe_id, F&& f, time_type tfrom = 0) {
+ void attach_sampler(cell_member_type probe_id, sampler_function f, time_type tfrom = 0) {
if (!algorithms::in_interval(probe_id.gid, gid_partition().bounds())) {
return;
}
const auto idx = gid_partition().index(probe_id.gid);
- cell_groups_[idx].add_sampler(probe_id, std::forward<F>(f), tfrom);
+ cell_groups_[idx]->add_sampler(probe_id, f, tfrom);
}
const std::vector<probe_record>& probes() const { return probes_; }
@@ -235,13 +250,13 @@ public:
// Set event binning policy on all our groups.
void set_binning_policy(binning_kind policy, time_type bin_interval) {
for (auto& group: cell_groups_) {
- group.set_binning_policy(policy, bin_interval);
+ group->set_binning_policy(policy, bin_interval);
}
}
// access cell_group directly
- cell_group_type& group(int i) {
- return cell_groups_[i];
+ cell_group& group(int i) {
+ return *cell_groups_[i];
}
// register a callback that will perform a export of the global
@@ -258,13 +273,14 @@ public:
private:
std::vector<cell_gid_type> cell_group_divisions_;
+ backend_policy backend_policy_;
auto gid_partition() const -> decltype(util::partition_view(cell_group_divisions_)) {
return util::partition_view(cell_group_divisions_);
}
time_type t_ = 0.;
- std::vector<cell_group_type> cell_groups_;
+ std::vector<std::unique_ptr<cell_group>> cell_groups_;
communicator_type communicator_;
std::vector<probe_record> probes_;
diff --git a/src/sampler_function.hpp b/src/sampler_function.hpp
new file mode 100644
index 00000000..6a042b58
--- /dev/null
+++ b/src/sampler_function.hpp
@@ -0,0 +1,14 @@
+#pragma once
+
+#include <functional>
+
+#include <common_types.hpp>
+#include <util/optional.hpp>
+
+namespace nest {
+namespace mc {
+
+using sampler_function = std::function<util::optional<time_type>(time_type, double)>;
+
+} // namespace mc
+} // namespace nest
diff --git a/src/simple_sampler.hpp b/src/simple_sampler.hpp
index cb055734..5ffc41d2 100644
--- a/src/simple_sampler.hpp
+++ b/src/simple_sampler.hpp
@@ -9,6 +9,7 @@
#include <vector>
#include <common_types.hpp>
+#include <sampler_function.hpp>
#include <util/optional.hpp>
#include <util/deduce_return.hpp>
#include <util/transform.hpp>
@@ -43,7 +44,7 @@ class simple_sampler {
public:
trace_data trace;
- simple_sampler(float dt, float t0=0):
+ simple_sampler(time_type dt, time_type t0=0):
t0_(t0),
sample_dt_(dt),
t_next_sample_(t0)
@@ -54,23 +55,22 @@ public:
t_next_sample_ = t0_;
}
- template <typename Time = float, typename Value = double>
- std::function<util::optional<Time> (Time, Value)> sampler() {
- return [&](Time t, Value v) -> util::optional<Time> {
- if (t<(Time)t_next_sample_) {
- return (Time)t_next_sample_;
+ sampler_function sampler() {
+ return [&](time_type t, double v) -> util::optional<time_type> {
+ if (t<t_next_sample_) {
+ return t_next_sample_;
}
else {
- trace.push_back({float(t), double(v)});
+ trace.push_back({t, v});
return t_next_sample_+=sample_dt_;
}
};
}
private:
- float t0_ = 0;
- float sample_dt_ = 0;
- float t_next_sample_ = 0;
+ time_type t0_ = 0;
+ time_type sample_dt_ = 0;
+ time_type t_next_sample_ = 0;
};
} // namespace mc
diff --git a/src/util/config.hpp b/src/util/config.hpp
index 4bd3adf3..2e113bf4 100644
--- a/src/util/config.hpp
+++ b/src/util/config.hpp
@@ -30,7 +30,7 @@ constexpr bool has_power_measurement = true;
constexpr bool has_power_measurement = false;
#endif
-#ifdef NMC_HAVE_CUDA
+#ifdef NMC_HAVE_GPU
constexpr bool has_cuda = true;
#else
constexpr bool has_cuda = false;
diff --git a/tests/performance/io/disk_io.cpp b/tests/performance/io/disk_io.cpp
index 05b64666..c671e907 100644
--- a/tests/performance/io/disk_io.cpp
+++ b/tests/performance/io/disk_io.cpp
@@ -17,8 +17,6 @@
using namespace nest::mc;
using global_policy = communication::global_policy;
-using lowered_cell = fvm::fvm_multicell<multicore::backend>;
-using cell_group_type = cell_group<lowered_cell>;
using timer = util::timer_type;
int main(int argc, char** argv) {
diff --git a/tests/unit/CMakeLists.txt b/tests/unit/CMakeLists.txt
index 3ac4c1ff..0bae169c 100644
--- a/tests/unit/CMakeLists.txt
+++ b/tests/unit/CMakeLists.txt
@@ -18,7 +18,7 @@ build_modules(
set(TEST_CUDA_SOURCES
test_atomics.cu
- test_cell_group.cu
+ test_mc_cell_group.cu
test_gpu_stack.cu
test_matrix.cu
test_spikes.cu
@@ -31,6 +31,7 @@ set(TEST_CUDA_SOURCES
set(TEST_SOURCES
# unit tests
test_algorithms.cpp
+ test_backend.cpp
test_double_buffer.cpp
test_cell.cpp
test_compartments.cpp
@@ -41,7 +42,7 @@ set(TEST_SOURCES
test_event_binner.cpp
test_filter.cpp
test_fvm_multi.cpp
- test_cell_group.cpp
+ test_mc_cell_group.cpp
test_lexcmp.cpp
test_mask_stream.cpp
test_math.cpp
diff --git a/tests/unit/test_backend.cpp b/tests/unit/test_backend.cpp
new file mode 100644
index 00000000..08679d0d
--- /dev/null
+++ b/tests/unit/test_backend.cpp
@@ -0,0 +1,23 @@
+#include <type_traits>
+
+#include <backends/fvm.hpp>
+#include <memory/memory.hpp>
+#include <util/config.hpp>
+
+#include "../gtest.h"
+
+TEST(backends, gpu_is_null) {
+ using backend = nest::mc::gpu::backend;
+
+ static_assert(std::is_same<backend, nest::mc::null_backend>::value || nest::mc::config::has_cuda,
+ "gpu back should be defined as null when compiling without gpu support.");
+
+ if (not nest::mc::config::has_cuda) {
+ EXPECT_FALSE(backend::is_supported());
+
+ EXPECT_FALSE(backend::has_mechanism("hh"));
+ EXPECT_THROW(
+ backend::make_mechanism("hh", backend::view(), backend::view(), {}, {}),
+ std::runtime_error);
+ }
+}
diff --git a/tests/unit/test_fvm_multi.cpp b/tests/unit/test_fvm_multi.cpp
index 66226d9e..86777590 100644
--- a/tests/unit/test_fvm_multi.cpp
+++ b/tests/unit/test_fvm_multi.cpp
@@ -2,8 +2,9 @@
#include "../gtest.h"
-#include <common_types.hpp>
+#include <backends/multicore/fvm.hpp>
#include <cell.hpp>
+#include <common_types.hpp>
#include <fvm_multicell.hpp>
#include <util/rangeutil.hpp>
diff --git a/tests/unit/test_cell_group.cpp b/tests/unit/test_mc_cell_group.cpp
similarity index 76%
rename from tests/unit/test_cell_group.cpp
rename to tests/unit/test_mc_cell_group.cpp
index 0016b24e..00491537 100644
--- a/tests/unit/test_cell_group.cpp
+++ b/tests/unit/test_mc_cell_group.cpp
@@ -1,8 +1,9 @@
#include "../gtest.h"
-#include <cell_group.hpp>
+#include <backends/multicore/fvm.hpp>
#include <common_types.hpp>
#include <fvm_multicell.hpp>
+#include <mc_cell_group.hpp>
#include <util/rangeutil.hpp>
#include "common.hpp"
@@ -11,19 +12,17 @@
using namespace nest::mc;
using fvm_cell = fvm::fvm_multicell<nest::mc::multicore::backend>;
-nest::mc::cell make_cell() {
- using namespace nest::mc;
+cell make_cell() {
+ auto c = make_cell_ball_and_stick();
- nest::mc::cell cell = make_cell_ball_and_stick();
+ c.add_detector({0, 0}, 0);
+ c.segment(1)->set_compartments(101);
- cell.add_detector({0, 0}, 0);
- cell.segment(1)->set_compartments(101);
-
- return cell;
+ return c;
}
-TEST(cell_group, test) {
- cell_group<fvm_cell> group{0, util::singleton_view(make_cell())};
+TEST(mc_cell_group, test) {
+ mc_cell_group<fvm_cell> group{0, util::singleton_view(make_cell())};
group.advance(50, 0.01);
@@ -32,8 +31,8 @@ TEST(cell_group, test) {
EXPECT_EQ(4u, group.spikes().size());
}
-TEST(cell_group, sources) {
- using cell_group_type = cell_group<fvm_cell>;
+TEST(mc_cell_group, sources) {
+ using cell_group_type = mc_cell_group<fvm_cell>;
auto cell = make_cell();
EXPECT_EQ(cell.detectors().size(), 1u);
diff --git a/tests/unit/test_cell_group.cu b/tests/unit/test_mc_cell_group.cu
similarity index 86%
rename from tests/unit/test_cell_group.cu
rename to tests/unit/test_mc_cell_group.cu
index 16bc124d..92f7af50 100644
--- a/tests/unit/test_cell_group.cu
+++ b/tests/unit/test_mc_cell_group.cu
@@ -1,6 +1,7 @@
#include "../gtest.h"
-#include <cell_group.hpp>
+#include <backends/gpu/fvm.hpp>
+#include <mc_cell_group.hpp>
#include <common_types.hpp>
#include <fvm_multicell.hpp>
#include <util/rangeutil.hpp>
@@ -25,7 +26,7 @@ nest::mc::cell make_cell() {
TEST(cell_group, test)
{
- using cell_group_type = cell_group<fvm_cell>;
+ using cell_group_type = mc_cell_group<fvm_cell>;
auto group = cell_group_type{0, util::singleton_view(make_cell())};
group.advance(50, 0.01);
diff --git a/tests/unit/test_probe.cpp b/tests/unit/test_probe.cpp
index 005eead2..8ea355ea 100644
--- a/tests/unit/test_probe.cpp
+++ b/tests/unit/test_probe.cpp
@@ -1,5 +1,6 @@
#include "../gtest.h"
+#include <backends/multicore/fvm.hpp>
#include <common_types.hpp>
#include <cell.hpp>
#include <fvm_multicell.hpp>
diff --git a/tests/validation/convergence_test.hpp b/tests/validation/convergence_test.hpp
index 4d8ea28d..7c9f5936 100644
--- a/tests/validation/convergence_test.hpp
+++ b/tests/validation/convergence_test.hpp
@@ -75,7 +75,7 @@ public:
// reset samplers and attach to probe locations
for (auto& se: cell_samplers_) {
se.sampler.reset();
- m.attach_sampler(se.probe, se.sampler.template sampler<>());
+ m.attach_sampler(se.probe, se.sampler.sampler());
}
m.run(t_end, dt);
diff --git a/tests/validation/validate_ball_and_stick.cpp b/tests/validation/validate_ball_and_stick.cpp
index 109155a6..c28530a1 100644
--- a/tests/validation/validate_ball_and_stick.cpp
+++ b/tests/validation/validate_ball_and_stick.cpp
@@ -3,24 +3,24 @@
#include <fvm_multicell.hpp>
-using lowered_cell = nest::mc::fvm::fvm_multicell<nest::mc::multicore::backend>;
+const auto backend = nest::mc::backend_policy::use_multicore;
TEST(ball_and_stick, neuron_ref) {
- validate_ball_and_stick<lowered_cell>();
+ validate_ball_and_stick(backend);
}
TEST(ball_and_taper, neuron_ref) {
- validate_ball_and_taper<lowered_cell>();
+ validate_ball_and_taper(backend);
}
TEST(ball_and_3stick, neuron_ref) {
- validate_ball_and_3stick<lowered_cell>();
+ validate_ball_and_3stick(backend);
}
TEST(rallpack1, numeric_ref) {
- validate_rallpack1<lowered_cell>();
+ validate_rallpack1(backend);
}
TEST(ball_and_squiggle, neuron_ref) {
- validate_ball_and_squiggle<lowered_cell>();
+ validate_ball_and_squiggle(backend);
}
diff --git a/tests/validation/validate_ball_and_stick.cu b/tests/validation/validate_ball_and_stick.cu
index 52d1bf0d..3f8e4427 100644
--- a/tests/validation/validate_ball_and_stick.cu
+++ b/tests/validation/validate_ball_and_stick.cu
@@ -3,24 +3,24 @@
#include <fvm_multicell.hpp>
-using lowered_cell = nest::mc::fvm::fvm_multicell<nest::mc::gpu::backend>;
+const auto backend = nest::mc::backend_policy::prefer_gpu;
TEST(ball_and_stick, neuron_ref) {
- validate_ball_and_stick<lowered_cell>();
+ validate_ball_and_stick(backend);
}
TEST(ball_and_taper, neuron_ref) {
- validate_ball_and_taper<lowered_cell>();
+ validate_ball_and_taper(backend);
}
TEST(ball_and_3stick, neuron_ref) {
- validate_ball_and_3stick<lowered_cell>();
+ validate_ball_and_3stick(backend);
}
TEST(rallpack1, numeric_ref) {
- validate_rallpack1<lowered_cell>();
+ validate_rallpack1(backend);
}
TEST(ball_and_squiggle, neuron_ref) {
- validate_ball_and_squiggle<lowered_cell>();
+ validate_ball_and_squiggle(backend);
}
diff --git a/tests/validation/validate_ball_and_stick.hpp b/tests/validation/validate_ball_and_stick.hpp
index 0a438f9d..da1652e6 100644
--- a/tests/validation/validate_ball_and_stick.hpp
+++ b/tests/validation/validate_ball_and_stick.hpp
@@ -15,13 +15,11 @@
#include "trace_analysis.hpp"
#include "validation_data.hpp"
-template <
- typename LoweredCell,
- typename SamplerInfoSeq
->
+template <typename SamplerInfoSeq>
void run_ncomp_convergence_test(
const char* model_name,
const nest::mc::util::path& ref_data_path,
+ nest::mc::backend_policy backend,
const nest::mc::cell& c,
SamplerInfoSeq& samplers,
float t_end=100.f)
@@ -37,7 +35,7 @@ void run_ncomp_convergence_test(
{"dt", dt},
{"sim", "nestmc"},
{"units", "mV"},
- {"backend", LoweredCell::backend::name()}
+ {"backend_policy", to_string(backend)}
};
auto exclude = stimulus_ends(c);
@@ -51,7 +49,7 @@ void run_ncomp_convergence_test(
seg->set_compartments(ncomp);
}
}
- model<LoweredCell> m(singleton_recipe{c});
+ model m(singleton_recipe{c}, backend);
runner.run(m, ncomp, t_end, dt, exclude);
}
@@ -59,8 +57,7 @@ void run_ncomp_convergence_test(
runner.assert_all_convergence();
}
-template <typename LoweredCell>
-void validate_ball_and_stick() {
+void validate_ball_and_stick(nest::mc::backend_policy backend) {
using namespace nest::mc;
cell c = make_cell_ball_and_stick();
@@ -73,15 +70,15 @@ void validate_ball_and_stick() {
{"dend.end", {0u, 2u}, simple_sampler(sample_dt)}
};
- run_ncomp_convergence_test<LoweredCell>(
+ run_ncomp_convergence_test(
"ball_and_stick",
"neuron_ball_and_stick.json",
+ backend,
c,
samplers);
}
-template <typename LoweredCell>
-void validate_ball_and_taper() {
+void validate_ball_and_taper(nest::mc::backend_policy backend) {
using namespace nest::mc;
cell c = make_cell_ball_and_taper();
@@ -94,15 +91,15 @@ void validate_ball_and_taper() {
{"taper.end", {0u, 2u}, simple_sampler(sample_dt)}
};
- run_ncomp_convergence_test<LoweredCell>(
+ run_ncomp_convergence_test(
"ball_and_taper",
"neuron_ball_and_taper.json",
+ backend,
c,
samplers);
}
-template <typename LoweredCell>
-void validate_ball_and_3stick() {
+void validate_ball_and_3stick(nest::mc::backend_policy backend) {
using namespace nest::mc;
cell c = make_cell_ball_and_3stick();
@@ -119,15 +116,15 @@ void validate_ball_and_3stick() {
{"dend3.end", {0u, 6u}, simple_sampler(sample_dt)}
};
- run_ncomp_convergence_test<LoweredCell>(
+ run_ncomp_convergence_test(
"ball_and_3stick",
"neuron_ball_and_3stick.json",
+ backend,
c,
samplers);
}
-template <typename LoweredCell>
-void validate_rallpack1() {
+void validate_rallpack1(nest::mc::backend_policy backend) {
using namespace nest::mc;
cell c = make_cell_simple_cable();
@@ -144,16 +141,16 @@ void validate_rallpack1() {
{"cable.x1.0", {0u, 2u}, simple_sampler(sample_dt)},
};
- run_ncomp_convergence_test<LoweredCell>(
+ run_ncomp_convergence_test(
"rallpack1",
"numeric_rallpack1.json",
+ backend,
c,
samplers,
250.f);
}
-template <typename LoweredCell>
-void validate_ball_and_squiggle() {
+void validate_ball_and_squiggle(nest::mc::backend_policy backend) {
using namespace nest::mc;
cell c = make_cell_ball_and_squiggle();
@@ -177,9 +174,10 @@ void validate_ball_and_squiggle() {
samplers);
#endif
- run_ncomp_convergence_test<LoweredCell>(
+ run_ncomp_convergence_test(
"ball_and_squiggle_integrator",
"neuron_ball_and_squiggle.json",
+ backend,
c,
samplers);
}
diff --git a/tests/validation/validate_kinetic.cpp b/tests/validation/validate_kinetic.cpp
index 1c200516..b5d97b23 100644
--- a/tests/validation/validate_kinetic.cpp
+++ b/tests/validation/validate_kinetic.cpp
@@ -2,12 +2,12 @@
#include "../gtest.h"
-using lowered_cell = nest::mc::fvm::fvm_multicell<nest::mc::multicore::backend>;
+const auto backend = nest::mc::backend_policy::use_multicore;
TEST(kinetic, kin1_numeric_ref) {
- validate_kinetic_kin1<lowered_cell>();
+ validate_kinetic_kin1(backend);
}
TEST(kinetic, kinlva_numeric_ref) {
- validate_kinetic_kinlva<lowered_cell>();
+ validate_kinetic_kinlva(backend);
}
diff --git a/tests/validation/validate_kinetic.cu b/tests/validation/validate_kinetic.cu
index 4c32cd93..a86847f8 100644
--- a/tests/validation/validate_kinetic.cu
+++ b/tests/validation/validate_kinetic.cu
@@ -2,12 +2,12 @@
#include "../gtest.h"
-using lowered_cell = nest::mc::fvm::fvm_multicell<nest::mc::gpu::backend>;
+const auto backend = nest::mc::backend_policy::prefer_gpu;
TEST(kinetic, kin1_numeric_ref) {
- validate_kinetic_kin1<lowered_cell>();
+ validate_kinetic_kin1(backend);
}
TEST(kinetic, kinlva_numeric_ref) {
- validate_kinetic_kinlva<lowered_cell>();
+ validate_kinetic_kinlva(backend);
}
diff --git a/tests/validation/validate_kinetic.hpp b/tests/validation/validate_kinetic.hpp
index 7ccde7c9..535ed869 100644
--- a/tests/validation/validate_kinetic.hpp
+++ b/tests/validation/validate_kinetic.hpp
@@ -13,8 +13,13 @@
#include "trace_analysis.hpp"
#include "validation_data.hpp"
-template <typename LoweredCell>
-void run_kinetic_dt(nest::mc::cell& c, float t_end, nlohmann::json meta, const std::string& ref_file) {
+void run_kinetic_dt(
+ nest::mc::backend_policy backend,
+ nest::mc::cell& c,
+ float t_end,
+ nlohmann::json meta,
+ const std::string& ref_file)
+{
using namespace nest::mc;
float sample_dt = .025f;
@@ -23,11 +28,11 @@ void run_kinetic_dt(nest::mc::cell& c, float t_end, nlohmann::json meta, const s
};
meta["sim"] = "nestmc";
- meta["backend"] = LoweredCell::backend::name();
+ meta["backend_policy"] = to_string(backend);
convergence_test_runner<float> runner("dt", samplers, meta);
runner.load_reference_data(ref_file);
- model<LoweredCell> model(singleton_recipe{c});
+ model model(singleton_recipe{c}, backend);
auto exclude = stimulus_ends(c);
@@ -49,8 +54,7 @@ end:
runner.assert_all_convergence();
}
-template <typename LoweredCell>
-void validate_kinetic_kin1() {
+void validate_kinetic_kin1(nest::mc::backend_policy backend) {
using namespace nest::mc;
// 20 µm diameter soma with single mechanism, current probe
@@ -65,11 +69,10 @@ void validate_kinetic_kin1() {
{"units", "nA"}
};
- run_kinetic_dt<LoweredCell>(c, 100.f, meta, "numeric_kin1.json");
+ run_kinetic_dt(backend, c, 100.f, meta, "numeric_kin1.json");
}
-template <typename LoweredCell>
-void validate_kinetic_kinlva() {
+void validate_kinetic_kinlva(nest::mc::backend_policy backend) {
using namespace nest::mc;
// 20 µm diameter soma with single mechanism, current probe
@@ -85,6 +88,6 @@ void validate_kinetic_kinlva() {
{"units", "mV"}
};
- run_kinetic_dt<LoweredCell>(c, 300.f, meta, "numeric_kinlva.json");
+ run_kinetic_dt(backend, c, 300.f, meta, "numeric_kinlva.json");
}
diff --git a/tests/validation/validate_soma.cpp b/tests/validation/validate_soma.cpp
index e4e58e7b..57b094b3 100644
--- a/tests/validation/validate_soma.cpp
+++ b/tests/validation/validate_soma.cpp
@@ -2,8 +2,9 @@
#include "../gtest.h"
-using lowered_cell = nest::mc::fvm::fvm_multicell<nest::mc::multicore::backend>;
+
+const auto backend = nest::mc::backend_policy::use_multicore;
TEST(soma, numeric_ref) {
- validate_soma<lowered_cell>();
+ validate_soma(backend);
}
diff --git a/tests/validation/validate_soma.cu b/tests/validation/validate_soma.cu
index 35355ab9..b31b91a4 100644
--- a/tests/validation/validate_soma.cu
+++ b/tests/validation/validate_soma.cu
@@ -2,8 +2,8 @@
#include "../gtest.h"
-using lowered_cell = nest::mc::fvm::fvm_multicell<nest::mc::gpu::backend>;
+const auto backend = nest::mc::backend_policy::prefer_gpu;
TEST(soma, numeric_ref) {
- validate_soma<lowered_cell>();
+ validate_soma(backend);
}
diff --git a/tests/validation/validate_soma.hpp b/tests/validation/validate_soma.hpp
index eee44e6b..0c533faa 100644
--- a/tests/validation/validate_soma.hpp
+++ b/tests/validation/validate_soma.hpp
@@ -13,13 +13,12 @@
#include "trace_analysis.hpp"
#include "validation_data.hpp"
-template <typename LoweredCell>
-void validate_soma() {
+void validate_soma(nest::mc::backend_policy backend) {
using namespace nest::mc;
cell c = make_cell_soma_only();
add_common_voltage_probes(c);
- model<LoweredCell> model(singleton_recipe{c});
+ model model(singleton_recipe{c}, backend);
float sample_dt = .025f;
sampler_info samplers[] = {{"soma.mid", {0u, 0u}, simple_sampler(sample_dt)}};
@@ -29,7 +28,7 @@ void validate_soma() {
{"model", "soma"},
{"sim", "nestmc"},
{"units", "mV"},
- {"backend", LoweredCell::backend::name()}
+ {"backend_policy", to_string(backend)}
};
convergence_test_runner<float> runner("dt", samplers, meta);
diff --git a/tests/validation/validate_synapses.cpp b/tests/validation/validate_synapses.cpp
index 23413cc9..d1331b70 100644
--- a/tests/validation/validate_synapses.cpp
+++ b/tests/validation/validate_synapses.cpp
@@ -3,14 +3,14 @@
#include "../gtest.h"
#include "validate_synapses.hpp"
-using lowered_cell = nest::mc::fvm::fvm_multicell<nest::mc::multicore::backend>;
+const auto backend = nest::mc::backend_policy::use_multicore;
TEST(simple_synapse, expsyn_neuron_ref) {
SCOPED_TRACE("expsyn");
- run_synapse_test<lowered_cell>("expsyn", "neuron_simple_exp_synapse.json");
+ run_synapse_test("expsyn", "neuron_simple_exp_synapse.json", backend);
}
TEST(simple_synapse, exp2syn_neuron_ref) {
SCOPED_TRACE("exp2syn");
- run_synapse_test<lowered_cell>("exp2syn", "neuron_simple_exp2_synapse.json");
+ run_synapse_test("exp2syn", "neuron_simple_exp2_synapse.json", backend);
}
diff --git a/tests/validation/validate_synapses.cu b/tests/validation/validate_synapses.cu
index 0dedd584..47f0cc67 100644
--- a/tests/validation/validate_synapses.cu
+++ b/tests/validation/validate_synapses.cu
@@ -3,14 +3,14 @@
#include "../gtest.h"
#include "validate_synapses.hpp"
-using lowered_cell = nest::mc::fvm::fvm_multicell<nest::mc::gpu::backend>;
+const auto backend = nest::mc::backend_policy::prefer_gpu;
TEST(simple_synapse, expsyn_neuron_ref) {
SCOPED_TRACE("expsyn");
- run_synapse_test<lowered_cell>("expsyn", "neuron_simple_exp_synapse.json");
+ run_synapse_test("expsyn", "neuron_simple_exp_synapse.json", backend);
}
TEST(simple_synapse, exp2syn_neuron_ref) {
SCOPED_TRACE("exp2syn");
- run_synapse_test<lowered_cell>("exp2syn", "neuron_simple_exp2_synapse.json");
+ run_synapse_test("exp2syn", "neuron_simple_exp2_synapse.json", backend);
}
diff --git a/tests/validation/validate_synapses.hpp b/tests/validation/validate_synapses.hpp
index cee90062..c3f7f294 100644
--- a/tests/validation/validate_synapses.hpp
+++ b/tests/validation/validate_synapses.hpp
@@ -15,10 +15,10 @@
#include "trace_analysis.hpp"
#include "validation_data.hpp"
-template <typename LoweredCell>
void run_synapse_test(
const char* syn_type,
const nest::mc::util::path& ref_data_path,
+ nest::mc::backend_policy backend,
float t_end=70.f,
float dt=0.001)
{
@@ -30,7 +30,7 @@ void run_synapse_test(
{"model", syn_type},
{"sim", "nestmc"},
{"units", "mV"},
- {"backend", LoweredCell::backend::name()}
+ {"backend_policy", to_string(backend)}
};
cell c = make_cell_ball_and_stick(false); // no stimuli
@@ -60,7 +60,7 @@ void run_synapse_test(
for (int ncomp = 10; ncomp<max_ncomp; ncomp*=2) {
c.cable(1)->set_compartments(ncomp);
- model<LoweredCell> m(singleton_recipe{c});
+ model m(singleton_recipe{c}, backend);
m.group(0).enqueue_events(synthetic_events);
runner.run(m, ncomp, t_end, dt, exclude);
--
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