VOR related models and provenance

neural_modelling/makefiles/neuron/IF_cond_exp_stdp_mad_mfvn_mfvn/Makefile

@@ -0,0 +1,28 @@
+# Copyright (c) 2017-2021 The University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+APP = $(notdir $(CURDIR))
+
+NEURON_MODEL_H = $(NEURON_DIR)/neuron/models/neuron_model_lif_impl.h
+INPUT_TYPE_H = $(NEURON_DIR)/neuron/input_types/input_type_conductance.h
+NEURON_IMPL_H = $(NEURON_DIR)/neuron/implementations/neuron_impl_standard.h
+THRESHOLD_TYPE_H = $(NEURON_DIR)/neuron/threshold_types/threshold_type_static.h
+SYNAPSE_TYPE_H = $(NEURON_DIR)/neuron/synapse_types/synapse_types_exponential_impl.h
+SYNAPSE_DYNAMICS = $(NEURON_DIR)/neuron/plasticity/stdp/synapse_dynamics_stdp_mad_mfvn_impl.c
+TIMING_DEPENDENCE = $(NEURON_DIR)/neuron/plasticity/stdp/timing_dependence/timing_mfvn_impl.c
+TIMING_DEPENDENCE_H = $(NEURON_DIR)/neuron/plasticity/stdp/timing_dependence/timing_mfvn_impl.h
+WEIGHT_DEPENDENCE = $(NEURON_DIR)/neuron/plasticity/stdp/weight_dependence/weight_mfvn_impl.c
+WEIGHT_DEPENDENCE_H = $(NEURON_DIR)/neuron/plasticity/stdp/weight_dependence/weight_mfvn_impl.h
+
+include ../neural_build.mk

neural_modelling/makefiles/neuron/IF_cond_exp_stdp_mad_pfpc_pfpc/Makefile

@@ -0,0 +1,28 @@
+# Copyright (c) 2017-2021 The University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+APP = $(notdir $(CURDIR))
+
+NEURON_MODEL_H = $(NEURON_DIR)/neuron/models/neuron_model_lif_impl.h
+INPUT_TYPE_H = $(NEURON_DIR)/neuron/input_types/input_type_conductance.h
+NEURON_IMPL_H = $(NEURON_DIR)/neuron/implementations/neuron_impl_standard.h
+THRESHOLD_TYPE_H = $(NEURON_DIR)/neuron/threshold_types/threshold_type_static.h
+SYNAPSE_TYPE_H = $(NEURON_DIR)/neuron/synapse_types/synapse_types_exponential_impl.h
+SYNAPSE_DYNAMICS = $(NEURON_DIR)/neuron/plasticity/stdp/synapse_dynamics_stdp_mad_pfpc_impl.c
+TIMING_DEPENDENCE = $(NEURON_DIR)/neuron/plasticity/stdp/timing_dependence/timing_pfpc_impl.c
+TIMING_DEPENDENCE_H = $(NEURON_DIR)/neuron/plasticity/stdp/timing_dependence/timing_pfpc_impl.h
+WEIGHT_DEPENDENCE = $(NEURON_DIR)/neuron/plasticity/stdp/weight_dependence/weight_pfpc_impl.c
+WEIGHT_DEPENDENCE_H = $(NEURON_DIR)/neuron/plasticity/stdp/weight_dependence/weight_pfpc_impl.h
+
+include ../neural_build.mk

neural_modelling/makefiles/synapse_only/Makefile

@@ -25,7 +25,9 @@ MODELS = synapses\
          synapses_stdp_mad_pair_additive_structural_random_distance_weight\
          synapses_stdp_mad_pair_additive_structural_last_neuron_distance_weight\
          synapses_stdp_mad_nearest_pair_additive_structural_random_distance_weight\
-         synapses_stdp_izhikevich_neuromodulation_pair_additive
+         synapses_stdp_izhikevich_neuromodulation_pair_additive\
+         synapses_stdp_mad_mfvn_mfvn\
+         synapses_stdp_mad_pfpc_pfpc
 
 ifneq ($(SPYNNAKER_DEBUG), DEBUG)
     MODELS += synapses_stdp_izhikevich_neuromodulation_pair_multiplicative\

neural_modelling/makefiles/synapse_only/synapses_stdp_mad_mfvn_mfvn/Makefile

@@ -0,0 +1,23 @@
+# Copyright (c) 2017-2019 The University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+APP = $(notdir $(CURDIR))
+
+SYNAPSE_DYNAMICS = $(NEURON_DIR)/neuron/plasticity/stdp/synapse_dynamics_stdp_mad_mfvn_impl.c
+TIMING_DEPENDENCE = $(NEURON_DIR)/neuron/plasticity/stdp/timing_dependence/timing_mfvn_impl.c
+TIMING_DEPENDENCE_H = $(NEURON_DIR)/neuron/plasticity/stdp/timing_dependence/timing_mfvn_impl.h
+WEIGHT_DEPENDENCE = $(NEURON_DIR)/neuron/plasticity/stdp/weight_dependence/weight_mfvn_impl.c
+WEIGHT_DEPENDENCE_H = $(NEURON_DIR)/neuron/plasticity/stdp/weight_dependence/weight_mfvn_impl.h
+
+include ../synapse_build.mk

neural_modelling/makefiles/synapse_only/synapses_stdp_mad_pfpc_pfpc/Makefile

@@ -0,0 +1,23 @@
+# Copyright (c) 2017-2019 The University of Manchester
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+APP = $(notdir $(CURDIR))
+
+SYNAPSE_DYNAMICS = $(NEURON_DIR)/neuron/plasticity/stdp/synapse_dynamics_stdp_mad_pfpc_impl.c
+TIMING_DEPENDENCE = $(NEURON_DIR)/neuron/plasticity/stdp/timing_dependence/timing_pfpc_impl.c
+TIMING_DEPENDENCE_H = $(NEURON_DIR)/neuron/plasticity/stdp/timing_dependence/timing_pfpc_impl.h
+WEIGHT_DEPENDENCE = $(NEURON_DIR)/neuron/plasticity/stdp/weight_dependence/weight_pfpc_impl.c
+WEIGHT_DEPENDENCE_H = $(NEURON_DIR)/neuron/plasticity/stdp/weight_dependence/weight_pfpc_impl.h
+
+include ../synapse_build.mk

neural_modelling/src/common/in_spikes.h

@@ -135,4 +135,16 @@ static inline void in_spikes_clear(void) {
 static inline spike_t in_spikes_value_at_index(uint32_t index) {
     return circular_buffer_value_at_index(buffer, index);
 }
+
+#if LOG_LEVEL >= LOG_DEBUG
+// FLUSH SPIKES
+static inline uint32_t in_spikes_flush_buffer(void) {
+
+	uint32_t num_spikes_left = circular_buffer_size(buffer);
+	circular_buffer_clear(buffer);
+
+	return num_spikes_left;
+}
+#endif
+
 #endif // _IN_SPIKES_H_

neural_modelling/src/neuron/c_main.c

@@ -39,6 +39,10 @@
 #include "profile_tags.h"
 #include "spike_processing.h"
 
+// FLUSH SPIKES
+//bool timer_callback_active = false;
+//extern volatile bool dma_busy;
+
 //! The combined provenance from synapses and neurons
 struct combined_provenance {
     struct neuron_provenance neuron_provenance;
@@ -179,7 +183,12 @@ void background_callback(uint timer_count, uint local_time) {
 //!            executed since start of simulation
 //! \param[in] unused: unused parameter kept for API consistency
 void timer_callback(uint timer_count, UNUSED uint unused) {
-    // Disable interrupts to stop DMAs and MC getting in the way of this bit
+//    // Get number of spikes in last tick, and reset spike counter
+//    spike_processing_get_and_reset_spikes_this_tick();
+//    spike_processing_get_and_reset_dmas_this_tick();
+//    spike_processing_get_and_reset_pipeline_restarts_this_tick();
+
+	// Disable interrupts to stop DMAs and MC getting in the way of this bit
     uint32_t state = spin1_int_disable();
 
     // Increment time step

neural_modelling/src/neuron/c_main_synapses.c

@@ -35,9 +35,14 @@
 #include "c_main_synapse_common.h"
 #include "c_main_common.h"
 #include "spike_processing_fast.h"
+#include "spike_profiling.h"
 #include "structural_plasticity/synaptogenesis_dynamics.h"
 #include <spin1_api_params.h>
 
+// FLUSH SPIKES
+bool timer_callback_active = false;
+extern volatile bool dma_busy;
+
 //! values for the priority for each callback
 typedef enum callback_priorities {
     MC = -1, DMA = -2, TIMER = 0, SDP = 0
@@ -90,6 +95,12 @@ const struct synapse_regions SYNAPSE_REGIONS = {
     .bitfield_filter = BIT_FIELD_FILTER_REGION
 };
 
+//! spike profiling
+struct spike_holder_t spike_counter;
+struct spike_holder_t spike_cache;
+struct spike_holder_t spike_counter_inh;
+struct spike_holder_t spike_cache_inh;
+
 //! The current timer tick value.
 // the timer tick callback returning the same value.
 uint32_t time;
@@ -129,7 +140,19 @@ void resume_callback(void) {
 //! \param[in] unused0: unused
 //! \param[in] unused1: unused
 void timer_callback(UNUSED uint unused0, UNUSED uint unused1) {
-    time++;
+    // Get number of spikes in last tick, and reset spike counter
+    spike_processing_get_and_reset_spikes_this_tick();
+    spike_processing_get_and_reset_dmas_this_tick();
+    spike_processing_get_and_reset_pipeline_restarts_this_tick();
+
+    // cache and flush spike counters
+    // functions in file neural_modelling/src/neuron/spike_profiling.h
+	spike_profiling_cache_and_flush_spike_holder(&spike_counter,
+			&spike_cache);
+	spike_profiling_cache_and_flush_spike_holder(&spike_counter_inh,
+			&spike_cache_inh);
+
+	time++;
     if (simulation_is_finished()) {
         // Enter pause and resume state to avoid another tick
         simulation_handle_pause_resume(resume_callback);

neural_modelling/src/neuron/models/neuron_model_lif_impl.h

@@ -189,20 +189,20 @@ static inline state_t neuron_model_get_membrane_voltage(const neuron_t *neuron)
 }
 
 static inline void neuron_model_print_state_variables(const neuron_t *neuron) {
-	log_info("V membrane    = %11.4k mv", neuron->V_membrane);
-	log_info("Refract timer = %u timesteps", neuron->refract_timer);
+	log_debug("V membrane    = %11.4k mv", neuron->V_membrane);
+	log_debug("Refract timer = %u timesteps", neuron->refract_timer);
 }
 
 static inline void neuron_model_print_parameters(const neuron_t *neuron) {
-    log_info("V reset       = %11.4k mv", neuron->V_reset);
-    log_info("V rest        = %11.4k mv", neuron->V_rest);
+    log_debug("V reset       = %11.4k mv", neuron->V_reset);
+    log_debug("V rest        = %11.4k mv", neuron->V_rest);
 
-    log_info("I offset      = %11.4k nA", neuron->I_offset);
-    log_info("R membrane    = %11.4k Mohm", neuron->R_membrane);
+    log_debug("I offset      = %11.4k nA", neuron->I_offset);
+    log_debug("R membrane    = %11.4k Mohm", neuron->R_membrane);
 
-    log_info("exp(-ms/(RC)) = %11.4k [.]", neuron->exp_TC);
+    log_debug("exp(-ms/(RC)) = %11.4k [.]", neuron->exp_TC);
 
-    log_info("T refract     = %u timesteps", neuron->T_refract);
+    log_debug("T refract     = %u timesteps", neuron->T_refract);
 }
 
 

neural_modelling/src/neuron/plasticity/stdp/maths.h

@@ -58,6 +58,7 @@ static inline int16_lut *maths_copy_int16_lut(address_t *address) {
     int16_lut *sdram_lut = (int16_lut *) *address;
     uint32_t size = sizeof(int16_lut) + (sdram_lut->size * sizeof(int16_t));
     int16_lut *lut = spin1_malloc(size);
+    log_debug("lut size %d sdram_lut size %d", size, sdram_lut->size);
     if (lut == NULL) {
         log_error("Not enough space to allocate LUT.  Try reducing the timestep,"
             " the number of neurons per core, or the tau value; size = %u", size);
@@ -77,14 +78,28 @@ static inline int16_lut *maths_copy_int16_lut(address_t *address) {
 //! \param[in] lut: The lookup table (result of maths_copy_int16_lut())
 //! \return The value from the LUT, or zero if out of range
 static inline int32_t maths_lut_exponential_decay(
-        uint32_t time, const int16_lut *lut) {
+        const uint32_t time, const int16_lut *lut) {
     // Calculate lut index
     uint32_t lut_index = time >> lut->shift;
 
     // Return value from LUT
     return (lut_index < lut->size) ? lut->values[lut_index] : 0;
 }
 
+//! \brief Get value from lookup table, time shifted
+//! \param[in] time: The time that we are mapping
+//! \param[in] time_shift: The time shift value
+//! \param[in] lut: The lookup table (result of maths_copy_int16_lut())
+//! \return The value from the LUT, or zero if out of range
+static inline int32_t maths_lut_exponential_decay_time_shifted(
+        const uint32_t time, const uint32_t time_shift, const int16_lut *lut) {
+    // Calculate lut index
+    uint32_t lut_index = (time >> lut->shift) >> time_shift;
+
+    // Return value from LUT
+    return (lut_index < lut->size) ? lut->values[lut_index] : 0;
+}
+
 //! \brief Clamp to fit in number of bits
 //! \param[in] x: The value to clamp
 //! \param[in] shift: Width of the field to clamp the value to fit in

neural_modelling/src/neuron/plasticity/stdp/post_events.h

@@ -84,6 +84,7 @@ static inline post_event_history_t *post_events_init_buffers(
         uint32_t n_neurons) {
     post_event_history_t *post_event_history =
             spin1_malloc(n_neurons * sizeof(post_event_history_t));
+
     // Check allocations succeeded
     if (post_event_history == NULL) {
         log_error("Unable to allocate global STDP structures - Out of DTCM: Try "
@@ -111,6 +112,7 @@ static inline post_event_history_t *post_events_init_buffers(
 static inline post_event_window_t post_events_get_window_delayed(
         const post_event_history_t *events, uint32_t begin_time,
         uint32_t end_time) {
+
     // Start at end event - beyond end of post-event history
     const uint32_t count = events->count_minus_one + 1;
     const uint32_t *end_event_time = events->times + count;

neural_modelling/src/neuron/plasticity/stdp/stdp_typedefs.h

@@ -37,6 +37,8 @@
 //! \return The product
 #define STDP_FIXED_MUL_16X16(a, b) maths_fixed_mul16(a, b, STDP_FIXED_POINT)
 
+//#define print_plasticity false
+
 //! The amount of right shift required to take a weight from s1615 format
 //! to STDP_FIXED_POINT format (s4,11)
 #define S1615_TO_STDP_RIGHT_SHIFT 4

neural_modelling/src/neuron/plasticity/stdp/synapse_dynamics_stdp_common.h

@@ -66,15 +66,6 @@
 //---------------------------------------
 // Structures
 //---------------------------------------
-//! \brief The type of history data of pre-events
-//!
-//! This data is stored in SDRAM in the plastic part of the synaptic matrix
-typedef struct {
-    //! The event time
-    uint32_t prev_time;
-    //! The event trace
-    pre_trace_t prev_trace;
-} pre_event_history_t;
 
 //! The type of configuration parameters in SDRAM (written by host)
 typedef struct stdp_params {

neural_modelling/src/neuron/plasticity/stdp/synapse_dynamics_stdp_izhikevich_neuromodulation.c

@@ -42,6 +42,16 @@ typedef struct nm_final_state_t {
     final_state_t final_state;
 } nm_final_state_t;
 
+//! \brief The type of history data of pre-events
+//!
+//! This data is stored in SDRAM in the plastic part of the synaptic matrix
+typedef struct {
+    //! The event time
+    uint32_t prev_time;
+    //! The event trace
+    pre_trace_t prev_trace;
+} pre_event_history_t;
+
 struct synapse_row_plastic_data_t {
     union {
         struct {

neural_modelling/src/neuron/plasticity/stdp/synapse_dynamics_stdp_mad_impl.c

@@ -19,6 +19,16 @@
 #include "post_events.h"
 #include "synapse_dynamics_stdp_common.h"
 
+//! \brief The type of history data of pre-events
+//!
+//! This data is stored in SDRAM in the plastic part of the synaptic matrix
+typedef struct {
+    //! The event time
+    uint32_t prev_time;
+    //! The event trace
+    pre_trace_t prev_trace;
+} pre_event_history_t;
+
 //! The format of the plastic data region of a synaptic row
 struct synapse_row_plastic_data_t {
     //! The pre-event history