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nest · Nov 6, 2024 · 34adbdc · 34adbdc
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diff --git a/.github/workflows/continuous_benchmarking.yml b/.github/workflows/continuous_benchmarking.yml
@@ -0,0 +1,171 @@
+on:
+  pull_request_target:
+    types: [opened, reopened, edited, synchronize]
+
+jobs:
+  fork_pr_requires_review:
+    environment: ${{ (github.event.pull_request.head.repo.full_name == github.repository && 'internal') || 'external' }}
+    runs-on: ubuntu-latest
+    steps:
+      - run: true
+
+  benchmark_fork_pr_branch:
+    needs: fork_pr_requires_review
+    name: Continuous Benchmarking Fork PRs with Bencher
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          ref: ${{ github.event.pull_request.head.sha }}
+          persist-credentials: false
+
+      - uses: bencherdev/bencher@main
+
+      # Setup Python version
+      - name: Setup Python 3.8
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.8
+
+      # Install dependencies
+      - name: Install apt dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install libltdl7-dev libgsl0-dev libncurses5-dev libreadline6-dev pkg-config
+          sudo apt-get install python3-all-dev python3-matplotlib python3-numpy python3-scipy ipython3
+
+      # Install Python dependencies
+      - name: Python dependencies
+        run: |
+          python -m pip install --upgrade pip pytest jupyterlab matplotlib pycodestyle scipy pandas pytest-benchmark
+          python -m pip install -r requirements.txt
+
+      # Install NEST simulator
+      - name: NEST simulator
+        run: |
+          python -m pip install cython
+          echo "GITHUB_WORKSPACE = $GITHUB_WORKSPACE"
+          NEST_SIMULATOR=$(pwd)/nest-simulator
+          NEST_INSTALL=$(pwd)/nest_install
+          echo "NEST_SIMULATOR = $NEST_SIMULATOR"
+          echo "NEST_INSTALL = $NEST_INSTALL"
+
+          git clone --depth=1 https://github.com/nest/nest-simulator
+          mkdir nest_install
+          echo "NEST_INSTALL=$NEST_INSTALL" >> $GITHUB_ENV
+          cd nest_install
+          cmake -DCMAKE_INSTALL_PREFIX=$NEST_INSTALL $NEST_SIMULATOR
+          make && make install
+          cd ..
+
+      # Install NESTML (repeated)
+      - name: Install NESTML
+        run: |
+          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.8/site-packages
+          #echo PYTHONPATH=`pwd` >> $GITHUB_ENV
+          echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
+          python setup.py install
+
+      - name: Track Fork PR Benchmarks with Bencher
+        env:
+          LD_LIBRARY_PATH: ${{ env.NEST_INSTALL }}/lib/nest
+        run: |
+          echo "NEST_INSTALL = $NEST_INSTALL"
+          LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${{ env.NEST_INSTALL }}/lib/nest bencher run \
+          --project nestml \
+          --token '${{ secrets.BENCHER_API_TOKEN }}' \
+          --branch '${{ github.event.number }}/merge' \
+          --branch-start-point '${{ github.base_ref }}' \
+          --branch-start-point-hash '${{ github.event.pull_request.base.sha }}' \
+          --branch-reset \
+          --github-actions "${{ secrets.GITHUB_TOKEN }}" \
+          --testbed ubuntu-latest \
+          --adapter python_pytest \
+          --file results.json \
+          --err \
+          'LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${{ env.NEST_INSTALL }}/lib/nest python3 -m pytest --benchmark-json results.json -s $GITHUB_WORKSPACE/tests/nest_continuous_benchmarking/test_nest_continuous_benchmarking.py'
+
+
+on:
+  push:
+    branches: master
+
+jobs:
+  benchmark_base_branch:
+    name: Continuous Benchmarking Fork PRs with Bencher
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          ref: ${{ github.event.pull_request.head.sha }}
+          persist-credentials: false
+
+      - uses: bencherdev/bencher@main
+
+      # Setup Python version
+      - name: Setup Python 3.8
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.8
+
+      # Install dependencies
+      - name: Install apt dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install libltdl7-dev libgsl0-dev libncurses5-dev libreadline6-dev pkg-config
+          sudo apt-get install python3-all-dev python3-matplotlib python3-numpy python3-scipy ipython3
+
+      # Install Python dependencies
+      - name: Python dependencies
+        run: |
+          python -m pip install --upgrade pip pytest jupyterlab matplotlib pycodestyle scipy pandas pytest-benchmark
+          python -m pip install -r requirements.txt
+
+      # Install NEST simulator
+      - name: NEST simulator
+        run: |
+          python -m pip install cython
+          echo "GITHUB_WORKSPACE = $GITHUB_WORKSPACE"
+          NEST_SIMULATOR=$(pwd)/nest-simulator
+          NEST_INSTALL=$(pwd)/nest_install
+          echo "NEST_SIMULATOR = $NEST_SIMULATOR"
+          echo "NEST_INSTALL = $NEST_INSTALL"
+
+          git clone --depth=1 https://github.com/nest/nest-simulator
+          mkdir nest_install
+          echo "NEST_INSTALL=$NEST_INSTALL" >> $GITHUB_ENV
+          cd nest_install
+          cmake -DCMAKE_INSTALL_PREFIX=$NEST_INSTALL $NEST_SIMULATOR
+          make && make install
+          cd ..
+
+      # Install NESTML (repeated)
+      - name: Install NESTML
+        run: |
+          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.8/site-packages
+          #echo PYTHONPATH=`pwd` >> $GITHUB_ENV
+          echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
+          python setup.py install
+
+      - name: Track Fork PR Benchmarks with Bencher
+        env:
+          LD_LIBRARY_PATH: ${{ env.NEST_INSTALL }}/lib/nest
+        run: |
+          echo "NEST_INSTALL = $NEST_INSTALL"
+          LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${{ env.NEST_INSTALL }}/lib/nest bencher run \
+          --project nestml \
+          --token '${{ secrets.BENCHER_API_TOKEN }}' \
+          --branch master \
+          --threshold-measure latency \
+          --threshold-test t_test \
+          --threshold-max-sample-size 64 \
+          --threshold-upper-boundary 0.99 \
+          --thresholds-reset \
+          --github-actions "${{ secrets.GITHUB_TOKEN }}" \
+          --testbed ubuntu-latest \
+          --adapter python_pytest \
+          --file results.json \
+          --err \
+          'LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${{ env.NEST_INSTALL }}/lib/nest python3 -m pytest --benchmark-json results.json -s $GITHUB_WORKSPACE/tests/nest_continuous_benchmarking/test_nest_continuous_benchmarking.py'
diff --git a/doc/models_library/aeif_cond_alpha_neuron.rst b/doc/models_library/aeif_cond_alpha_neuron.rst
@@ -22,10 +22,17 @@ and
 
 .. math::
 
- \tau_w \frac{dw}{dt} = a(V_m-E_L) - w
+   \tau_w \frac{dw}{dt} = a(V_m-E_L) - w
 
 Note that the membrane potential can diverge to positive infinity due to the exponential term. To avoid numerical instabilities, instead of :math:`V_m`, the value :math:`\min(V_m,V_{peak})` is used in the dynamical equations.
 
+.. note::
+
+   The default refractory period for ``aeif`` models is zero, consistent with the model definition in
+   Brette & Gerstner [1]_.  Thus, an ``aeif`` neuron with default parameters can fire multiple spikes in a single
+   time step, which can lead to exploding spike numbers and extreme slow-down of simulations.
+   To avoid such unphysiological behavior, you should set a refractory time ``refr_t > 0``.
+
 
 References
 ++++++++++
@@ -108,4 +115,4 @@ The model source code can be found in the NESTML models repository here: `aeif_c
 
 .. footer::
 
-   Generated at 2024-05-22 14:51:14.532753
+   Generated at 2024-05-22 14:51:14.532753
diff --git a/doc/models_library/aeif_cond_exp_neuron.rst b/doc/models_library/aeif_cond_exp_neuron.rst
@@ -27,6 +27,12 @@ and
 
 Note that the membrane potential can diverge to positive infinity due to the exponential term. To avoid numerical instabilities, instead of :math:`V_m`, the value :math:`\min(V_m,V_{peak})` is used in the dynamical equations.
 
+.. note::
+    The default refractory period for ``aeif`` models is zero, consistent with the model definition in
+    Brette & Gerstner [1]_.  Thus, an ``aeif`` neuron with default parameters can fire multiple spikes in a single
+    time step, which can lead to exploding spike numbers and extreme slow-down of simulations.
+    To avoid such unphysiological behavior, you should set a refractory time ``refr_t > 0``.
+
 
 References
 ++++++++++
@@ -109,4 +115,4 @@ The model source code can be found in the NESTML models repository here: `aeif_c
 
 .. footer::
 
-   Generated at 2024-05-22 14:51:14.484055
+   Generated at 2024-05-22 14:51:14.484055
diff --git a/doc/models_library/output.html b/doc/models_library/output.html
@@ -424,10 +424,4 @@ <h3 id="stdp_triplet_synapse-stdp_triplet_synapse"><code
 <p>Synapse type with triplet spike-timing dependent plasticity</p>
 <p>Source file: <a
 href="https://www.github.com/nest/nestml/blob/master/models/synapses/stdp_triplet_synapse.nestml">stdp_triplet_synapse.nestml</a></p>
-<h3 id="third_factor_stdp_synapse-third_factor_stdp_synapse"><code
-class="interpreted-text"
-role="doc">third_factor_stdp_synapse &lt;third_factor_stdp_synapse&gt;</code></h3>
-<p>Synapse model for spike-timing dependent plasticity with postsynaptic
-third-factor modulation</p>
-<p>Source file: <a
-href="https://www.github.com/nest/nestml/blob/master/models/synapses/third_factor_stdp_synapse.nestml">third_factor_stdp_synapse.nestml</a></p>
+
diff --git a/doc/nestml_language/nestml_language_concepts.rst b/doc/nestml_language/nestml_language_concepts.rst
@@ -907,6 +907,30 @@ Each model can only send a single type of event. The type of the event has to be
 
 Calling the ``emit_spike()`` function in the ``update`` block results in firing a spike to all target neurons and devices time stamped with the simulation time at the end of the time interval ``t + timestep()``.
 
+Event attributes
+~~~~~~~~~~~~~~~~
+
+Each spiking output event can be parameterised by one or more attributes. For example, a synapse could assign a weight (as a real number) and delay (in milliseconds) to its spike events by including these values in the call to ``emit_spike()``:
+
+.. code-block:: nestml
+
+   parameters:
+       weight real = 10.
+
+   update:
+       emit_spike(weight, 1 ms)
+
+If spike event attributes are used, their names and types must be given as part of the output port specification, for example:
+
+.. code-block:: nestml
+
+   output:
+       spike(weight real, delay ms)
+
+The names are only used externally, so that other models can refer to the correct attribute (such as a downstream neuron that is receiving the spike through its input port). It is thus allowed to have a state variable called ``weight`` and an output port attribute by the same name; the output port attribute name does not refer to names declared inside the model.
+
+Specific code generators may support a specific set of attributes; please check the documentation of each individual code generator for more details.
+
 
 Equations
 ---------

diff --git a/doc/nestml_language/synapses_in_nestml.rst b/doc/nestml_language/synapses_in_nestml.rst
@@ -122,8 +122,8 @@ For example:
 .. code-block:: nestml
 
    parameters:
-       a real = 3.14159   @homogeneous
-       b real = 100.      @heterogeneous  # the default!
+       a real = pi        @homogeneous
+       b integer = 42     @heterogeneous  # the default!
 
 
 Third-factor plasticity

diff --git a/doc/running/running_nest.rst b/doc/running/running_nest.rst
@@ -182,6 +182,14 @@ For a full example, please see `iaf_psc_exp_multisynapse_vectors.nestml <https:/
 Generating code
 ---------------
 
+Output event attributes
+~~~~~~~~~~~~~~~~~~~~~~~
+
+In neuron models, no spike event attributes are supported.
+
+In synapse models, precisely two spike event attributes are supported: a synaptic weight (as a real number) and a synaptic (dendritic) delay (in milliseconds).
+
+
 Generating code for plastic synapses
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 

diff --git a/doc/tutorials/stdp_dopa_synapse/stdp_dopa_synapse.ipynb b/doc/tutorials/stdp_dopa_synapse/stdp_dopa_synapse.ipynb
@@ -179,7 +179,7 @@
     "        mod_spikes <- spike\n",
     "\n",
     "    output:\n",
-    "        spike\n",
+    "        spike(weight real, delay ms)\n",
     "\n",
     "    onReceive(mod_spikes):\n",
     "        n += A_vt / tau_n\n",

diff --git a/doc/tutorials/stdp_third_factor_active_dendrite/stdp_third_factor_active_dendrite.ipynb b/doc/tutorials/stdp_third_factor_active_dendrite/stdp_third_factor_active_dendrite.ipynb
@@ -444,7 +444,7 @@
     "        I_post_dend pA <- continuous\n",
     "\n",
     "    output:\n",
-    "        spike\n",
+    "        spike(weight real, delay ms)\n",
     "\n",
     "    onReceive(post_spikes):\n",
     "        # potentiate synapse\n",

diff --git a/doc/tutorials/stdp_windows/stdp_windows.ipynb b/doc/tutorials/stdp_windows/stdp_windows.ipynb
@@ -249,7 +249,7 @@
     "        post_spikes <- spike\n",
     "\n",
     "    output:\n",
-    "        spike\n",
+    "        spike(weight real, delay ms)\n",
     "\n",
     "    onReceive(post_spikes):\n",
     "        # potentiate synapse\n",
@@ -3214,7 +3214,7 @@
     "        post_spikes <- spike\n",
     "\n",
     "    output:\n",
-    "        spike\n",
+    "        spike(weight real, delay ms)\n",
     "\n",
     "    onReceive(post_spikes):\n",
     "        post_nn_trace = 1\n",
@@ -4805,7 +4805,7 @@
     "        post_spikes <- spike\n",
     "\n",
     "    output:\n",
-    "        spike\n",
+    "        spike(weight real, delay ms)\n",
     "\n",
     "    onReceive(post_spikes, priority=2):\n",
     "        w += lambda * (pre_trace + post_trace)\n",

diff --git a/doc/tutorials/triplet_stdp_synapse/triplet_stdp_synapse.ipynb b/doc/tutorials/triplet_stdp_synapse/triplet_stdp_synapse.ipynb
@@ -216,7 +216,7 @@
     "        post_spikes <- spike\n",
     "\n",
     "    output:\n",
-    "        spike\n",
+    "        spike(weight real, delay ms)\n",
     "\n",
     "    onReceive(post_spikes):\n",
     "        # increment post trace values\n",
@@ -1120,7 +1120,7 @@
     "        post_spikes <- spike\n",
     "\n",
     "    output:\n",
-    "        spike\n",
+    "        spike(weight real, delay ms)\n",
     "\n",
     "    onReceive(post_spikes):\n",
     "        # increment post trace values\n",

diff --git a/models/neurons/aeif_cond_alpha_neuron.nestml b/models/neurons/aeif_cond_alpha_neuron.nestml
@@ -20,10 +20,17 @@ and
 
 .. math::
 
- \tau_w \frac{dw}{dt} = a(V_m-E_L) - w
+   \tau_w \frac{dw}{dt} = a(V_m-E_L) - w
 
 Note that the membrane potential can diverge to positive infinity due to the exponential term. To avoid numerical instabilities, instead of :math:`V_m`, the value :math:`\min(V_m,V_{peak})` is used in the dynamical equations.
 
+.. note::
+
+   The default refractory period for ``aeif`` models is zero, consistent with the model definition in
+   Brette & Gerstner [1]_.  Thus, an ``aeif`` neuron with default parameters can fire multiple spikes in a single
+   time step, which can lead to exploding spike numbers and extreme slow-down of simulations.
+   To avoid such unphysiological behavior, you should set a refractory time ``refr_t > 0``.
+
 
 References
 ++++++++++

diff --git a/models/neurons/aeif_cond_exp_neuron.nestml b/models/neurons/aeif_cond_exp_neuron.nestml
@@ -25,6 +25,13 @@ and
 
 Note that the membrane potential can diverge to positive infinity due to the exponential term. To avoid numerical instabilities, instead of :math:`V_m`, the value :math:`\min(V_m,V_{peak})` is used in the dynamical equations.
 
+.. note::
+
+   The default refractory period for ``aeif`` models is zero, consistent with the model definition in
+   Brette & Gerstner [1]_.  Thus, an ``aeif`` neuron with default parameters can fire multiple spikes in a single
+   time step, which can lead to exploding spike numbers and extreme slow-down of simulations.
+   To avoid such unphysiological behavior, you should set a refractory time ``refr_t > 0``.
+
 
 References
 ++++++++++

diff --git a/models/synapses/neuromodulated_stdp_synapse.nestml b/models/synapses/neuromodulated_stdp_synapse.nestml
@@ -56,7 +56,7 @@ model neuromodulated_stdp_synapse:
         mod_spikes <- spike
 
     output:
-        spike
+        spike(weight real, delay ms)
 
     onReceive(mod_spikes):
         n += 1. / tau_n