From 9acd8131e62b6a04aea88a1e4bc94e88308ea69b Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Thu, 3 Mar 2022 13:03:38 +0100
Subject: [PATCH 01/25] Pull up to arbor 0.6.

---
 .../engines/busyring/arbor/CMakeLists.txt     |   5 +
 benchmarks/engines/busyring/arbor/ring.cpp    | 118 ++++++++----------
 install-local.sh                              |   4 +-
 systems/juwels-gpu.sh                         |  36 ++----
 4 files changed, 66 insertions(+), 97 deletions(-)

diff --git a/benchmarks/engines/busyring/arbor/CMakeLists.txt b/benchmarks/engines/busyring/arbor/CMakeLists.txt
index b90ee9b..a6abc38 100644
--- a/benchmarks/engines/busyring/arbor/CMakeLists.txt
+++ b/benchmarks/engines/busyring/arbor/CMakeLists.txt
@@ -1,12 +1,17 @@
 cmake_minimum_required(VERSION 3.9)
 project(arbor-ring LANGUAGES CXX)
 
+find_package(CUDAToolkit)
 set (CMAKE_CXX_STANDARD 17)
 
+enable_language(CUDA)
+
 find_package(arbor REQUIRED)
 
 add_executable(ring ring.cpp)
+target_link_libraries(ring PRIVATE ${CUDA_LIBRARIES})
 target_link_libraries(ring PRIVATE arbor::arbor arbor::arborenv)
+
 target_include_directories(ring PRIVATE ../../../../common/cpp/include)
 
 set_target_properties(ring PROPERTIES OUTPUT_NAME arbor-busyring)
diff --git a/benchmarks/engines/busyring/arbor/ring.cpp b/benchmarks/engines/busyring/arbor/ring.cpp
index d3a0bfa..3f453b1 100644
--- a/benchmarks/engines/busyring/arbor/ring.cpp
+++ b/benchmarks/engines/busyring/arbor/ring.cpp
@@ -16,9 +16,11 @@
 #include <arbor/recipe.hpp>
 #include <arbor/version.hpp>
 
-#include <arborenv/concurrency.hpp>
+#include <arborenv/default_env.hpp>
 #include <arborenv/gpu_env.hpp>
 
+#include <arborio/label_parse.hpp>
+
 #include "parameters.hpp"
 
 #ifdef ARB_MPI_ENABLED
@@ -34,6 +36,8 @@ using arb::cell_kind;
 using arb::time_type;
 using arb::cable_probe_membrane_voltage;
 
+using namespace arborio::literals;
+
 // Writes voltage trace as a json file.
 void write_trace_json(std::string fname, const arb::trace_data<double>& trace);
 
@@ -46,12 +50,10 @@ class ring_recipe: public arb::recipe {
     ring_recipe(ring_params params):
         num_cells_(params.num_cells),
         min_delay_(params.min_delay),
-        params_(params),
-        cat(arb::global_allen_catalogue())
+        params_(params)
     {
-        cat.import(arb::global_default_catalogue(), "");
         gprop.default_parameters = arb::neuron_parameter_defaults;
-        gprop.catalogue = &cat;
+        gprop.catalogue.import(arb::global_allen_catalogue(), "");
 
         if (params.cell.complex_cell) {
             gprop.default_parameters.reversal_potential_method["ca"] = "nernst/ca";
@@ -62,10 +64,9 @@ class ring_recipe: public arb::recipe {
         }
     }
 
-    cell_size_type num_cells() const override {
-        return num_cells_;
-    }
-
+    std::any get_global_properties(cell_kind kind) const override { return gprop; }
+    cell_size_type num_cells() const override { return num_cells_; }
+    cell_kind get_cell_kind(cell_gid_type gid) const override { return cell_kind::cable; }
     arb::util::unique_any get_cell_description(cell_gid_type gid) const override {
         if (params_.cell.complex_cell) {
             return complex_cell(gid, params_.cell);
@@ -73,24 +74,6 @@ class ring_recipe: public arb::recipe {
         return branch_cell(gid, params_.cell);
     }
 
-    cell_kind get_cell_kind(cell_gid_type gid) const override {
-        return cell_kind::cable;
-    }
-
-    // Each cell has one spike detector (at the soma).
-    cell_size_type num_sources(cell_gid_type gid) const override {
-        return 1;
-    }
-
-    // The cell has one target synapse, which will be connected to cell gid-1.
-    cell_size_type num_targets(cell_gid_type gid) const override {
-        return params_.cell.synapses;
-    }
-
-    std::any get_global_properties(cell_kind kind) const override {
-        return gprop;
-    }
-
     // Each cell has one incoming connection, from cell with gid-1,
     // and fan_in-1 random connections with very low weight.
     std::vector<arb::cell_connection> connections_on(cell_gid_type gid) const override {
@@ -103,7 +86,7 @@ class ring_recipe: public arb::recipe {
         const auto group_start = s*group;
         const auto group_end = std::min(group_start+s, num_cells_);
         cell_gid_type src = gid==group_start? group_end-1: gid-1;
-        cons.push_back(arb::cell_connection({src, 0}, {gid, 0}, event_weight_, min_delay_));
+        cons.push_back(arb::cell_connection({src, "detector"}, {"p_syn"}, event_weight_, min_delay_));
 
         // Used to pick source cell for a connection.
         std::uniform_int_distribution<cell_gid_type> dist(0, num_cells_-2);
@@ -116,24 +99,20 @@ class ring_recipe: public arb::recipe {
             src = dist(src_gen);
             if (src==gid) ++src;
             const float delay = min_delay_+delay_dist(src_gen);
-            //const float delay = min_delay_;
             cons.push_back(
-                arb::cell_connection({src, 0}, {gid, i}, 0.f, delay));
+                arb::cell_connection({src, "detector"}, {"p_syn"}, 0.f, delay));
         }
-
         return cons;
     }
 
     // Return one event generator on the first cell of each ring.
     // This generates a single event that will kick start the spiking on the sub-ring.
     std::vector<arb::event_generator> event_generators(cell_gid_type gid) const override {
-        std::vector<arb::event_generator> gens;
         if (gid%params_.ring_size == 0) {
-            gens.push_back(
-                arb::explicit_generator(
-                    arb::pse_vector{{{gid, 0}, 1.0, event_weight_}}));
+            return {arb::explicit_generator({{{"p_syn"}, 1.0, event_weight_}})};
+        } else {
+            return {};
         }
-        return gens;
     }
 
     std::vector<arb::probe_info> get_probes(cell_gid_type gid) const override {
@@ -149,7 +128,6 @@ class ring_recipe: public arb::recipe {
     float event_weight_ = 0.01;
 
     arb::cable_cell_global_properties gprop;
-    arb::mechanism_catalogue cat;
 };
 
 struct cell_stats {
@@ -203,12 +181,7 @@ int main(int argc, char** argv) {
         auto params = read_options(argc, argv);
 
         arb::proc_allocation resources;
-        if (auto nt = arbenv::get_env_num_threads()) {
-            resources.num_threads = nt;
-        }
-        else {
-            resources.num_threads = arbenv::thread_concurrency();
-        }
+        resources.num_threads = arbenv::default_concurrency();
 
 #ifdef ARB_MPI_ENABLED
         arbenv::with_mpi guard(argc, argv, false);
@@ -411,38 +384,43 @@ arb::cable_cell complex_cell (arb::cell_gid_type gid, const cell_parameters& par
        dict.set("synapses",  arb::ls::uniform(arb::reg::all(), 0, params.synapses-2, gid));
     }
 
+    auto soma = "soma"_lab;
+    auto dend = "dend"_lab;
+    auto cntr = "center"_lab;
+    auto syns = "synapses"_lab;
+
     arb::decor decor;
 
     decor.paint(all(), arb::init_reversal_potential{"k",  -107.0});
     decor.paint(all(), arb::init_reversal_potential{"na", 53.0});
 
-    decor.paint("\"soma\"", arb::axial_resistivity{133.577});
-    decor.paint("\"soma\"", arb::membrane_capacitance{4.21567e-2});
+    decor.paint(soma, arb::axial_resistivity{133.577});
+    decor.paint(soma, arb::membrane_capacitance{4.21567e-2});
 
-    decor.paint("\"dend\"", arb::axial_resistivity{68.355});
-    decor.paint("\"dend\"", arb::membrane_capacitance{2.11248e-2});
+    decor.paint(dend, arb::axial_resistivity{68.355});
+    decor.paint(dend, arb::membrane_capacitance{2.11248e-2});
 
-    decor.paint("\"soma\"", mech("pas").set("g", 0.000119174).set("e", -76.4024));
-    decor.paint("\"soma\"", mech("NaV").set("gbar", 0.0499779));
-    decor.paint("\"soma\"", mech("SK").set("gbar", 0.000733676));
-    decor.paint("\"soma\"", mech("Kv3_1").set("gbar", 0.186718));
-    decor.paint("\"soma\"", mech("Ca_HVA").set("gbar", 9.96973e-05));
-    decor.paint("\"soma\"", mech("Ca_LVA").set("gbar", 0.00344495));
-    decor.paint("\"soma\"", mech("CaDynamics").set("gamma", 0.0177038).set("decay", 42.2507));
-    decor.paint("\"soma\"", mech("Ih").set("gbar", 1.07608e-07));
+    decor.paint(soma, arb::density("pas",        {{"g", 0.000119174}, {"e", -76.4024}}));
+    decor.paint(soma, arb::density("NaV",        {{"gbar", 0.0499779}}));
+    decor.paint(soma, arb::density("SK",         {{"gbar", 0.000733676}}));
+    decor.paint(soma, arb::density("Kv3_1",      {{"gbar", 0.186718}}));
+    decor.paint(soma, arb::density("Ca_HVA",     {{"gbar", 9.96973e-05}}));
+    decor.paint(soma, arb::density("Ca_LVA",     {{"gbar", 0.00344495}}));
+    decor.paint(soma, arb::density("CaDynamics", {{"gamma", 0.0177038}, {"decay", 42.2507}}));
+    decor.paint(soma, arb::density("Ih",         {{"gbar", 1.07608e-07}}));
 
-    decor.paint("\"dend\"", mech("pas").set("g", 9.57001e-05).set("e", -88.2554));
-    decor.paint("\"dend\"", mech("NaV").set("gbar", 0.0472215));
-    decor.paint("\"dend\"", mech("Kv3_1").set("gbar", 0.186859));
-    decor.paint("\"dend\"", mech("Im_v2").set("gbar", 0.00132163));
-    decor.paint("\"dend\"", mech("Ih").set("gbar", 9.18815e-06));
+    decor.paint(dend, arb::density("pas",   {{"g", 9.57001e-05}, {"e", -88.2554}}));
+    decor.paint(dend, arb::density("NaV",   {{"gbar", 0.0472215}}));
+    decor.paint(dend, arb::density("Kv3_1", {{"gbar", 0.186859}}));
+    decor.paint(dend, arb::density("Im_v2", {{"gbar", 0.00132163}}));
+    decor.paint(dend, arb::density("Ih",    {{"gbar", 9.18815e-06}}));
 
-    decor.place("\"center\"", mech("expsyn"));
+    decor.place(cntr, arb::synapse("expsyn"), "p_syn");
     if (params.synapses>1) {
-       decor.place("\"synapses\"", "expsyn");
+        decor.place(syns, arb::synapse("expsyn"), "s_syn");
     }
 
-    decor.place("\"center\"", arb::threshold_detector{-20.0});
+    decor.place(cntr, arb::threshold_detector{-20.0}, "detector");
 
     decor.set_default(arb::cv_policy_every_segment());
 
@@ -500,6 +478,10 @@ arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& param
 
     arb::label_dict labels;
 
+    auto soma = "soma"_lab;
+    auto dnds = "dendrites"_lab;
+    auto syns = "synapses"_lab;
+
     using arb::reg::tagged;
     labels.set("soma",      tagged(1));
     labels.set("dendrites", join(tagged(3), tagged(4)));
@@ -509,19 +491,19 @@ arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& param
 
     arb::decor decor;
 
-    decor.paint("\"soma\"", "hh");
-    decor.paint("\"dendrites\"", "pas");
+    decor.paint(soma, arb::density{"hh"});
+    decor.paint(dnds, arb::density{"pas"});
     decor.set_default(arb::axial_resistivity{100}); // [Ω·cm]
 
     // Add spike threshold detector at the soma.
-    decor.place(arb::mlocation{0,0}, arb::threshold_detector{10});
+    decor.place(arb::mlocation{0,0}, arb::threshold_detector{10}, "detector");
 
     // Add a synapse to proximal end of first dendrite.
-    decor.place(arb::mlocation{1, 0}, "expsyn");
+    decor.place(arb::mlocation{1, 0}, arb::synapse{"expsyn"}, "p_syn");
 
     // Add additional synapses that will not be connected to anything.
     if (params.synapses>1) {
-        decor.place("\"synapses\"", "expsyn");
+        decor.place(syns, arb::synapse{"expsyn"}, "s_syn");
     }
 
     // Make a CV between every sample in the sample tree.
diff --git a/install-local.sh b/install-local.sh
index 877cbb0..971b973 100755
--- a/install-local.sh
+++ b/install-local.sh
@@ -194,8 +194,8 @@ fi
 
 # Build simulator targets.
 
-export CC="$ns_cc"
-export CXX="$ns_cxx"
+# export CC="$ns_cc"
+# export CXX="$ns_cxx"
 
 [ "$ns_build_arbor"  = true ] && echo && source "$ns_base_path/scripts/build_arbor.sh"
 cd "$ns_base_path"
diff --git a/systems/juwels-gpu.sh b/systems/juwels-gpu.sh
index ceb9c17..625144f 100644
--- a/systems/juwels-gpu.sh
+++ b/systems/juwels-gpu.sh
@@ -3,47 +3,29 @@
 # record system name
 ns_sysname="juwels-gpu"
 
-# set up environment for building on the multicore part of juwels
-module purge
-module use /gpfs/software/juwels/otherstages/
-module load Stages/2019a
+# set up environment for building on the booster part of juwels
+ml CMake/3.21.1 Python/3.9.6 NVHPC/22.1 ParaStationMPI/5.5.0-1
+ml Python/3.9.6 mpi4py/3.1.3
 
-module load GCC
-module load MVAPICH2
-module load CMake
+ns_validate=disable
 
-module load CUDA
-export MV2_ENABLE_AFFINITY=0
-export MV2_USE_GPUDIRECT_GDRCOPY=0
-
-module load Python/3.6.8
-module load SciPy-Stack/2019a-Python-3.6.8
 ns_python=$(which python3)
-
-# for (core)neuron
-module load mpi4py/3.0.1-Python-3.6.8
-module load flex/2.6.4
-
-# for validation tests
-module load netCDF/4.6.3-serial
-
-### compilation options ###
 ns_cc=$(which mpicc)
 ns_cxx=$(which mpicxx)
 ns_with_mpi=ON
 
 ns_arb_gpu=cuda
-ns_arb_arch=skylake-avx512
+ns_arb_vectorize=ON
+ns_arb_arch=native
 
 ns_arb_branch=master
 
 ns_makej=20
 
-### benchmark execution options ###
 ns_threads_per_core=2
-ns_cores_per_socket=20
-ns_sockets=1
-ns_threads_per_socket=20
+ns_cores_per_socket=24
+ns_sockets=2
+ns_threads_per_socket=24
 
 # activate budget via jutil env activate -p <cproject> -A <budget> before running the benchmark
 run_with_mpi() {

From 46c4e9fe393fbf6cc748ed0b0fc36bc1ccca89ce Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Wed, 16 Mar 2022 09:51:57 +0100
Subject: [PATCH 02/25] add booster, bump arbor

---
 systems/{juwels-gpu.sh => juwels-booster.sh} | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename systems/{juwels-gpu.sh => juwels-booster.sh} (100%)

diff --git a/systems/juwels-gpu.sh b/systems/juwels-booster.sh
similarity index 100%
rename from systems/juwels-gpu.sh
rename to systems/juwels-booster.sh

From dcb3e4cb8c96b86c286614a80472fc1c49b7b727 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Wed, 16 Mar 2022 09:55:25 +0100
Subject: [PATCH 03/25] Bump Arbor, add jwb.

---
 benchmarks/engines/busyring/arbor/ring.cpp | 125 +++++++++------------
 systems/juwels-booster.sh                  |  46 +++-----
 2 files changed, 70 insertions(+), 101 deletions(-)

diff --git a/benchmarks/engines/busyring/arbor/ring.cpp b/benchmarks/engines/busyring/arbor/ring.cpp
index d3a0bfa..f2984cf 100644
--- a/benchmarks/engines/busyring/arbor/ring.cpp
+++ b/benchmarks/engines/busyring/arbor/ring.cpp
@@ -1,6 +1,11 @@
 #include <fstream>
 #include <iomanip>
 #include <iostream>
+#include <sstream>
+#include <algorithm>
+#include <array>
+#include <cstring>
+#include <functional>
 
 #include <nlohmann/json.hpp>
 
@@ -16,9 +21,11 @@
 #include <arbor/recipe.hpp>
 #include <arbor/version.hpp>
 
-#include <arborenv/concurrency.hpp>
+#include <arborenv/default_env.hpp>
 #include <arborenv/gpu_env.hpp>
 
+#include <arborio/label_parse.hpp>
+
 #include "parameters.hpp"
 
 #ifdef ARB_MPI_ENABLED
@@ -34,6 +41,8 @@ using arb::cell_kind;
 using arb::time_type;
 using arb::cable_probe_membrane_voltage;
 
+using namespace arborio::literals;
+
 // Writes voltage trace as a json file.
 void write_trace_json(std::string fname, const arb::trace_data<double>& trace);
 
@@ -46,12 +55,10 @@ class ring_recipe: public arb::recipe {
     ring_recipe(ring_params params):
         num_cells_(params.num_cells),
         min_delay_(params.min_delay),
-        params_(params),
-        cat(arb::global_allen_catalogue())
+        params_(params)
     {
-        cat.import(arb::global_default_catalogue(), "");
         gprop.default_parameters = arb::neuron_parameter_defaults;
-        gprop.catalogue = &cat;
+        gprop.catalogue.import(arb::global_allen_catalogue(), "");
 
         if (params.cell.complex_cell) {
             gprop.default_parameters.reversal_potential_method["ca"] = "nernst/ca";
@@ -62,10 +69,9 @@ class ring_recipe: public arb::recipe {
         }
     }
 
-    cell_size_type num_cells() const override {
-        return num_cells_;
-    }
-
+    std::any get_global_properties(cell_kind kind) const override { return gprop; }
+    cell_size_type num_cells() const override { return num_cells_; }
+    cell_kind get_cell_kind(cell_gid_type gid) const override { return cell_kind::cable; }
     arb::util::unique_any get_cell_description(cell_gid_type gid) const override {
         if (params_.cell.complex_cell) {
             return complex_cell(gid, params_.cell);
@@ -73,24 +79,6 @@ class ring_recipe: public arb::recipe {
         return branch_cell(gid, params_.cell);
     }
 
-    cell_kind get_cell_kind(cell_gid_type gid) const override {
-        return cell_kind::cable;
-    }
-
-    // Each cell has one spike detector (at the soma).
-    cell_size_type num_sources(cell_gid_type gid) const override {
-        return 1;
-    }
-
-    // The cell has one target synapse, which will be connected to cell gid-1.
-    cell_size_type num_targets(cell_gid_type gid) const override {
-        return params_.cell.synapses;
-    }
-
-    std::any get_global_properties(cell_kind kind) const override {
-        return gprop;
-    }
-
     // Each cell has one incoming connection, from cell with gid-1,
     // and fan_in-1 random connections with very low weight.
     std::vector<arb::cell_connection> connections_on(cell_gid_type gid) const override {
@@ -103,7 +91,7 @@ class ring_recipe: public arb::recipe {
         const auto group_start = s*group;
         const auto group_end = std::min(group_start+s, num_cells_);
         cell_gid_type src = gid==group_start? group_end-1: gid-1;
-        cons.push_back(arb::cell_connection({src, 0}, {gid, 0}, event_weight_, min_delay_));
+        cons.push_back(arb::cell_connection({src, "detector"}, {"p_syn"}, event_weight_, min_delay_));
 
         // Used to pick source cell for a connection.
         std::uniform_int_distribution<cell_gid_type> dist(0, num_cells_-2);
@@ -116,24 +104,20 @@ class ring_recipe: public arb::recipe {
             src = dist(src_gen);
             if (src==gid) ++src;
             const float delay = min_delay_+delay_dist(src_gen);
-            //const float delay = min_delay_;
             cons.push_back(
-                arb::cell_connection({src, 0}, {gid, i}, 0.f, delay));
+                arb::cell_connection({src, "detector"}, {"p_syn"}, 0.f, delay));
         }
-
         return cons;
     }
 
     // Return one event generator on the first cell of each ring.
     // This generates a single event that will kick start the spiking on the sub-ring.
     std::vector<arb::event_generator> event_generators(cell_gid_type gid) const override {
-        std::vector<arb::event_generator> gens;
         if (gid%params_.ring_size == 0) {
-            gens.push_back(
-                arb::explicit_generator(
-                    arb::pse_vector{{{gid, 0}, 1.0, event_weight_}}));
+            return {arb::explicit_generator({{{"p_syn"}, 1.0, event_weight_}})};
+        } else {
+            return {};
         }
-        return gens;
     }
 
     std::vector<arb::probe_info> get_probes(cell_gid_type gid) const override {
@@ -149,7 +133,6 @@ class ring_recipe: public arb::recipe {
     float event_weight_ = 0.01;
 
     arb::cable_cell_global_properties gprop;
-    arb::mechanism_catalogue cat;
 };
 
 struct cell_stats {
@@ -203,12 +186,7 @@ int main(int argc, char** argv) {
         auto params = read_options(argc, argv);
 
         arb::proc_allocation resources;
-        if (auto nt = arbenv::get_env_num_threads()) {
-            resources.num_threads = nt;
-        }
-        else {
-            resources.num_threads = arbenv::thread_concurrency();
-        }
+        resources.num_threads = arbenv::default_concurrency();
 
 #ifdef ARB_MPI_ENABLED
         arbenv::with_mpi guard(argc, argv, false);
@@ -411,38 +389,43 @@ arb::cable_cell complex_cell (arb::cell_gid_type gid, const cell_parameters& par
        dict.set("synapses",  arb::ls::uniform(arb::reg::all(), 0, params.synapses-2, gid));
     }
 
+    auto soma = "soma"_lab;
+    auto dend = "dend"_lab;
+    auto cntr = "center"_lab;
+    auto syns = "synapses"_lab;
+
     arb::decor decor;
 
     decor.paint(all(), arb::init_reversal_potential{"k",  -107.0});
     decor.paint(all(), arb::init_reversal_potential{"na", 53.0});
 
-    decor.paint("\"soma\"", arb::axial_resistivity{133.577});
-    decor.paint("\"soma\"", arb::membrane_capacitance{4.21567e-2});
+    decor.paint(soma, arb::axial_resistivity{133.577});
+    decor.paint(soma, arb::membrane_capacitance{4.21567e-2});
 
-    decor.paint("\"dend\"", arb::axial_resistivity{68.355});
-    decor.paint("\"dend\"", arb::membrane_capacitance{2.11248e-2});
+    decor.paint(dend, arb::axial_resistivity{68.355});
+    decor.paint(dend, arb::membrane_capacitance{2.11248e-2});
 
-    decor.paint("\"soma\"", mech("pas").set("g", 0.000119174).set("e", -76.4024));
-    decor.paint("\"soma\"", mech("NaV").set("gbar", 0.0499779));
-    decor.paint("\"soma\"", mech("SK").set("gbar", 0.000733676));
-    decor.paint("\"soma\"", mech("Kv3_1").set("gbar", 0.186718));
-    decor.paint("\"soma\"", mech("Ca_HVA").set("gbar", 9.96973e-05));
-    decor.paint("\"soma\"", mech("Ca_LVA").set("gbar", 0.00344495));
-    decor.paint("\"soma\"", mech("CaDynamics").set("gamma", 0.0177038).set("decay", 42.2507));
-    decor.paint("\"soma\"", mech("Ih").set("gbar", 1.07608e-07));
+    decor.paint(soma, arb::density("pas/e=-76.4024", {{"g", 0.000119174}}));
+    decor.paint(soma, arb::density("NaV",            {{"gbar", 0.0499779}}));
+    decor.paint(soma, arb::density("SK",             {{"gbar", 0.000733676}}));
+    decor.paint(soma, arb::density("Kv3_1",          {{"gbar", 0.186718}}));
+    decor.paint(soma, arb::density("Ca_HVA",         {{"gbar", 9.96973e-05}}));
+    decor.paint(soma, arb::density("Ca_LVA",         {{"gbar", 0.00344495}}));
+    decor.paint(soma, arb::density("CaDynamics",     {{"gamma", 0.0177038}, {"decay", 42.2507}}));
+    decor.paint(soma, arb::density("Ih",             {{"gbar", 1.07608e-07}}));
 
-    decor.paint("\"dend\"", mech("pas").set("g", 9.57001e-05).set("e", -88.2554));
-    decor.paint("\"dend\"", mech("NaV").set("gbar", 0.0472215));
-    decor.paint("\"dend\"", mech("Kv3_1").set("gbar", 0.186859));
-    decor.paint("\"dend\"", mech("Im_v2").set("gbar", 0.00132163));
-    decor.paint("\"dend\"", mech("Ih").set("gbar", 9.18815e-06));
+    decor.paint(dend, arb::density("pas/e=-88.2554", {{"g", 9.57001e-05}}));
+    decor.paint(dend, arb::density("NaV",            {{"gbar", 0.0472215}}));
+    decor.paint(dend, arb::density("Kv3_1",          {{"gbar", 0.186859}}));
+    decor.paint(dend, arb::density("Im_v2",          {{"gbar", 0.00132163}}));
+    decor.paint(dend, arb::density("Ih",             {{"gbar", 9.18815e-06}}));
 
-    decor.place("\"center\"", mech("expsyn"));
+    decor.place(cntr, arb::synapse("expsyn"), "p_syn");
     if (params.synapses>1) {
-       decor.place("\"synapses\"", "expsyn");
+        decor.place(syns, arb::synapse("expsyn"), "s_syn");
     }
 
-    decor.place("\"center\"", arb::threshold_detector{-20.0});
+    decor.place(cntr, arb::threshold_detector{-20.0}, "detector");
 
     decor.set_default(arb::cv_policy_every_segment());
 
@@ -500,6 +483,10 @@ arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& param
 
     arb::label_dict labels;
 
+    auto soma = "soma"_lab;
+    auto dnds = "dendrites"_lab;
+    auto syns = "synapses"_lab;
+
     using arb::reg::tagged;
     labels.set("soma",      tagged(1));
     labels.set("dendrites", join(tagged(3), tagged(4)));
@@ -509,19 +496,19 @@ arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& param
 
     arb::decor decor;
 
-    decor.paint("\"soma\"", "hh");
-    decor.paint("\"dendrites\"", "pas");
+    decor.paint(soma, arb::density{"hh"});
+    decor.paint(dnds, arb::density{"pas"});
     decor.set_default(arb::axial_resistivity{100}); // [Ω·cm]
 
     // Add spike threshold detector at the soma.
-    decor.place(arb::mlocation{0,0}, arb::threshold_detector{10});
+    decor.place(arb::mlocation{0,0}, arb::threshold_detector{10}, "detector");
 
-    // Add a synapse to proximal end of first dendrite.
-    decor.place(arb::mlocation{1, 0}, "expsyn");
+    // Add a synapse to proximal end of fqirst dendrite.
+    decor.place(arb::mlocation{1, 0}, arb::synapse{"expsyn"}, "p_syn");
 
     // Add additional synapses that will not be connected to anything.
     if (params.synapses>1) {
-        decor.place("\"synapses\"", "expsyn");
+        decor.place(syns, arb::synapse{"expsyn"}, "s_syn");
     }
 
     // Make a CV between every sample in the sample tree.
diff --git a/systems/juwels-booster.sh b/systems/juwels-booster.sh
index ceb9c17..28855e6 100644
--- a/systems/juwels-booster.sh
+++ b/systems/juwels-booster.sh
@@ -1,54 +1,36 @@
 ### environment ###
 
-# record system name
-ns_sysname="juwels-gpu"
+# As of March 2022
 
-# set up environment for building on the multicore part of juwels
-module purge
-module use /gpfs/software/juwels/otherstages/
-module load Stages/2019a
+# record system name
+ns_sysname="juwels-booster"
 
-module load GCC
-module load MVAPICH2
-module load CMake
+# set up environment for building on the booster part of juwels
+ml CMake/3.21.1 Python/3.9.6 NVHPC/22.1 ParaStationMPI/5.5.0-1
+ml Python/3.9.6 mpi4py/3.1.3
 
-module load CUDA
-export MV2_ENABLE_AFFINITY=0
-export MV2_USE_GPUDIRECT_GDRCOPY=0
+ns_validate=disable
 
-module load Python/3.6.8
-module load SciPy-Stack/2019a-Python-3.6.8
 ns_python=$(which python3)
-
-# for (core)neuron
-module load mpi4py/3.0.1-Python-3.6.8
-module load flex/2.6.4
-
-# for validation tests
-module load netCDF/4.6.3-serial
-
-### compilation options ###
 ns_cc=$(which mpicc)
 ns_cxx=$(which mpicxx)
 ns_with_mpi=ON
 
 ns_arb_gpu=cuda
-ns_arb_arch=skylake-avx512
+ns_arb_vectorize=ON
+ns_arb_arch=native
 
 ns_arb_branch=master
 
 ns_makej=20
 
-### benchmark execution options ###
 ns_threads_per_core=2
-ns_cores_per_socket=20
-ns_sockets=1
-ns_threads_per_socket=20
+ns_cores_per_socket=24
+ns_sockets=2
+ns_threads_per_socket=24
 
 # activate budget via jutil env activate -p <cproject> -A <budget> before running the benchmark
 run_with_mpi() {
-    export ARB_NUM_THREADS=$ns_threads_per_socket
-    export OMP_NUM_THREADS=$ns_threads_per_socket
-    echo srun -n$ns_sockets -N1 -c$ns_threads_per_socket "${@}"
-    srun -n$ns_sockets -N1 -c$ns_threads_per_socket "${@}"
+    echo srun "${@}"
+    srun "${@}"
 }

From d5529d88e8eca35cdd19320717630180da396aff Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Wed, 16 Mar 2022 10:16:13 +0100
Subject: [PATCH 04/25] Add CI.

---
 .github/workflows/main.yml | 41 ++++++++++++++++++++++++++++++++++++++
 systems/gh.sh              | 29 +++++++++++++++++++++++++++
 2 files changed, 70 insertions(+)
 create mode 100644 .github/workflows/main.yml
 create mode 100644 systems/gh.sh

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
new file mode 100644
index 0000000..4a294f7
--- /dev/null
+++ b/.github/workflows/main.yml
@@ -0,0 +1,41 @@
+name: Test
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  testallconfigs:
+    name: "Tests across OSes, versions, compilers, and build configs."
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      matrix:
+        config:
+        - {
+            name:  "Linux Min GCC",
+            os:    "ubuntu-22.04",
+            cc:    "gcc-10",
+            cxx:   "g++-10",
+            cmake: "3.22.x",
+          }
+    env:
+        CC:         ${{ matrix.config.cc }}
+        CXX:        ${{ matrix.config.cxx }}
+    steps:
+      - name: "Linux: get clang/gcc, libxml2"
+        if: ${{ startsWith(matrix.config.os, 'ubuntu') }}
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y g++-10
+      - name: Set up cmake
+        uses: jwlawson/actions-setup-cmake@v1.12
+        with:
+          cmake-version: ${{ matrix.config.cmake }}
+      - name: Install
+        run: |
+          ./install-local arbor --env=systems/gh.sh
+      - name: Run
+        run: |
+          ./run-bench.sh arbor --config=small
diff --git a/systems/gh.sh b/systems/gh.sh
new file mode 100644
index 0000000..d68e922
--- /dev/null
+++ b/systems/gh.sh
@@ -0,0 +1,29 @@
+### environment ###
+
+# record system name
+ns_sysname="GH"
+
+### compilation options ###
+# -DPYTHON_EXECUTABLE=/usr/local/bin/python3.8
+ns_cc="gcc"
+ns_cxx="g++"
+ns_with_mpi=OFF
+ns_arb_arch=native
+
+ns_arb_git_repo='https://github.com/arbor-sim/arbor.git'
+ns_arb_branch='master'
+
+ns_makej=4
+
+### benchmark execution options ###
+ns_threads_per_core=2
+ns_cores_per_socket=12
+ns_sockets=1
+ns_threads_per_socket=2
+
+run_with_mpi() {
+    export ARB_NUM_THREADS=$ns_threads_per_socket
+    export OMP_NUM_THREADS=$ns_threads_per_socket
+    echo ${@}
+    ${@}
+}

From e32658a6521165113851a1f5fa11ae823303c371 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Mon, 21 Mar 2022 14:07:38 +0100
Subject: [PATCH 05/25] Update main.yml

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 4a294f7..e3220c8 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -15,7 +15,7 @@ jobs:
         config:
         - {
             name:  "Linux Min GCC",
-            os:    "ubuntu-22.04",
+            os:    "ubuntu-20.04",
             cc:    "gcc-10",
             cxx:   "g++-10",
             cmake: "3.22.x",

From 5e48cddba68d7dbc302a11d1439ae9b3e7dea1c9 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Mon, 21 Mar 2022 14:13:06 +0100
Subject: [PATCH 06/25] Update main.yml

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index e3220c8..52d6a1f 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -35,7 +35,7 @@ jobs:
           cmake-version: ${{ matrix.config.cmake }}
       - name: Install
         run: |
-          ./install-local arbor --env=systems/gh.sh
+          ./install-local.sh arbor --env=systems/gh.sh
       - name: Run
         run: |
           ./run-bench.sh arbor --config=small

From 295390a3b367dc9a8a19ff1e4844aabf4a33a67d Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Mon, 21 Mar 2022 14:14:19 +0100
Subject: [PATCH 07/25] Update main.yml

---
 .github/workflows/main.yml | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 52d6a1f..c948ce5 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -35,6 +35,8 @@ jobs:
           cmake-version: ${{ matrix.config.cmake }}
       - name: Install
         run: |
+           pwd
+           ls
           ./install-local.sh arbor --env=systems/gh.sh
       - name: Run
         run: |

From 3e3174ca72e964dcc20ec814c7423365351c7b2f Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Mon, 21 Mar 2022 14:15:09 +0100
Subject: [PATCH 08/25] Update main.yml

---
 .github/workflows/main.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index c948ce5..0dc7603 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -37,7 +37,7 @@ jobs:
         run: |
            pwd
            ls
-          ./install-local.sh arbor --env=systems/gh.sh
+           ./install-local.sh arbor --env=systems/gh.sh
       - name: Run
         run: |
           ./run-bench.sh arbor --config=small

From 33d5a7d4661702aea76914c0e53cbe20365759f3 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Mon, 21 Mar 2022 14:17:43 +0100
Subject: [PATCH 09/25] Update main.yml

---
 .github/workflows/main.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 0dc7603..27a7a20 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -33,6 +33,10 @@ jobs:
         uses: jwlawson/actions-setup-cmake@v1.12
         with:
           cmake-version: ${{ matrix.config.cmake }}
+      - name: Clone
+        uses: actions/checkout@v2
+        with:
+          submodules: recursive
       - name: Install
         run: |
            pwd

From a1185cd6e77a18de4f274f19ec17534e8a8bd74d Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Mon, 21 Mar 2022 14:23:15 +0100
Subject: [PATCH 10/25] Update main.yml

---
 .github/workflows/main.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 27a7a20..3d730d4 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -41,7 +41,8 @@ jobs:
         run: |
            pwd
            ls
-           ./install-local.sh arbor --env=systems/gh.sh
+           ./install-local.sh arbor --env=systems/gh.sh || echo 'fail'
+           cat /home/runner/work/nsuite/nsuite/build/log_arbor
       - name: Run
         run: |
           ./run-bench.sh arbor --config=small

From ff713293a4aac518469be52a7b5d245a37382d88 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Mon, 21 Mar 2022 14:31:44 +0100
Subject: [PATCH 11/25] Drop CUDA.

---
 .github/workflows/main.yml                       | 2 +-
 benchmarks/engines/busyring/arbor/CMakeLists.txt | 3 ---
 systems/gh.sh                                    | 1 +
 3 files changed, 2 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 4a294f7..c2eb01c 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -29,7 +29,7 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install -y g++-10
-      - name: Set up cmake
+      - name: Set up CMake
         uses: jwlawson/actions-setup-cmake@v1.12
         with:
           cmake-version: ${{ matrix.config.cmake }}
diff --git a/benchmarks/engines/busyring/arbor/CMakeLists.txt b/benchmarks/engines/busyring/arbor/CMakeLists.txt
index a6abc38..49890c7 100644
--- a/benchmarks/engines/busyring/arbor/CMakeLists.txt
+++ b/benchmarks/engines/busyring/arbor/CMakeLists.txt
@@ -1,11 +1,8 @@
 cmake_minimum_required(VERSION 3.9)
 project(arbor-ring LANGUAGES CXX)
 
-find_package(CUDAToolkit)
 set (CMAKE_CXX_STANDARD 17)
 
-enable_language(CUDA)
-
 find_package(arbor REQUIRED)
 
 add_executable(ring ring.cpp)
diff --git a/systems/gh.sh b/systems/gh.sh
index d68e922..217f3ba 100644
--- a/systems/gh.sh
+++ b/systems/gh.sh
@@ -9,6 +9,7 @@ ns_cc="gcc"
 ns_cxx="g++"
 ns_with_mpi=OFF
 ns_arb_arch=native
+ns_arb_gpu=none
 
 ns_arb_git_repo='https://github.com/arbor-sim/arbor.git'
 ns_arb_branch='master'

From 43a1dbd405f132dc04195da9259c195b21449b10 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Mon, 21 Mar 2022 14:39:12 +0100
Subject: [PATCH 12/25] Do not validate. Ever.

---
 systems/gh.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/systems/gh.sh b/systems/gh.sh
index 217f3ba..f3f483a 100644
--- a/systems/gh.sh
+++ b/systems/gh.sh
@@ -15,13 +15,14 @@ ns_arb_git_repo='https://github.com/arbor-sim/arbor.git'
 ns_arb_branch='master'
 
 ns_makej=4
-
+ns_validate=disable
 ### benchmark execution options ###
 ns_threads_per_core=2
 ns_cores_per_socket=12
 ns_sockets=1
 ns_threads_per_socket=2
 
+
 run_with_mpi() {
     export ARB_NUM_THREADS=$ns_threads_per_socket
     export OMP_NUM_THREADS=$ns_threads_per_socket

From b89ddf049aedfb9ed73bb9ea170961be8889ed97 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Mon, 21 Mar 2022 14:44:21 +0100
Subject: [PATCH 13/25] Remove debug.

---
 .github/workflows/main.yml | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 3ca3793..393ddbd 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -39,10 +39,7 @@ jobs:
           submodules: recursive
       - name: Install
         run: |
-           pwd
-           ls
-           ./install-local.sh arbor --env=systems/gh.sh || echo 'fail'
-           cat /home/runner/work/nsuite/nsuite/build/log_arbor
+           ./install-local.sh arbor --env=systems/gh.sh
       - name: Run
         run: |
           ./run-bench.sh arbor --config=small

From 2a1969d362886f09d25bf82902403ff50d170328 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Wed, 27 Apr 2022 15:08:07 +0200
Subject: [PATCH 14/25] Fix review comment: export CC/CXX.

---
 install-local.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/install-local.sh b/install-local.sh
index 971b973..877cbb0 100755
--- a/install-local.sh
+++ b/install-local.sh
@@ -194,8 +194,8 @@ fi
 
 # Build simulator targets.
 
-# export CC="$ns_cc"
-# export CXX="$ns_cxx"
+export CC="$ns_cc"
+export CXX="$ns_cxx"
 
 [ "$ns_build_arbor"  = true ] && echo && source "$ns_base_path/scripts/build_arbor.sh"
 cd "$ns_base_path"

From 0f65be5a696db039d96ecea76b1e94cc3b0850a8 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Sat, 25 Jun 2022 08:25:23 +0200
Subject: [PATCH 15/25] Bump to 0.7pre.

---
 benchmarks/engines/busyring/arbor/ring.cpp | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/benchmarks/engines/busyring/arbor/ring.cpp b/benchmarks/engines/busyring/arbor/ring.cpp
index 98499f3..98fc190 100644
--- a/benchmarks/engines/busyring/arbor/ring.cpp
+++ b/benchmarks/engines/busyring/arbor/ring.cpp
@@ -218,13 +218,10 @@ int main(int argc, char** argv) {
         cell_stats stats(recipe);
         if (root) std::cout << stats << "\n";
 
-        //arb::partition_hint_map hints;
-        //hints[cell_kind::cable1d_neuron].cpu_group_size = 4;
-        //auto decomp = arb::partition_load_balance(recipe, context, hints);
         auto decomp = arb::partition_load_balance(recipe, context);
 
         // Construct the model.
-        arb::simulation sim(recipe, decomp, context);
+        arb::simulation sim(recipe, context, decomp);
 
         // Set up the probe that will measure voltage in the cell.
 

From ca977fad0da762cc515f7b3511e9e20b9acd3b30 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Tue, 9 Aug 2022 09:20:45 +0200
Subject: [PATCH 16/25] Driver spikes 1/ms.

---
 benchmarks/engines/busyring/arbor/ring.cpp | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/benchmarks/engines/busyring/arbor/ring.cpp b/benchmarks/engines/busyring/arbor/ring.cpp
index 98fc190..1752bdd 100644
--- a/benchmarks/engines/busyring/arbor/ring.cpp
+++ b/benchmarks/engines/busyring/arbor/ring.cpp
@@ -114,7 +114,8 @@ class ring_recipe: public arb::recipe {
     // This generates a single event that will kick start the spiking on the sub-ring.
     std::vector<arb::event_generator> event_generators(cell_gid_type gid) const override {
         if (gid%params_.ring_size == 0) {
-            return {arb::explicit_generator({{{"p_syn"}, 1.0, event_weight_}})};
+            return {arb::regular_generator({"p_syn"}, event_weight_, 1.0, 1.0)};
+            // return {arb::explicit_generator({{{"p_syn"}, 1.0, event_weight_}})};
         } else {
             return {};
         }
@@ -185,6 +186,8 @@ int main(int argc, char** argv) {
 
         auto params = read_options(argc, argv);
 
+        std::cout << "cell.complex=" << params.cell.complex_cell << '\n';
+
         arb::proc_allocation resources;
         resources.num_threads = arbenv::default_concurrency();
 
@@ -221,7 +224,7 @@ int main(int argc, char** argv) {
         auto decomp = arb::partition_load_balance(recipe, context);
 
         // Construct the model.
-        arb::simulation sim(recipe, context, decomp);
+        arb::simulation sim(recipe, decomp, context);
 
         // Set up the probe that will measure voltage in the cell.
 

From 3265ae2f8e9749e8f9780a4f95f54cf31058362a Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Tue, 9 Aug 2022 09:22:08 +0200
Subject: [PATCH 17/25] Clean-up.

---
 benchmarks/engines/busyring/arbor/ring.cpp | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/benchmarks/engines/busyring/arbor/ring.cpp b/benchmarks/engines/busyring/arbor/ring.cpp
index 1752bdd..39307bf 100644
--- a/benchmarks/engines/busyring/arbor/ring.cpp
+++ b/benchmarks/engines/busyring/arbor/ring.cpp
@@ -115,7 +115,6 @@ class ring_recipe: public arb::recipe {
     std::vector<arb::event_generator> event_generators(cell_gid_type gid) const override {
         if (gid%params_.ring_size == 0) {
             return {arb::regular_generator({"p_syn"}, event_weight_, 1.0, 1.0)};
-            // return {arb::explicit_generator({{{"p_syn"}, 1.0, event_weight_}})};
         } else {
             return {};
         }
@@ -186,8 +185,6 @@ int main(int argc, char** argv) {
 
         auto params = read_options(argc, argv);
 
-        std::cout << "cell.complex=" << params.cell.complex_cell << '\n';
-
         arb::proc_allocation resources;
         resources.num_threads = arbenv::default_concurrency();
 

From 63e4a3b566b787d743d8cea020cc36b1249f920e Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Tue, 9 Aug 2022 16:14:21 +0200
Subject: [PATCH 18/25] Clean-up.

---
 benchmarks/engines/busyring/arbor/ring.cpp | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/benchmarks/engines/busyring/arbor/ring.cpp b/benchmarks/engines/busyring/arbor/ring.cpp
index 39307bf..0b8aebe 100644
--- a/benchmarks/engines/busyring/arbor/ring.cpp
+++ b/benchmarks/engines/busyring/arbor/ring.cpp
@@ -218,10 +218,8 @@ int main(int argc, char** argv) {
         cell_stats stats(recipe);
         if (root) std::cout << stats << "\n";
 
-        auto decomp = arb::partition_load_balance(recipe, context);
-
         // Construct the model.
-        arb::simulation sim(recipe, decomp, context);
+        arb::simulation sim(recipe, context);
 
         // Set up the probe that will measure voltage in the cell.
 

From 480547eeaca4121ec2e9c88403c14bf4e9b75f2e Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Tue, 30 Aug 2022 14:45:57 +0200
Subject: [PATCH 19/25] Tweak spiking patterns.

---
 benchmarks/engines/busyring/arbor/ring.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/benchmarks/engines/busyring/arbor/ring.cpp b/benchmarks/engines/busyring/arbor/ring.cpp
index 0b8aebe..b882510 100644
--- a/benchmarks/engines/busyring/arbor/ring.cpp
+++ b/benchmarks/engines/busyring/arbor/ring.cpp
@@ -114,7 +114,7 @@ class ring_recipe: public arb::recipe {
     // This generates a single event that will kick start the spiking on the sub-ring.
     std::vector<arb::event_generator> event_generators(cell_gid_type gid) const override {
         if (gid%params_.ring_size == 0) {
-            return {arb::regular_generator({"p_syn"}, event_weight_, 1.0, 1.0)};
+            return {arb::regular_generator({"p_syn"}, event_weight_, 0.0, 1.0)};
         } else {
             return {};
         }
@@ -130,7 +130,7 @@ class ring_recipe: public arb::recipe {
     cell_size_type num_cells_;
     double min_delay_;
     ring_params params_;
-    float event_weight_ = 0.01;
+    float event_weight_ = 0.05;
 
     arb::cable_cell_global_properties gprop;
 };

From a40b5a1bbeb3ea8282e4953967a1f4c547117a1e Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Thu, 1 Sep 2022 09:15:54 +0200
Subject: [PATCH 20/25] Toggle spike recording.

---
 .../engines/busyring/arbor/parameters.hpp     |  2 ++
 benchmarks/engines/busyring/arbor/ring.cpp    | 24 ++++++++++---------
 2 files changed, 15 insertions(+), 11 deletions(-)

diff --git a/benchmarks/engines/busyring/arbor/parameters.hpp b/benchmarks/engines/busyring/arbor/parameters.hpp
index 124ecf1..1f286a7 100644
--- a/benchmarks/engines/busyring/arbor/parameters.hpp
+++ b/benchmarks/engines/busyring/arbor/parameters.hpp
@@ -38,6 +38,7 @@ struct ring_params {
     double duration = 100;
     double dt = 0.025;
     bool record_voltage = false;
+    bool record_spikes  = true;
     std::string odir = ".";
     cell_parameters cell;
 };
@@ -77,6 +78,7 @@ ring_params read_options(int argc, char** argv) {
     param_from_json(params.dt, "dt", json);
     param_from_json(params.min_delay, "min-delay", json);
     param_from_json(params.record_voltage, "record", json);
+    param_from_json(params.record_spikes,  "spikes", json);
     param_from_json(params.cell.complex_cell, "complex", json);
     param_from_json(params.cell.max_depth, "depth", json);
     param_from_json(params.cell.branch_probs, "branch-probs", json);
diff --git a/benchmarks/engines/busyring/arbor/ring.cpp b/benchmarks/engines/busyring/arbor/ring.cpp
index b882510..a70edd1 100644
--- a/benchmarks/engines/busyring/arbor/ring.cpp
+++ b/benchmarks/engines/busyring/arbor/ring.cpp
@@ -259,17 +259,19 @@ int main(int argc, char** argv) {
         if (root) {
             std::cout << "\n" << ns << " spikes generated at rate of "
                       << params.duration/ns << " ms between spikes\n";
-            std::ofstream fid(params.odir + "/" + params.name + "_spikes.gdf");
-            if (!fid.good()) {
-                std::cerr << "Warning: unable to open file spikes.gdf for spike output\n";
-            }
-            else {
-                char linebuf[45];
-                for (auto spike: recorded_spikes) {
-                    auto n = std::snprintf(
-                        linebuf, sizeof(linebuf), "%u %.4f\n",
-                        unsigned{spike.source.gid}, float(spike.time));
-                    fid.write(linebuf, n);
+            if (!recorded_spikes.empty()) {
+                std::ofstream fid(params.odir + "/" + params.name + "_spikes.gdf");
+                if (!fid.good()) {
+                    std::cerr << "Warning: unable to open file spikes.gdf for spike output\n";
+                }
+                else {
+                    char linebuf[45];
+                    for (auto spike: recorded_spikes) {
+                        auto n = std::snprintf(
+                            linebuf, sizeof(linebuf), "%u %.4f\n",
+                            unsigned{spike.source.gid}, float(spike.time));
+                        fid.write(linebuf, n);
+                    }
                 }
             }
         }

From ab1bc51539cf5b1341913fffd9d8edfd000ac403 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Thu, 1 Sep 2022 10:10:19 +0200
Subject: [PATCH 21/25] Tweaking the weight again.

---
 benchmarks/engines/busyring/arbor/ring.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/benchmarks/engines/busyring/arbor/ring.cpp b/benchmarks/engines/busyring/arbor/ring.cpp
index a70edd1..e32c9e1 100644
--- a/benchmarks/engines/busyring/arbor/ring.cpp
+++ b/benchmarks/engines/busyring/arbor/ring.cpp
@@ -130,7 +130,7 @@ class ring_recipe: public arb::recipe {
     cell_size_type num_cells_;
     double min_delay_;
     ring_params params_;
-    float event_weight_ = 0.05;
+    float event_weight_ = 0.025;
 
     arb::cable_cell_global_properties gprop;
 };

From 9582e3d217aa0cced701434794a689fb724a9727 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Thu, 29 Sep 2022 09:17:26 +0200
Subject: [PATCH 22/25] Bump spikes to 702/200ms/ring.

---
 benchmarks/engines/busyring/arbor/ring.cpp | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/benchmarks/engines/busyring/arbor/ring.cpp b/benchmarks/engines/busyring/arbor/ring.cpp
index e32c9e1..29323b6 100644
--- a/benchmarks/engines/busyring/arbor/ring.cpp
+++ b/benchmarks/engines/busyring/arbor/ring.cpp
@@ -65,7 +65,8 @@ class ring_recipe: public arb::recipe {
             gprop.default_parameters.axial_resistivity = 100;
             gprop.default_parameters.temperature_K = 34 + 273.15;
             gprop.default_parameters.init_membrane_potential = -90;
-            event_weight_*=5;
+            event_weight_ = 0.2;
+            event_freq_ = 0.2;
         }
     }
 
@@ -114,7 +115,7 @@ class ring_recipe: public arb::recipe {
     // This generates a single event that will kick start the spiking on the sub-ring.
     std::vector<arb::event_generator> event_generators(cell_gid_type gid) const override {
         if (gid%params_.ring_size == 0) {
-            return {arb::regular_generator({"p_syn"}, event_weight_, 0.0, 1.0)};
+            return {arb::regular_generator({"p_syn"}, event_weight_, 0.0, event_freq_)};
         } else {
             return {};
         }
@@ -131,6 +132,7 @@ class ring_recipe: public arb::recipe {
     double min_delay_;
     ring_params params_;
     float event_weight_ = 0.025;
+    float event_freq_ = 1.0;
 
     arb::cable_cell_global_properties gprop;
 };

From 454e8d58eb404dffe081383ff4c9391597d2bc7d Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Thu, 29 Sep 2022 11:52:46 +0200
Subject: [PATCH 23/25] Dont recorded spikes if not asked.

---
 benchmarks/engines/busyring/arbor/ring.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/benchmarks/engines/busyring/arbor/ring.cpp b/benchmarks/engines/busyring/arbor/ring.cpp
index 29323b6..b5ccc8a 100644
--- a/benchmarks/engines/busyring/arbor/ring.cpp
+++ b/benchmarks/engines/busyring/arbor/ring.cpp
@@ -239,7 +239,7 @@ int main(int argc, char** argv) {
 
         // Set up recording of spikes to a vector on the root process.
         std::vector<arb::spike> recorded_spikes;
-        if (root) {
+        if (root && params.record_spikes) {
             sim.set_global_spike_callback(
                 [&recorded_spikes](const std::vector<arb::spike>& spikes) {
                     recorded_spikes.insert(recorded_spikes.end(), spikes.begin(), spikes.end());

From 26a8903eeaa9ac1330a7661136cc7e30d2619fd0 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Fri, 26 Apr 2024 18:37:48 +0200
Subject: [PATCH 24/25] Fix up for v0.8.1. Use voltage_cell probe, validation
 fails.

---
 benchmarks/engines/busyring/arbor/ring.cpp    |  63 +++++------
 common/bin/comparex                           |   6 +-
 common/bin/thresholdx                         |  12 +--
 scripts/build_arbor.sh                        |   2 +-
 .../generate-rc-exp2syn-spike                 |   2 +-
 .../arbor-cable-steadystate.cpp               | 101 +++++++++---------
 .../src/arbor-rallpack1/arbor-rallpack1.cpp   |  29 ++---
 .../arbor-rc-exp2syn-spike.cpp                |  54 +++-------
 .../src/arbor-rc-expsyn/arbor-rc-expsyn.cpp   |  41 ++-----
 9 files changed, 118 insertions(+), 192 deletions(-)

diff --git a/benchmarks/engines/busyring/arbor/ring.cpp b/benchmarks/engines/busyring/arbor/ring.cpp
index b5ccc8a..10dedb4 100644
--- a/benchmarks/engines/busyring/arbor/ring.cpp
+++ b/benchmarks/engines/busyring/arbor/ring.cpp
@@ -92,7 +92,7 @@ class ring_recipe: public arb::recipe {
         const auto group_start = s*group;
         const auto group_end = std::min(group_start+s, num_cells_);
         cell_gid_type src = gid==group_start? group_end-1: gid-1;
-        cons.push_back(arb::cell_connection({src, "detector"}, {"p_syn"}, event_weight_, min_delay_));
+        cons.push_back(arb::cell_connection({src, "d"}, {"p"}, event_weight_, min_delay_));
 
         // Used to pick source cell for a connection.
         std::uniform_int_distribution<cell_gid_type> dist(0, num_cells_-2);
@@ -106,7 +106,7 @@ class ring_recipe: public arb::recipe {
             if (src==gid) ++src;
             const float delay = min_delay_+delay_dist(src_gen);
             cons.push_back(
-                arb::cell_connection({src, "detector"}, {"p_syn"}, 0.f, delay));
+                arb::cell_connection({src, "d"}, {"p"}, 0.f, delay));
         }
         return cons;
     }
@@ -115,7 +115,7 @@ class ring_recipe: public arb::recipe {
     // This generates a single event that will kick start the spiking on the sub-ring.
     std::vector<arb::event_generator> event_generators(cell_gid_type gid) const override {
         if (gid%params_.ring_size == 0) {
-            return {arb::regular_generator({"p_syn"}, event_weight_, 0.0, event_freq_)};
+            return {arb::regular_generator({"p"}, event_weight_, 0.0, event_freq_)};
         } else {
             return {};
         }
@@ -377,26 +377,19 @@ arb::cable_cell complex_cell (arb::cell_gid_type gid, const cell_parameters& par
         dist_from_soma += l;
     }
 
-    arb::label_dict dict;
-
-    dict.set("soma", tagged(1));
-    dict.set("axon", tagged(2));
-    dict.set("dend", tagged(3));
-    dict.set("apic", tagged(4));
-    dict.set("center", location(0, 0.5));
-    if (params.synapses>1) {
-       dict.set("synapses",  arb::ls::uniform(arb::reg::all(), 0, params.synapses-2, gid));
-    }
-
-    auto soma = "soma"_lab;
-    auto dend = "dend"_lab;
-    auto cntr = "center"_lab;
-    auto syns = "synapses"_lab;
+    using arb::reg::tagged;
+    auto rall  = arb::reg::all();
+    auto soma = tagged(1);
+    auto axon = tagged(2);
+    auto dend = tagged(3);
+    auto apic = tagged(4);
+    auto cntr = location(0, 0.5);
+    auto syns = arb::ls::uniform(rall, 0, params.synapses-2, gid);
 
     arb::decor decor;
 
-    decor.paint(all(), arb::init_reversal_potential{"k",  -107.0});
-    decor.paint(all(), arb::init_reversal_potential{"na", 53.0});
+    decor.paint(rall, arb::init_reversal_potential{"k",  -107.0});
+    decor.paint(rall, arb::init_reversal_potential{"na", 53.0});
 
     decor.paint(soma, arb::axial_resistivity{133.577});
     decor.paint(soma, arb::membrane_capacitance{4.21567e-2});
@@ -419,16 +412,16 @@ arb::cable_cell complex_cell (arb::cell_gid_type gid, const cell_parameters& par
     decor.paint(dend, arb::density("Im_v2",          {{"gbar", 0.00132163}}));
     decor.paint(dend, arb::density("Ih",             {{"gbar", 9.18815e-06}}));
 
-    decor.place(cntr, arb::synapse("expsyn"), "p_syn");
+    decor.place(cntr, arb::synapse("expsyn"), "p");
     if (params.synapses>1) {
-        decor.place(syns, arb::synapse("expsyn"), "s_syn");
+        // decor.place(syns, arb::synapse("expsyn"), "s");
     }
 
-    decor.place(cntr, arb::threshold_detector{-20.0}, "detector");
+    decor.place(cntr, arb::threshold_detector{-20.0}, "d");
 
     decor.set_default(arb::cv_policy_every_segment());
 
-    return {arb::morphology(tree), dict, decor};
+    return {arb::morphology(tree), decor};
 }
 
 arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& params) {
@@ -480,18 +473,10 @@ arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& param
         dist_from_soma += l;
     }
 
-    arb::label_dict labels;
-
-    auto soma = "soma"_lab;
-    auto dnds = "dendrites"_lab;
-    auto syns = "synapses"_lab;
-
     using arb::reg::tagged;
-    labels.set("soma",      tagged(1));
-    labels.set("dendrites", join(tagged(3), tagged(4)));
-    if (params.synapses>1) {
-       labels.set("synapses",  arb::ls::uniform(arb::reg::all(), 0, params.synapses-2, gid));
-    }
+    auto soma = tagged(1);
+    auto dnds = join(tagged(3), tagged(4));
+    auto syns = arb::ls::uniform(arb::reg::all(), 0, params.synapses-2, gid);
 
     arb::decor decor;
 
@@ -500,18 +485,18 @@ arb::cable_cell branch_cell(arb::cell_gid_type gid, const cell_parameters& param
     decor.set_default(arb::axial_resistivity{100}); // [Ω·cm]
 
     // Add spike threshold detector at the soma.
-    decor.place(arb::mlocation{0,0}, arb::threshold_detector{10}, "detector");
+    decor.place(arb::mlocation{0,0}, arb::threshold_detector{10}, "d");
 
     // Add a synapse to proximal end of first dendrite.
-    decor.place(arb::mlocation{1, 0}, arb::synapse{"expsyn"}, "p_syn");
+    decor.place(arb::mlocation{1, 0}, arb::synapse{"expsyn"}, "p");
 
     // Add additional synapses that will not be connected to anything.
     if (params.synapses>1) {
-        decor.place(syns, arb::synapse{"expsyn"}, "s_syn");
+        decor.place(syns, arb::synapse{"expsyn"}, "s");
     }
 
     // Make a CV between every sample in the sample tree.
     decor.set_default(arb::cv_policy_every_segment());
 
-    return {arb::morphology(tree), labels, decor};
+    return {arb::morphology(tree), decor};
 }
diff --git a/common/bin/comparex b/common/bin/comparex
index 5704e93..f0fe4db 100755
--- a/common/bin/comparex
+++ b/common/bin/comparex
@@ -8,7 +8,7 @@ import sys
 import numpy as np
 import xarray
 import scipy.interpolate as interpolate
-import scipy.ndimage.filters as filters
+from scipy.ndimage import maximum_filter1d
 
 def parse_clargs():
     P = argparse.ArgumentParser()
@@ -92,10 +92,10 @@ def interpolate_array(x, t, tnew):
     x4_est[0] *= 3  # end-interval fudge factors
     x4_est[-1] *= 3
 
-    x4_windowmax = np.pad(filters.maximum_filter1d(x4_est, 4, origin=-2), (1, 0), mode='edge')
+    x4_windowmax = np.pad(maximum_filter1d(x4_est, 4, origin=-2), (1, 0), mode='edge')
     local_x4max = interpolate.interp1d(t, np.resize(x4_windowmax, x.size), assume_sorted=True, kind='previous', fill_value='extrapolate')
 
-    dt_windowmax = np.pad(filters.maximum_filter1d(np.ediff1d(t), 3, origin=-1), (1, 0), mode='edge')
+    dt_windowmax = np.pad(maximum_filter1d(np.ediff1d(t), 3, origin=-1), (1, 0), mode='edge')
     local_dtmax = interpolate.interp1d(t, np.resize(dt_windowmax, x.size), assume_sorted=True, kind='previous', fill_value='extrapolate')
 
     xi_err = 5./384.*pow(local_dtmax(tnew), 4)*local_x4max(tnew)
diff --git a/common/bin/thresholdx b/common/bin/thresholdx
index 1775abe..60bb5bc 100755
--- a/common/bin/thresholdx
+++ b/common/bin/thresholdx
@@ -63,17 +63,17 @@ for var, op, value in opts.exprs:
     else:
         v = opts.input[var]
         if op=='<':
-            status = np.asscalar(np.all(v<value))
+            status = np.all(v<value).item()
         elif op=='<=':
-            status = np.asscalar(np.all(v<=value))
+            status = (np.all(v<=value)).item()
         elif op=='>':
-            status = np.asscalar(np.all(v>value))
+            status = (np.all(v>value)).item()
         elif op=='>=':
-            status = np.asscalar(np.all(v>=value))
+            status = (np.all(v>=value)).item()
         elif op=='==' or op=='=':
-            status = np.asscalar(np.all(v==value))
+            status = (np.all(v==value)).item()
         elif op=='!=':
-            status = np.asscalar(np.all(v!=value))
+            status = (np.all(v!=value)).item()
         else:
             status = 'unknown operation'
 
diff --git a/scripts/build_arbor.sh b/scripts/build_arbor.sh
index 74d01f1..4454ca6 100644
--- a/scripts/build_arbor.sh
+++ b/scripts/build_arbor.sh
@@ -48,7 +48,7 @@ fi
 cd "$arb_build_path"
 cmake_args=-DCMAKE_INSTALL_PREFIX:PATH="$ns_install_path"
 cmake_args="$cmake_args -DARB_WITH_MPI=$ns_with_mpi"
-cmake_args="$cmake_args -DARB_USE_BUNDLED_LIBS=ON"
+cmake_args="$cmake_args -DARB_USE_BUNDLED_LIBS=ON -DCMAKE_INTERPROCEDURAL_OPTIMIZATION=OFF"
 cmake_args="$cmake_args -DARB_GPU=$ns_arb_gpu"
 cmake_args="$cmake_args -DARB_ARCH=$ns_arb_arch"
 cmake_args="$cmake_args -DARB_VECTORIZE=$ns_arb_vectorize"
diff --git a/validation/rc-exp2syn-spike/generate-rc-exp2syn-spike b/validation/rc-exp2syn-spike/generate-rc-exp2syn-spike
index 03ad389..287ec39 100755
--- a/validation/rc-exp2syn-spike/generate-rc-exp2syn-spike
+++ b/validation/rc-exp2syn-spike/generate-rc-exp2syn-spike
@@ -67,7 +67,7 @@ def run_integration():
     crossing.direction = 1
 
     r = integrate.solve_ivp(dv_dt, (0., tend), [Erev], method='LSODA', t_eval=ts, jac=jacobian, atol=1e-10/nsamp, rtol=1e-10/nsamp, events=crossing)
-    spike = np.asscalar(r.t_events[0]) if r.t_events[0].size>0 else np.NaN
+    spike = (r.t_events[0]).item() if r.t_events[0].size>0 else np.NaN
 
     return (r.y[0], spike)
 
diff --git a/validation/src/arbor-cable-steadystate/arbor-cable-steadystate.cpp b/validation/src/arbor-cable-steadystate/arbor-cable-steadystate.cpp
index d7144ad..ec7f76f 100644
--- a/validation/src/arbor-cable-steadystate/arbor-cable-steadystate.cpp
+++ b/validation/src/arbor-cable-steadystate/arbor-cable-steadystate.cpp
@@ -14,6 +14,8 @@
 #include <arbor/simple_sampler.hpp>
 #include <arbor/simulation.hpp>
 #include <arbor/version.hpp>
+#include <arbor/util/any_cast.hpp>
+#include <arbor/util/any_ptr.hpp>
 
 #include "common_args.h"
 #include "common_attr.h"
@@ -48,9 +50,9 @@ struct rc_cable_recipe: public arb::recipe {
     {}
 
     cell_size_type num_cells() const override { return 1; }
-    cell_size_type num_targets(cell_gid_type) const override { return 0; }
     cell_kind get_cell_kind(cell_gid_type) const override { return cell_kind::cable; }
-    cell_size_type num_probes(cell_gid_type) const { return n; }
+    cell_size_type num_cvs_per_branch(cell_gid_type) const { return n; }
+    std::vector<arb::probe_info> get_probes(cell_gid_type gid) const override { return {cable_probe_membrane_voltage_cell()}; }
 
     std::any get_global_properties(cell_kind kind) const override {
         cable_cell_global_properties prop;
@@ -58,87 +60,80 @@ struct rc_cable_recipe: public arb::recipe {
         prop.default_parameters.init_membrane_potential = 0;
         prop.default_parameters.axial_resistivity = 100*rl; // [Ω·cm]
         prop.default_parameters.membrane_capacitance = (double)cm;  // [F/m²]
-        prop.default_parameters.temperature_K = 0;
+        prop.default_parameters.temperature_K = 300;
         prop.ion_species.clear();
         return prop;
     }
 
-    std::vector<arb::probe_info> get_probes(cell_gid_type gid) const override {
-        std::vector<arb::probe_info> probes; 
-
-        // n probes, centred over CVs.
-        for (unsigned i = 0; i < num_probes(gid); ++i) {
-          arb::mlocation loc{0, probe_x(i)/length};
-          probes.push_back(cable_probe_membrane_voltage{loc});
-        } 
-        return probes; 
-    }
 
     util::unique_any get_cell_description(cell_gid_type) const override {
         segment_tree tree;
         tree.append(arb::mnpos, {0., 0., 0., d0/2}, {0., 0., length, d1/2}, 0);
 
-        mechanism_desc pas("pas");
+        mechanism_desc pas("pas/e=0");
         pas["g"] = 1e-4/rm; // [S/cm^2]
-        pas["e"] = 0; // erev=0
+        // pas["e"] = 0; // erev=0
 
         decor D;
-        D.paint(reg::all(), pas);
-        D.place(mlocation{0, 1.}, i_clamp{0, INFINITY, iinj});
+        D.paint(reg::all(), arb::density{pas});
+        D.place(mlocation{0, 1.}, i_clamp{iinj}, "ic");
         D.set_default(cv_policy_fixed_per_branch(n));
 
-        return cable_cell(tree, {}, D);
+        return cable_cell(tree, D);
     }
 
     // time constant in [ms]
     static double tau() { return rm*cm*1000; }
-
-    // probe position in [µm]
-    double probe_x(unsigned i) const {
-        return length*((2.0*i+1.0)/(2.0*n));
-    }
-
 };
 
-domain_decomposition trivial_dd(const recipe& r) {
-    cell_size_type ncell = r.num_cells();
-
-    std::vector<cell_gid_type> all_gids(ncell);
-    std::iota(all_gids.begin(), all_gids.end(), cell_gid_type(0));
-
-    return domain_decomposition{
-        [](cell_gid_type) { return 0; },   // gid_domain map
-        1,                                 // num_domains
-        0,                                 // domain_id
-        ncell,                             // num_local_cells
-        ncell,                             // num_global_cells
-        {{r.get_cell_kind(0), all_gids, backend_kind::multicore}}  // groups
-    };
-}
-
 int main(int argc, char** argv) {
     common_args A;
     A.params = default_parameters;
     parse_common_args(A, argc, argv, {"binevents"});
 
-    auto ctx = make_context();
     rc_cable_recipe rec(A.params);
-    simulation sim(rec, trivial_dd(rec), ctx);
+    simulation sim(rec);
 
     time_type dt = A.params["dt"];
     time_type t_end = 20*rec.tau(); // transient amplitudes are proportional to exp(-t/tau).
 
-    std::vector<double> voltage(rec.num_probes(0));
-    std::vector<double> x(rec.num_probes(0));
-    for (unsigned i = 0; i<x.size(); ++i) x[i] = rec.probe_x(i);
+    auto n_entities = rec.num_cvs_per_branch(0);
+    std::vector<double> voltage(n_entities);
+    std::vector<double> xs(n_entities);
 
     double t_sample = 0;
-    auto sampler = [&voltage,&t_sample] (probe_metadata pm, std::size_t n, const sample_record* rec) {
-        voltage.at(pm.id.index) = *rec[0].data.as<const double*>();
-        t_sample = rec[0].time;
-    }; 
+    auto sampler = [&voltage,
+                    &t_sample,
+                    &xs,
+                    n_entities=n_entities] (probe_metadata pm,
+                                            std::size_t n_samples,
+                                            const sample_record* samples) {
+        auto* cables = arb::util::any_cast<const arb::mcable_list*>(pm.meta);
+        assert(cables);
+        for (std::size_t ix = 0; ix < n_samples; ++ix) {
+            auto* value_range = arb::util::any_cast<const arb::cable_sample_range*>(samples[ix].data);
+            assert(value_range);
+            const auto& [lo, hi] = *value_range;
+            assert(n_entities == hi - lo);
+            t_sample = samples[ix].time;
+            for (unsigned jx = 0; jx < n_entities; ++jx) {
+                arb::mcable where = (*cables)[jx];
+                assert(where.branch_id == 0);
+                xs[jx] = 0.5*(where.prox_pos + where.dist_pos);
+
+                voltage[jx] = lo[jx];
+                std::cout << "t=" << t_sample << ", x=" << xs[jx] << ", U=" << voltage[jx] << '\n';
+            }
+            // Just taking the _first_ time.
+            break;
+        }
+    };
 
-    sim.add_sampler(all_probes, explicit_schedule({t_end-dt}), sampler, sampling_policy::exact);
+        // voltage.at(pm.id.index) = *rec[0].data.as<const double*>();
+        // t_sample = rec[0].time;
+    // };
+
+    sim.add_sampler(all_probes, explicit_schedule({t_end-dt}), sampler);
 
     sim.run(t_end, dt);
 
@@ -155,6 +150,10 @@ int main(int argc, char** argv) {
     nc_check(nc_def_var, ncid, "v", NC_DOUBLE, 1, &x_dimid, &vid);
     nc_check(nc_def_var, ncid, "t_sample", NC_DOUBLE, 0, nullptr, &tid);
 
+    for (int ix = 0; ix < n_entities; ++ix) {
+        // std::cout << t_sample << ", " << xs[ix] << ", " << voltage[ix] << '\n';
+    }
+
     auto nc_put_att_cstr = [](int ncid, int varid, const char* name, const char* value) {
         nc_check(nc_put_att_text, ncid, varid, name, std::strlen(value), value);
     };
@@ -175,6 +174,6 @@ int main(int argc, char** argv) {
 
     nc_check(nc_put_var_double, ncid, tid, &t_sample)
     nc_check(nc_put_var_double, ncid, vid, voltage.data())
-    nc_check(nc_put_var_double, ncid, xid, x.data())
+    nc_check(nc_put_var_double, ncid, xid, xs.data())
     nc_check(nc_close, ncid);
 }
diff --git a/validation/src/arbor-rallpack1/arbor-rallpack1.cpp b/validation/src/arbor-rallpack1/arbor-rallpack1.cpp
index 7591251..48cef79 100644
--- a/validation/src/arbor-rallpack1/arbor-rallpack1.cpp
+++ b/validation/src/arbor-rallpack1/arbor-rallpack1.cpp
@@ -49,7 +49,6 @@ struct rc_rallpack1_recipe: public arb::recipe {
     {}
 
     cell_size_type num_cells() const override { return 1; }
-    cell_size_type num_targets(cell_gid_type) const override { return 0; }
     cell_kind get_cell_kind(cell_gid_type) const override { return cell_kind::cable; }
     cell_size_type num_probes(cell_gid_type) const { return 2; }
 
@@ -79,35 +78,19 @@ struct rc_rallpack1_recipe: public arb::recipe {
         segment_tree tree;
         tree.append(arb::mnpos, {0., 0., 0., d/2}, {0., 0., length, d/2}, 0);
 
-        mechanism_desc pas("pas");
+        mechanism_desc pas("pas/e=-65");
         pas["g"] = 1e-4/rm; // [S/cm^2]
-        pas["e"] = (double)erev;
+        // pas["e"] = (double)erev;
 
         decor D;
-        D.paint(reg::all(), pas);
-        D.place(mlocation{0, 0}, i_clamp{0, INFINITY, iinj});
+        D.paint(reg::all(), arb::density{pas});
+        D.place(mlocation{0, 0}, i_clamp{0, INFINITY, iinj}, "ic");
         D.set_default(cv_policy_fixed_per_branch(n));
 
-        return cable_cell(tree, {}, D);
+        return cable_cell(tree, D);
     }
 };
 
-domain_decomposition trivial_dd(const recipe& r) {
-    cell_size_type ncell = r.num_cells();
-
-    std::vector<cell_gid_type> all_gids(ncell);
-    std::iota(all_gids.begin(), all_gids.end(), cell_gid_type(0));
-
-    return domain_decomposition{
-        [](cell_gid_type) { return 0; },   // gid_domain map
-        1,                                 // num_domains
-        0,                                 // domain_id
-        ncell,                             // num_local_cells
-        ncell,                             // num_global_cells
-        {{r.get_cell_kind(0), all_gids, backend_kind::multicore}}  // groups
-    };
-}
-
 int main(int argc, char** argv) {
     common_args A;
     A.params = default_parameters;
@@ -115,7 +98,7 @@ int main(int argc, char** argv) {
 
     auto ctx = make_context();
     rc_rallpack1_recipe rec(A.params);
-    simulation sim(rec, trivial_dd(rec), ctx);
+    simulation sim(rec);
 
     time_type dt = A.params["dt"];
     time_type t_end = A.params["tend"];
diff --git a/validation/src/arbor-rc-exp2syn-spike/arbor-rc-exp2syn-spike.cpp b/validation/src/arbor-rc-exp2syn-spike/arbor-rc-exp2syn-spike.cpp
index e13c638..e80c4c8 100644
--- a/validation/src/arbor-rc-exp2syn-spike/arbor-rc-exp2syn-spike.cpp
+++ b/validation/src/arbor-rc-exp2syn-spike/arbor-rc-exp2syn-spike.cpp
@@ -12,12 +12,14 @@
 #include <arbor/simple_sampler.hpp>
 #include <arbor/simulation.hpp>
 #include <arbor/version.hpp>
+#include <arborio/label_parse.hpp>
 
 #include "common_args.h"
 #include "common_attr.h"
 #include "netcdf_wrap.h"
 
 using namespace arb;
+using namespace arborio::literals;
 
 paramset default_parameters = {
     {"dt", 0.01},
@@ -64,11 +66,7 @@ struct rc_exp2syn_spike_recipe: public arb::recipe {
     }
 
     cell_size_type num_cells() const override { return ncell; }
-    cell_size_type num_sources(cell_gid_type) const override { return 1; }
-    cell_size_type num_targets(cell_gid_type) const override { return 1; }
-    cell_size_type num_probes(cell_gid_type gid) const {
-        return gid==0? 1: 0;
-    }
+    cell_size_type num_probes(cell_gid_type gid) const { return gid==0? 1: 0; }
     cell_kind get_cell_kind(cell_gid_type) const override { return cell_kind::cable; }
 
     std::any get_global_properties(cell_kind kind) const override {
@@ -89,22 +87,18 @@ struct rc_exp2syn_spike_recipe: public arb::recipe {
 
     std::vector<event_generator> event_generators(cell_gid_type gid) const override {
         if (gid!=0) return {};
-
-        spike_event ev;
-        ev.target = {0u, 0u};
-        ev.time = 0;
-        ev.weight = g0;
-
-        return {explicit_generator(pse_vector{{ev}})};
+        return {explicit_generator(arb::cell_local_label_type("syn"),
+                                   g0,
+                                   std::vector<float>{0.0f})};
     }
 
     util::unique_any get_cell_description(cell_gid_type) const override {
         segment_tree tree;
         tree.append(arb::mnpos, {0., 0., 0., r*1e6}, {0., 0., 2*r*1e6,  r*1e6}, 1);
 
-        mechanism_desc pas("pas");
+        mechanism_desc pas("pas/e=-65");
         pas["g"] = 1e-10/(rm*area);    // [S/cm^2]
-        pas["e"] = erev;
+        // pas["e"] = erev;
 
         mechanism_desc exp2syn("exp2syn");
         exp2syn["tau1"] = tau1;
@@ -117,44 +111,30 @@ struct rc_exp2syn_spike_recipe: public arb::recipe {
 
         decor D;
         D.set_default(membrane_capacitance{cm*1e-9/area}); // [F/m^2]
-        D.paint("\"soma\"", pas);
-        D.place("\"midpoint\"", exp2syn);
-        D.place("\"midpoint\"", threshold_detector{threshold});
+        D.paint(arb::reg::named("soma"), arb::density{pas});
+        D.place(arb::ls::named("midpoint"), arb::synapse{exp2syn}, "syn");
+        D.place(arb::ls::named("midpoint"), threshold_detector{threshold}, "det");
 
-        return cable_cell(tree, labels, D);
+        return cable_cell(tree, D, labels);
     }
 
     std::vector<arb::cell_connection> connections_on(cell_gid_type gid) const override {
         if (gid==0) return {};
 
-        return {arb::cell_connection({0, 0}, {gid, 0}, g0, delay[gid])};
+        return {arb::cell_connection(arb::cell_global_label_type{0, "det"},
+                                     arb::cell_local_label_type{"syn"},
+                                     g0,
+                                     delay[gid])};
     }
 };
 
-domain_decomposition trivial_dd(const recipe& r) {
-    cell_size_type ncell = r.num_cells();
-
-    std::vector<cell_gid_type> all_gids(ncell);
-    std::iota(all_gids.begin(), all_gids.end(), cell_gid_type(0));
-
-    return domain_decomposition{
-        [](cell_gid_type) { return 0; },   // gid_domain map
-        1,                                 // num_domains
-        0,                                 // domain_id
-        ncell,                             // num_local_cells
-        ncell,                             // num_global_cells
-        {{r.get_cell_kind(0), all_gids, backend_kind::multicore}}  // groups
-    };
-}
-
 int main(int argc, char** argv) {
     common_args A;
     A.params = default_parameters;
     parse_common_args(A, argc, argv, {"binevents"});
 
-    auto ctx = make_context();
     rc_exp2syn_spike_recipe rec(A.params);
-    simulation sim(rec, trivial_dd(rec), ctx);
+    simulation sim(rec);
 
     time_type t_end = 10., sample_dt = 0.05; // [ms]
     time_type dt = A.params["dt"];
diff --git a/validation/src/arbor-rc-expsyn/arbor-rc-expsyn.cpp b/validation/src/arbor-rc-expsyn/arbor-rc-expsyn.cpp
index 72573f8..66ddd2f 100644
--- a/validation/src/arbor-rc-expsyn/arbor-rc-expsyn.cpp
+++ b/validation/src/arbor-rc-expsyn/arbor-rc-expsyn.cpp
@@ -42,7 +42,6 @@ struct rc_expsyn_recipe: public arb::recipe {
     explicit rc_expsyn_recipe(const paramset& ps): g0(ps.at("g0")) {}
 
     cell_size_type num_cells() const override { return 1; }
-    cell_size_type num_targets(cell_gid_type) const override { return 1; }
     cell_kind get_cell_kind(cell_gid_type) const override { return cell_kind::cable; }
     cell_size_type num_probes(cell_gid_type) const { return 1; }
 
@@ -62,22 +61,19 @@ struct rc_expsyn_recipe: public arb::recipe {
         return {cable_probe_membrane_voltage{ls::named("midpoint")}};
     }
 
-    std::vector<event_generator> event_generators(cell_gid_type) const override {
-        spike_event ev;
-        ev.target = {0u, 0u};
-        ev.time = 0;
-        ev.weight = g0;
-
-        return {explicit_generator(pse_vector{{ev}})};
+    std::vector<event_generator> event_generators(cell_gid_type gid) const override {
+        return {explicit_generator(arb::cell_local_label_type("syn"),
+                                   g0,
+                                   std::vector<float>{0.0f})};
     }
 
     util::unique_any get_cell_description(cell_gid_type) const override {
         segment_tree tree;
         tree.append(arb::mnpos, {0., 0., 0., r*1e6}, {0., 0., 2*r*1e6,  r*1e6}, 1);
 
-        mechanism_desc pas("pas");
+        mechanism_desc pas("pas/e=-65");
         pas["g"] = 1e-10/(rm*area);    // [S/cm^2]
-        pas["e"] = erev;
+        // pas["e"] = erev;
 
         mechanism_desc expsyn("expsyn");
         expsyn["tau"] = syntau;
@@ -89,37 +85,20 @@ struct rc_expsyn_recipe: public arb::recipe {
 
         decor D;
         D.set_default(membrane_capacitance{cm*1e-9/area}); // [F/m^2]
-        D.paint("\"soma\"", pas);
-        D.place("\"midpoint\"", expsyn);
+        D.paint(arb::reg::named("soma"), arb::density{pas});
+        D.place(arb::ls::named("midpoint"), arb::synapse{expsyn}, "syn");
 
-        return cable_cell(tree, labels, D);
+        return cable_cell(tree, D, labels);
     }
 };
 
-domain_decomposition trivial_dd(const recipe& r) {
-    cell_size_type ncell = r.num_cells();
-
-    std::vector<cell_gid_type> all_gids(ncell);
-    std::iota(all_gids.begin(), all_gids.end(), cell_gid_type(0));
-
-    return domain_decomposition{
-        [](cell_gid_type) { return 0; },   // gid_domain map
-        1,                                 // num_domains
-        0,                                 // domain_id
-        ncell,                             // num_local_cells
-        ncell,                             // num_global_cells
-        {{r.get_cell_kind(0), all_gids, backend_kind::multicore}}  // groups
-    };
-}
-
 int main(int argc, char** argv) {
     common_args A;
     A.params = default_parameters;
     parse_common_args(A, argc, argv, {"binevents"});
 
-    auto ctx = make_context();
     rc_expsyn_recipe rec(A.params);
-    simulation sim(rec, trivial_dd(rec), ctx);
+    simulation sim(rec);
 
     time_type t_end = 10., sample_dt = 0.05; // [ms]
     time_type dt = A.params["dt"];

From 779a8fb24778750310152b63ac66ca6b5c5ab553 Mon Sep 17 00:00:00 2001
From: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>
Date: Fri, 26 Apr 2024 19:22:37 +0200
Subject: [PATCH 25/25] Fix up for v0.8.1. Use old probe style, all pass.

---
 .../arbor-cable-steadystate.cpp               | 57 +++++++------------
 1 file changed, 20 insertions(+), 37 deletions(-)

diff --git a/validation/src/arbor-cable-steadystate/arbor-cable-steadystate.cpp b/validation/src/arbor-cable-steadystate/arbor-cable-steadystate.cpp
index ec7f76f..c4be69d 100644
--- a/validation/src/arbor-cable-steadystate/arbor-cable-steadystate.cpp
+++ b/validation/src/arbor-cable-steadystate/arbor-cable-steadystate.cpp
@@ -52,7 +52,16 @@ struct rc_cable_recipe: public arb::recipe {
     cell_size_type num_cells() const override { return 1; }
     cell_kind get_cell_kind(cell_gid_type) const override { return cell_kind::cable; }
     cell_size_type num_cvs_per_branch(cell_gid_type) const { return n; }
-    std::vector<arb::probe_info> get_probes(cell_gid_type gid) const override { return {cable_probe_membrane_voltage_cell()}; }
+    std::vector<arb::probe_info> get_probes(cell_gid_type gid) const override {
+        std::vector<arb::probe_info> probes;
+
+        // n probes, centred over CVs.
+        for (unsigned i = 0; i < num_probes(gid); ++i) {
+          arb::mlocation loc{0, probe_x(i)/length};
+          probes.push_back(cable_probe_membrane_voltage{loc});
+        }
+        return probes;
+    }
 
     std::any get_global_properties(cell_kind kind) const override {
         cable_cell_global_properties prop;
@@ -84,6 +93,10 @@ struct rc_cable_recipe: public arb::recipe {
 
     // time constant in [ms]
     static double tau() { return rm*cm*1000; }
+
+    // probe position in [µm]
+    double probe_x(unsigned i) const { return length*((2.0*i+1.0)/(2.0*n)); }
+    cell_size_type num_probes(cell_gid_type) const { return n; }
 };
 
 int main(int argc, char** argv) {
@@ -99,40 +112,14 @@ int main(int argc, char** argv) {
 
     auto n_entities = rec.num_cvs_per_branch(0);
     std::vector<double> voltage(n_entities);
-    std::vector<double> xs(n_entities);
+    std::vector<double> x(n_entities);
+    for (unsigned i = 0; i<x.size(); ++i) x[i] = rec.probe_x(i);
 
     double t_sample = 0;
-    auto sampler = [&voltage,
-                    &t_sample,
-                    &xs,
-                    n_entities=n_entities] (probe_metadata pm,
-                                            std::size_t n_samples,
-                                            const sample_record* samples) {
-        auto* cables = arb::util::any_cast<const arb::mcable_list*>(pm.meta);
-        assert(cables);
-        for (std::size_t ix = 0; ix < n_samples; ++ix) {
-            auto* value_range = arb::util::any_cast<const arb::cable_sample_range*>(samples[ix].data);
-            assert(value_range);
-            const auto& [lo, hi] = *value_range;
-            assert(n_entities == hi - lo);
-            t_sample = samples[ix].time;
-            for (unsigned jx = 0; jx < n_entities; ++jx) {
-                arb::mcable where = (*cables)[jx];
-                assert(where.branch_id == 0);
-                xs[jx] = 0.5*(where.prox_pos + where.dist_pos);
-
-                voltage[jx] = lo[jx];
-                std::cout << "t=" << t_sample << ", x=" << xs[jx] << ", U=" << voltage[jx] << '\n';
-            }
-            // Just taking the _first_ time.
-            break;
-        }
+    auto sampler = [&voltage,&t_sample] (probe_metadata pm, std::size_t n, const sample_record* rec) {
+        voltage.at(pm.id.index) = *rec[0].data.as<const double*>();
+        t_sample = rec[0].time;
     };
-
-        // voltage.at(pm.id.index) = *rec[0].data.as<const double*>();
-        // t_sample = rec[0].time;
-    // };
-
     sim.add_sampler(all_probes, explicit_schedule({t_end-dt}), sampler);
 
     sim.run(t_end, dt);
@@ -150,10 +137,6 @@ int main(int argc, char** argv) {
     nc_check(nc_def_var, ncid, "v", NC_DOUBLE, 1, &x_dimid, &vid);
     nc_check(nc_def_var, ncid, "t_sample", NC_DOUBLE, 0, nullptr, &tid);
 
-    for (int ix = 0; ix < n_entities; ++ix) {
-        // std::cout << t_sample << ", " << xs[ix] << ", " << voltage[ix] << '\n';
-    }
-
     auto nc_put_att_cstr = [](int ncid, int varid, const char* name, const char* value) {
         nc_check(nc_put_att_text, ncid, varid, name, std::strlen(value), value);
     };
@@ -174,6 +157,6 @@ int main(int argc, char** argv) {
 
     nc_check(nc_put_var_double, ncid, tid, &t_sample)
     nc_check(nc_put_var_double, ncid, vid, voltage.data())
-    nc_check(nc_put_var_double, ncid, xid, xs.data())
+    nc_check(nc_put_var_double, ncid, xid, x.data())
     nc_check(nc_close, ncid);
 }