Update ubench benchmarks (#1453)

* fix mech_vec
* fix fvm_discretize
* small fixes

doc/install/build_install.rst

@@ -557,7 +557,6 @@ installation comprises:
 
 - The static libraries ``libarbor.a`` and ``libarborenv.a``.
 - Public header files.
-- The ``lmorpho`` l-system morphology generation utility
 - The ``modcc`` NMODL compiler if built.
 - The python module if built.
 - The HTML documentation if built.

test/ubench/CMakeLists.txt

@@ -7,8 +7,8 @@ set(bench_sources
     default_construct.cpp
     event_setup.cpp
     event_binning.cpp
-    #    fvm_discretize.cpp
-    #    mech_vec.cpp
+    fvm_discretize.cpp
+    mech_vec.cpp
     task_system.cpp
 )
 
@@ -25,9 +25,9 @@ foreach(bench_src ${bench_sources})
     string(REGEX REPLACE "\\.[^.]*$" "" bench_exe ${bench_src})
     add_executable(${bench_exe} EXCLUDE_FROM_ALL "${bench_src}")
 
-    target_link_libraries(${bench_exe} arbor arbor-private-headers ext-benchmark)
+    target_link_libraries(${bench_exe} arbor arborio arbor-private-headers ext-benchmark)
     target_compile_options(${bench_exe} PRIVATE ${ARB_CXXOPT_ARCH})
-    target_compile_definitions(${bench_exe} PRIVATE "-DDATADIR=\"${CMAKE_CURRENT_SOURCE_DIR}/swc\"")
+    target_compile_definitions(${bench_exe} PRIVATE "-DDATADIR=\"${CMAKE_CURRENT_SOURCE_DIR}/../swc\"")
     list(APPEND bench_exe_list ${bench_exe})
 endforeach()
 

test/ubench/fvm_discretize.cpp

@@ -17,10 +17,8 @@
 #define DATADIR "."
 #endif
 
-#define STRING(s) #s
-
 #undef SWCFILE
-#define SWCFILE STRING(DATADIR) "/motoneuron.swc"
+#define SWCFILE DATADIR "/pyramidal.swc"
 
 using namespace arb;
 
@@ -71,35 +69,37 @@ void run_discretize(benchmark::State& state) {
     auto gdflt = neuron_parameter_defaults;
     const std::size_t ncv_per_branch = state.range(0);
 
-    cable_cell c(from_swc(SWCFILE));
-    c.default_parameters.discretization = cv_policy_fixed_per_branch(ncv_per_branch);
+    decor dec;
+    auto morpho = from_swc(SWCFILE);
+    dec.set_default(cv_policy_fixed_per_branch(ncv_per_branch));
 
     while (state.KeepRunning()) {
-        benchmark::DoNotOptimize(fvm_cv_discretize(c, gdflt));
+        benchmark::DoNotOptimize(fvm_cv_discretize(cable_cell{morpho, {}, dec}, gdflt));
     }
 }
 
 void run_discretize_every_segment(benchmark::State& state) {
     auto gdflt = neuron_parameter_defaults;
 
-    cable_cell c(from_swc(SWCFILE));
-    c.default_parameters.discretization = cv_policy_every_segment();
+    decor dec;
+    auto morpho = from_swc(SWCFILE);
+    dec.set_default(cv_policy_every_segment());
 
     while (state.KeepRunning()) {
-        benchmark::DoNotOptimize(fvm_cv_discretize(c, gdflt));
+        benchmark::DoNotOptimize(fvm_cv_discretize(cable_cell{morpho, {}, dec}, gdflt));
     }
 }
 
 void run_discretize_explicit(benchmark::State& state) {
     auto gdflt = neuron_parameter_defaults;
 
-    cable_cell c(from_swc(SWCFILE));
+    decor dec;
+    auto morpho = from_swc(SWCFILE);
+    auto ends = cv_policy_every_segment().cv_boundary_points(cable_cell{morpho});
+    dec.set_default(cv_policy_explicit(std::move(ends)));
 
     while (state.KeepRunning()) {
-        auto ends = cv_policy_every_segment().cv_boundary_points(c);
-        c.default_parameters.discretization = cv_policy_explicit(std::move(ends));
-
-        benchmark::DoNotOptimize(fvm_cv_discretize(c, gdflt));
+        benchmark::DoNotOptimize(fvm_cv_discretize(cable_cell{morpho, {}, dec}, gdflt));
     }
 }
 

test/ubench/mech_vec.cpp

@@ -57,25 +57,21 @@ public:
 
         // Add soma.
         auto s0 = tree.append(arb::mnpos, {0,0,-soma_radius,soma_radius}, {0,0,soma_radius,soma_radius}, 1);
-
         // Add dendrite
         auto s1 = tree.append(s0, {0,0,soma_radius,dend_radius}, 3);
         tree.append(s1, {0,0,soma_radius+dend_length,dend_radius}, 3);
 
-        arb::label_dict d;
-        d.set("soma", arb::reg::tagged(1));
-        arb::cable_cell cell{arb::morphology(tree), d};
-        cell.paint("soma", "pas");
+        arb::decor decor;
+        decor.paint(arb::reg::tagged(1), "pas");
+        decor.set_default(arb::cv_policy_max_extent((dend_length+soma_radius*2)/num_comp_));
 
         auto distribution = std::uniform_real_distribution<float>(0.f, 1.0f);
         for(unsigned i = 0; i < num_synapse_; i++) {
             auto gen = std::mt19937(i);
-            cell.place(arb::mlocation{1, distribution(gen)}, "expsyn");
+            decor.place(arb::mlocation{0, distribution(gen)}, "expsyn");
         }
 
-        cell.default_parameters = arb::neuron_parameter_defaults;
-        cell.default_parameters.discretization = arb::cv_policy_max_extent(dend_length/num_comp_);
-        return std::move(cell);
+        return arb::cable_cell{arb::morphology(tree), {}, decor};
     }
 
     virtual cell_kind get_cell_kind(cell_gid_type) const override {
@@ -108,17 +104,15 @@ public:
 
         // Add soma.
         auto s0 = tree.append(arb::mnpos, {0,0,-soma_radius,soma_radius}, {0,0,soma_radius,soma_radius}, 1);
-
         // Add dendrite
         auto s1 = tree.append(s0, {0,0,soma_radius,dend_radius}, 3);
         tree.append(s1, {0,0,soma_radius+dend_length,dend_radius}, 3);
 
-        arb::cable_cell cell{arb::morphology(tree)};
-        cell.paint(arb::reg::all(), "pas");
+        arb::decor decor;
+        decor.paint(arb::reg::all(), "pas");
+        decor.set_default(arb::cv_policy_max_extent((dend_length+soma_radius*2)/num_comp_));
 
-        cell.default_parameters = arb::neuron_parameter_defaults;
-        cell.default_parameters.discretization = arb::cv_policy_max_extent(dend_length/num_comp_);
-        return std::move(cell);
+        return arb::cable_cell {arb::morphology(tree), {}, decor};
     }
 
     virtual cell_kind get_cell_kind(cell_gid_type) const override {
@@ -151,19 +145,17 @@ public:
 
         // Add soma.
         auto s0 = tree.append(arb::mnpos, {0,0,-soma_radius,soma_radius}, {0,0,soma_radius,soma_radius}, 1);
-
         // Add dendrite
         auto s1 = tree.append(s0, {0          ,0          ,soma_radius,             dend_radius}, 3);
         auto s2 = tree.append(s1, {0          ,0          ,soma_radius+dend_length, dend_radius}, 3);
         tree.append(s2,           {0          ,dend_length,soma_radius+dend_length, dend_radius}, 3);
         tree.append(s2,           {dend_length,0          ,soma_radius+dend_length, dend_radius}, 3);
 
-        arb::cable_cell cell{arb::morphology(tree)};
-        cell.paint(arb::reg::all(), "pas");
+        arb::decor decor;
+        decor.paint(arb::reg::all(), "pas");
+        decor.set_default(arb::cv_policy_max_extent((dend_length*3+soma_radius*2)/num_comp_));
 
-        cell.default_parameters = arb::neuron_parameter_defaults;
-        cell.default_parameters.discretization = arb::cv_policy_max_extent(dend_length*3/num_comp_);
-        return std::move(cell);
+        return arb::cable_cell{arb::morphology(tree), {}, decor};
     }
 
     virtual cell_kind get_cell_kind(cell_gid_type) const override {
@@ -196,17 +188,15 @@ public:
 
         // Add soma.
         auto s0 = tree.append(arb::mnpos, {0,0,-soma_radius,soma_radius}, {0,0,soma_radius,soma_radius}, 1);
-
         // Add dendrite
         auto s1 = tree.append(s0, {0          ,0          ,soma_radius,             dend_radius}, 3);
         tree.append(s1,           {0          ,0          ,soma_radius+dend_length, dend_radius}, 3);
 
-        arb::cable_cell cell{arb::morphology(tree)};
-        cell.paint(arb::reg::all(), "hh");
+        arb::decor decor;
+        decor.paint(arb::reg::all(), "hh");
+        decor.set_default(arb::cv_policy_max_extent((dend_length+soma_radius*2)/num_comp_));
 
-        cell.default_parameters = arb::neuron_parameter_defaults;
-        cell.default_parameters.discretization = arb::cv_policy_max_extent(dend_length/num_comp_);
-        return std::move(cell);
+        return arb::cable_cell{arb::morphology(tree), {}, decor};
     }
 
     virtual cell_kind get_cell_kind(cell_gid_type) const override {
@@ -239,19 +229,17 @@ public:
 
         // Add soma.
         auto s0 = tree.append(arb::mnpos, {0,0,-soma_radius,soma_radius}, {0,0,soma_radius,soma_radius}, 1);
-
         // Add dendrite
         auto s1 = tree.append(s0, {0          ,0          ,soma_radius,             dend_radius}, 3);
         auto s2 = tree.append(s1, {0          ,0          ,soma_radius+dend_length, dend_radius}, 3);
         tree.append(          s2, {0          ,dend_length,soma_radius+dend_length, dend_radius}, 3);
         tree.append(          s2, {dend_length,0          ,soma_radius+dend_length, dend_radius}, 3);
 
-        arb::cable_cell cell{arb::morphology(tree)};
-        cell.paint(arb::reg::all(), "hh");
+        arb::decor decor;
+        decor.paint(arb::reg::all(), "hh");
+        decor.set_default(arb::cv_policy_max_extent((dend_length*3+soma_radius*2)/num_comp_));
 
-        cell.default_parameters = arb::neuron_parameter_defaults;
-        cell.default_parameters.discretization = arb::cv_policy_max_extent(dend_length*3/num_comp_);
-        return std::move(cell);
+        return arb::cable_cell{arb::morphology(tree), {}, decor};
     }
 
     virtual cell_kind get_cell_kind(cell_gid_type) const override {

test/unit/CMakeLists.txt

@@ -236,7 +236,7 @@ if(ARB_WITH_HIP_CLANG)
 endif()
 
 target_compile_options(unit PRIVATE ${ARB_CXXOPT_ARCH})
-target_compile_definitions(unit PRIVATE "-DDATADIR=\"${CMAKE_CURRENT_SOURCE_DIR}/swc\"")
+target_compile_definitions(unit PRIVATE "-DDATADIR=\"${CMAKE_CURRENT_SOURCE_DIR}/../swc\"")
 target_compile_definitions(unit PRIVATE "-DLIBDIR=\"${PROJECT_BINARY_DIR}/lib\"")
 target_include_directories(unit PRIVATE "${CMAKE_CURRENT_BINARY_DIR}")
 target_link_libraries(unit PRIVATE gtest arbor arborenv arborio arborio-private-headers arbor-private-headers arbor-sup)