Implement mechanism ABI

Implements #1376.

* Provide a common C linkage ABI for externally compiled mechanisms, for both CPU and GPU.
* Remove mechanism type hierarchy (`concrete_mechanism` etc.), and move corresponding functionality to the back-end shared state objects. Mechanism catalogue is no longer indexed by type id.
* Distinguish between SIMD optimal alignment and SIMD width with new `min_align` attribute. Mechanisms provide both pieces of information via ABI.

.gitmodules

@@ -4,3 +4,6 @@
 [submodule "python/pybind11"]
 	path = python/pybind11
 	url = https://github.com/pybind/pybind11.git
+[submodule "ext/fmt"]
+	path = ext/fmt
+	url = https://github.com/fmtlib/fmt.git

CMakeLists.txt

@@ -8,6 +8,8 @@ string(REGEX MATCH "^[0-9]+(\\.[0-9]+)?(\\.[0-9]+)?(\\.[0-9]+)?" numeric_version
 project(arbor VERSION ${numeric_version})
 enable_language(CXX)
 
+include(GNUInstallDirs)
+
 # Turn on this option to force the compilers to produce color output when output is
 # redirected from the terminal (e.g. when using ninja or a pager).
 
@@ -171,6 +173,9 @@ set(CMAKE_CXX_EXTENSIONS OFF)
 # to the 'export set', even the private ones, and this must be done
 # in the same CMakeLists.txt in which the target is defined.
 
+# Data and internal scripts go here
+set(ARB_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATAROOTDIR}/arbor)
+
 # Interface library `arbor-config-defs` collects configure-time defines
 # for arbor, arborenv, arborio, of the form ARB_HAVE_XXX. These
 # defines should _not_ be used in any installed public headers.
@@ -212,6 +217,12 @@ install(TARGETS arbor-public-deps EXPORT arbor-targets)
 add_library(arborio-public-deps INTERFACE)
 install(TARGETS arborio-public-deps EXPORT arborio-targets)
 
+# Add scripts and supporting CMake for setting up external catalogues
+
+configure_file(scripts/build-catalogue.in ${CMAKE_CURRENT_BINARY_DIR}/build-catalogue @ONLY)
+install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/build-catalogue DESTINATION ${CMAKE_INSTALL_FULL_BINDIR})
+install(FILES mechanisms/BuildModules.cmake DESTINATION ${ARB_INSTALL_DATADIR})
+install(FILES mechanisms/generate_catalogue DESTINATION ${ARB_INSTALL_DATADIR} PERMISSIONS OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE)
 # External libraries in `ext` sub-directory: json, tinyopt and randon123.
 # Creates interface libraries `ext-json`, `ext-tinyopt` and `ext-random123`
 
@@ -224,6 +235,8 @@ else()
 endif()
 add_subdirectory(ext)
 
+cmake_dependent_option(ARB_USE_BUNDLED_FMT "Use bundled FMT lib." ON "ARB_USE_BUNDLED_LIBS" OFF)
+
 # Keep track of packages we need to add to the generated CMake config
 # file for arbor.
 

arbor/CMakeLists.txt

@@ -3,8 +3,6 @@
 set(arbor_sources
     arbexcept.cpp
     assert.cpp
-    backends/multicore/fvm.cpp
-    backends/multicore/mechanism.cpp
     backends/multicore/shared_state.cpp
     communication/communicator.cpp
     communication/dry_run_context.cpp
@@ -27,6 +25,7 @@ set(arbor_sources
     lif_cell_group.cpp
     mc_cell_group.cpp
     mechcat.cpp
+    mechinfo.cpp
     memory/gpu_wrappers.cpp
     memory/util.cpp
     morph/embed_pwlin.cpp
@@ -63,9 +62,6 @@ set(arbor_sources
 
 if(ARB_WITH_GPU)
     list(APPEND arbor_sources
-        backends/gpu/fvm.cpp
-        backends/gpu/mechanism.cpp
-        backends/gpu/mechanism.cu
         backends/gpu/shared_state.cpp
         backends/gpu/stimulus.cu
         backends/gpu/threshold_watcher.cu

arbor/arbexcept.cpp

@@ -134,5 +134,13 @@ bad_catalogue_error::bad_catalogue_error(const std::string &fn, const std::strin
       failed_call{call}
 {}
 
+unsupported_abi_error::unsupported_abi_error(size_t v):
+    arbor_exception(pprintf("ABI version is not supported by this version of arbor '{}'", v)),
+    version{v} {}
+
+bad_alignment::bad_alignment(size_t a):
+    arbor_exception(pprintf("Mechanism reported unsupported alignment '{}'", a)),
+    alignment{a} {}
+
 } // namespace arb
 

arbor/backends/event.hpp

@@ -22,13 +22,12 @@ struct target_handle {
 
 struct deliverable_event {
     time_type time;
-    target_handle handle;
     float weight;
+    target_handle handle;
 
     deliverable_event() {}
     deliverable_event(time_type time, target_handle handle, float weight):
-        time(time), handle(handle), weight(weight)
-    {}
+        time(time), weight(weight), handle(handle) {}
 };
 
 // Stream index accessor function for multi_event_stream:

arbor/backends/gpu/fvm.hpp

@@ -32,6 +32,8 @@ struct backend {
     using array  = arb::gpu::array;
     using iarray = arb::gpu::iarray;
 
+    static constexpr arb_backend_kind kind = arb_backend_kind_gpu;
+
     static memory::host_vector<value_type> host_view(const array& v) {
         return memory::on_host(v);
     }
@@ -65,8 +67,6 @@ struct backend {
             thresholds,
             context);
     }
-
-    static value_type* mechanism_field_data(arb::mechanism* mptr, const std::string& field);
 };
 
 } // namespace gpu

arbor/backends/gpu/matrix_assemble.cu

@@ -1,6 +1,6 @@
 #include <arbor/fvm_types.hpp>
 
-#include "gpu_common.hpp"
+#include <arbor/gpu/gpu_common.hpp>
 #include "matrix_common.hpp"
 
 namespace arb {

arbor/backends/gpu/matrix_common.hpp

@@ -3,7 +3,7 @@
 #include <cfloat>
 #include <climits>
 
-#include "gpu_api.hpp"
+#include <arbor/gpu/gpu_api.hpp>
 
 #if defined(__CUDACC__) || defined(__HIPCC__)
 #   define HOST_DEVICE_IF_GPU __host__ __device__

arbor/backends/gpu/matrix_fine.cu

@@ -1,7 +1,7 @@
 #include <arbor/fvm_types.hpp>
+#include <arbor/gpu/gpu_api.hpp>
+#include <arbor/gpu/gpu_common.hpp>
 
-#include "gpu_api.hpp"
-#include "gpu_common.hpp"
 #include "matrix_common.hpp"
 #include "matrix_fine.hpp"
 

arbor/backends/gpu/matrix_solve.cu

@@ -1,6 +1,6 @@
 #include <arbor/fvm_types.hpp>
+#include <arbor/gpu/gpu_common.hpp>
 
-#include "gpu_common.hpp"
 #include "matrix_common.hpp"
 
 namespace arb {