Feature/lib install target part i (#506)
CMake and build refactoring * Use CUDA as first-class language (leading to CMake 3.9 minimum version requirement). * Use 'modern CMake' interface libraries for compiler options, include file and library dependency tracking. Interface library targets: * `arbor-deps`: compiler options and library requirements for the `libarbor.a` static library, as governed by configure-time options and environment. * `arbor-private-headers`: include path for non-installed headers, as required by unit tests and arbor itself. * `arbor-aux`: helper classes and utilities used across tests and examples. * `ext-json`, `ext-tclap`, `ext-tbb`, `ext-benchmark`, `ext-sphinx_rtd_theme`: externally maintained software that we include (directly or via submodule) in the `ext/` subdirectory. * Single static library `libarbor.a` includes all built-in modules and CUDA objects. * Simply configuration options: * `ARB_WITH_TRACE`, `ARB_AUTORUN_MODCC_ON_CHANGES` `ARB_SYSTEM_TYPE` removed. * External `modcc` is provided by `ARB_MODCC` configuration option; if provided `modcc` is still buildable, but is not included in the default target. * `ARB_PRIVATE_TBBLIB`, defaulting to `OFF`, instructs the build to make TBB from the included submodule. * Extend `ErrorTarget` functionality to provide a dummy target or an error target based on a condition. * Generate header version defines and library version variables based on git status and project version, via new script `include/git-source-id`. * All generated binaries now placed in `bin/` subdirectory at build. * Install targets installs: public headers (incomplete); static library; `modcc` tool; `lmorpho` executable; `html` documentation (examples, tests and validation data are currently not installed). * Executable targets have had the `.exe` suffix removed; unit tests are labelled `unit` (arbor unit tests), `unit-modcc` (modcc unit tests), `unit-local` (distributed tests with local context), `unit-mpi` (distributed tests with MPI context). * More graceful handling of configure-time detection of `nrniv`, Julia and required Julia modules for validation data generation. * Add `cmake/FindJulia.cmake`, `cmake/FindTBB.cmake` package finders, and adjust `cmake/FindUnwind.cmake` to use link library-style properties. * Adjust travis script to test `unit-local` and `unit-mpi` if appropriate. * Simply documentation `conf.py`. Source relocation and reorganization * All external project sources and files moved to `ext/`. * Source code refactoring to decouple library-using code from the configure-time definitions that govern arbor behaviour: removes conditional code in public headers that depends upon `ARB_WITH_X`-type definitions at compile time. Affected code is is in the public interfaces for MPI, the threading implementation, and the profiler. * Remove `util/debug.hpp`; split out functionality for pretty-printing from assertion handling. * Make FVM cell non-physical voltage check a run-time cell-group parameter. * Move spike double buffer implementation to `simulation.cpp`. * Make timer utility wrap POSIX `clock_gettime` independent of threading configuration. * Make `mpi_error` derive from `system_error` and follow C++11 `system_error` semantics. * `EXPECTS` macro replaced by `arb_assert` macro. * JSON dependency removed from `libarbor.a` and header files: moved to auxiliary library. * Publicly visible macros garner an `ARB_` prefix as required. * Move SWC test file to `test/unit` directory. * Work-in-progress splitting of public from private includes: as a convention not entirely adhered to as yet, private headers within arbor source are included with `""`, public headers with `<>`. Modcc interface changes * Expose via `--namespace` option the functionality that sets the namespace in generated code. * Use `--profile` option to add profiler hooks to generated code; uses public function interface directly rather than `PE/PL` macros in order to avoid public `PE` and `PL` defines.
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- .gitmodules 5 additions, 5 deletions.gitmodules
- CMakeLists.txt 192 additions, 242 deletionsCMakeLists.txt
- arbor/CMakeLists.txt 102 additions, 0 deletionsarbor/CMakeLists.txt
- arbor/algorithms.hpp 7 additions, 6 deletionsarbor/algorithms.hpp
- arbor/assert.cpp 34 additions, 0 deletionsarbor/assert.cpp
- arbor/backends.hpp 0 additions, 0 deletionsarbor/backends.hpp
- arbor/backends/builtin_mech_proto.hpp 2 additions, 2 deletionsarbor/backends/builtin_mech_proto.hpp
- arbor/backends/event.hpp 2 additions, 2 deletionsarbor/backends/event.hpp
- arbor/backends/event_delivery.md 0 additions, 0 deletionsarbor/backends/event_delivery.md
- arbor/backends/gpu/cuda_atomic.hpp 0 additions, 0 deletionsarbor/backends/gpu/cuda_atomic.hpp
- arbor/backends/gpu/cuda_common.hpp 0 additions, 0 deletionsarbor/backends/gpu/cuda_common.hpp
- arbor/backends/gpu/fvm.hpp 8 additions, 8 deletionsarbor/backends/gpu/fvm.hpp
- arbor/backends/gpu/gpu_store_types.hpp 5 additions, 5 deletionsarbor/backends/gpu/gpu_store_types.hpp
- arbor/backends/gpu/managed_ptr.cpp 12 additions, 0 deletionsarbor/backends/gpu/managed_ptr.cpp
- arbor/backends/gpu/managed_ptr.hpp 28 additions, 12 deletionsarbor/backends/gpu/managed_ptr.hpp
- arbor/backends/gpu/math_cu.hpp 0 additions, 0 deletionsarbor/backends/gpu/math_cu.hpp
- arbor/backends/gpu/matrix_assemble.cu 1 addition, 1 deletionarbor/backends/gpu/matrix_assemble.cu
- arbor/backends/gpu/matrix_common.hpp 0 additions, 0 deletionsarbor/backends/gpu/matrix_common.hpp
- arbor/backends/gpu/matrix_interleave.cu 1 addition, 1 deletionarbor/backends/gpu/matrix_interleave.cu
- arbor/backends/gpu/matrix_interleave.hpp 0 additions, 0 deletionsarbor/backends/gpu/matrix_interleave.hpp
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