- Jul 06, 2018
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Who broke the build? Sam did!
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- Jul 05, 2018
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Fixes issue #517. Deprecate the IBM xlC compiler. xlC generates code that is an order of a magnitude slower than gcc, while generating spurious warnings, and requiring hacks and workarounds to pass all tests. Supporting it makes no sense. * Add test and fatal error for xlC detection in CheckCompilerXLC.cmake. * Move xlC 13 misdetection work around to CheckCompilerXLC.cmake. * Remove xlC-specific compatibility workarounds from code.
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This time we're moving `recipe.hpp` and `simulation.hpp`, plus the requirements they bring. Code changes: * Pimplize `simulation`. * Consolidate arbor exceptions: all non-cell kind specific exceptions that might be expected to reach user code now have consistent messages and fit in an exception hierarchy based at `arb::arbor_exception`. Internal errors throw an `arb::arbor_internal_error` exception. * Renamed `postsynaptic_spike_event` to `spike_event`. (Note: `pse_vector` name is unchanged.) * Repurposed `pprintf` and moved it into `strprintf.h` — further consolidation is a TODO. * Made a generic `util::to_string` to avoid redundancy of `operator<<` overloads and other `to_string` definitions. Defaults to ADL `to_string`, `std::to_string`, and finally tries using `operator<<`.
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- Jul 03, 2018
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Further work to public install target. * Move SIMD classes, cell description classes, simple sampler to public include. * Rename `cell` to `mc_cell`, `segment` to `mc_segment`, and remove `_description` from cell description class names and includes. * Move `compartment_model` out of `mc_cell` interface and use only in `fvm_layout.cpp`. * (Provisionally) remove area/volume methods on `mc_cell` and `mc_segment`.
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- Jun 25, 2018
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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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