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  1. Apr 05, 2018
    • Ben Cumming's avatar
      Add C++ docs for recipe (#461) · bc6fcffd
      Ben Cumming authored and Sam Yates's avatar Sam Yates committed
      Add some C++ API documentation.
      
      * Create C++ API section in docs.
      * Document `arb::recipe`: both a class reference along with more explanatory text and best practices guide.
      * Add some class documentation of basic types required to understand recipe definition.
      * Some in-code comment clean up.
      * Change `arb::cell_kind` from a vanilla enum to a scoped enum.
      bc6fcffd
  2. Mar 29, 2018
    • Ben Cumming's avatar
      rename class 'model' to 'simulation' (#462) · 2b2044a6
      Ben Cumming authored and Sam Yates's avatar Sam Yates committed
      The name `arb::model` did not clearly describe the role of the class, while `arb::simulation` better captures that this is an instantiation of a model for the purpose of running a simulation, as distinct from the description of a model represented by an `arb::recipe` instance.
      
      * Rename sources `model.{hpp,cpp}` to `simulation.{hpp,cpp}`.
      * Rename class `arb::model` to `arb::simulation`.
      * Update docs and tests to suit.
      2b2044a6
    • Ben Cumming's avatar
      merge all SIMD docs into a single topic (#463) · 3d83af5b
      Ben Cumming authored and Sam Yates's avatar Sam Yates committed
      Put all the SIMD docs in a single topic, to simplify the documentation tree.
      3d83af5b
  3. Mar 27, 2018
    • Ben Cumming's avatar
      Installation Guide (#459) · 0cf65a4c
      Ben Cumming authored
      Added an installation guide to the Read The Docs
      Removed the outdated build/install information from README.md
      Link from README to Read The Docs
      Updated the splash page for Read The Docs
      0cf65a4c
    • Ben Cumming's avatar
      wrap warp intrinsics to fix depricated warnings (#456) · 7e6ea389
      Ben Cumming authored
      CUDA 9 introduced new, fine-grained, thread synchronization primitives.
      In doing so, it introduced new forms of the warp intrinsics like __shfl_up, depricating the old symbols in the process.
      
      It will be a while before we can use 9 as the default minimum, so we have to support compilers that expect the new and old behavior.
      
      There are two options: wrap the intrinsics in question, or pass nvcc a flag to not issue warnings about depricated symbols. I go for the approach of wrapping, because I would rather keep the compiler warning turned on.
      
      Fixes #379.
      7e6ea389
  4. Mar 26, 2018
    • Sam Yates's avatar
      Add padded allocator for aligned and padded vectors. (#460) · 581c4ef3
      Sam Yates authored
      Padded vectors with run-time padding/alignment guarantees will form the basis of the storage class for the new CPU and SIMD generated mechanisms.
      
      * Add `padded_allocator` that aligns and pads allocations.
      * Make microbenchmark for `default_construct_adaptor` that overrides the allocator construct() to default- instead of value-initialization on values.
      * Add `with_instrumented_malloc` class for tracking malloc, realloc, etc. calls.
      * Add unit tests for `padded_allocator`.
      581c4ef3
  5. Mar 20, 2018
  6. Mar 19, 2018
    • Sam Yates's avatar
      Avoid intermediate underflow in expm1 calc with ftz. (#454) · 1499bf1e
      Sam Yates authored
      Intel compiler with default options does not guarantee correct fp behaviour with subnormals; it presumably sets the fp state to flush to zero.
      
      Reordering a multiply and divide in the expm1 calculation avoids a transient subnormal value that was causing the routine to incorrectly return zero for very small, but normal, arguments.
      1499bf1e
  7. Mar 16, 2018
    • Sam Yates's avatar
      Fix broken namespace renaming in SIMD (#453) · f3be6dff
      Sam Yates authored
      f3be6dff
    • Sam Yates's avatar
      SIMD wrappers for Arbor generated mechanisms. (#450) · 2dff9c41
      Sam Yates authored
      This provides a bunch of SIMD intrinsic wrappers as a precursor to the SIMD printers.
      
      The aim is that the SIMD printer can be agnostic regarding the particular vector architecture.
      
      The design is based rather loosely on the proposal P0214R6 for C++ Parallelism TS 2. The transcendental function implementations are adapted from the existing SIMD architecture-specific code, which in turn are based on the Cephes library algorithms.
      
      The custom CSS for the html documentation have been tweaked.
      2dff9c41
    • Ben Cumming's avatar
      5fe81e83
    • Ben Cumming's avatar
      refactor git submodule support in cmake (#448) · 4c66432f
      Ben Cumming authored
      In some places our CMake scripts were attempting to check out git submodules when required, if they have not already been checked out. The code that does this was cut and pasted, and was getting unwieldy.
      
      To minimise the responsibilities of CMake, this PR
      
      removes calls to git
      introduces a function check_git_submodule that can be used to test if a git submodule is installed, and print a helpful message that informs the user how to check it out if needed.
      introduces a function add_error_target that makes a target that prints a message then quits with an error. This can be used to generate a proxy target when a problem is detected during CMake setup. This means that an error is only generated when building a target with a missing dependency, instead of an error during CMake setup.
      refactors the CMake setup for the docs and ubenches targets to use these new features.
      4c66432f
  8. Mar 15, 2018
    • Ben Cumming's avatar
      Improve TBB vs. CMake (#451) · 459d6562
      Ben Cumming authored
      This replaces the CMake templates provided by TBB with a much more sane alternative!
      
      The TBB CMake templates had a very strange workflow, that involved downloading the TBB source and compiling it, which made it impossible to configure the TBB build, and caused problems on systems without connection to the internet.
      
      We replace this with a fork of the TBB repository maintained by Github user @wjakob:
      https://github.com/wjakob/tbb
      This fork provides a sane CMakeLists.txt that can be configured from our CMake setup.
      It is added as a git submodule, so it can be downloaded with the rest of the repository, hence not requiring connection to the internet during CMake configuration.
      
      It could be extended to use a user-provided build of TBB to use instead of building it.
      
      fixes #332.
      459d6562
    • Ben Cumming's avatar
      Multithreading friendly profiler (#447) · 1e461b1b
      Ben Cumming authored and Sam Yates's avatar Sam Yates committed
      Replace the profiler with a simpler design that works for nested multi-threaded regions.
      
      * Replace hierarchical profiler accounting with strictly exclusive regions.
      * Make tree grouping of profile data a presentation concern.
      * Uncouple profiler semantics from Arbor classes such as `model`.
      * Add thorough documentation for the new profiler to the library documentation.
      1e461b1b
  9. Feb 28, 2018
    • Ben Cumming's avatar
      Value semantics for event_generators · aca84730
      Ben Cumming authored
      Use type erasure tricks to remove abstract base class for `event_generator`.
      
      This simplifies all the code that uses `event_generator`s (not radically, but it is simpler).
      aca84730
  10. Jan 29, 2018
  11. Jan 26, 2018
    • kabicm's avatar
      LIF neurons: CPU backend with Brunel Network miniapp (#441) · 2d4bd154
      kabicm authored
      Two main contributions:
      
      1) Implementation of LIF neuron model with no kernel and no external input (I_e=0)
      
      The input current to each neuron is therefore just the sum of all the weights of incoming spikes. We integrate in jumps dt = min(t_final - t, t_event - t), since we know the exact solution of the differential equal describing the membrane potential.
      
      2) Miniapp for simulating the Brunel network of LIF neurons. 
      
      The network consists of 2 main populations: excitatory and inhibitory populations. Each neuron from the network receives a fixed number (proportional to the size of the population) of incoming connections from both of these groups. In addition to the input from excitatory and inhibitory populations, each neuron receives a fixed number of connections from the Poisson neurons producing the Poisson-like input that is integrated into the LIF cell group so that the communication of Poisson events is bypassed. 
      2d4bd154
  12. Jan 25, 2018
  13. Jan 18, 2018
  14. Jan 15, 2018
    • Sam Yates's avatar
      Fix improper brace-initialization in unit test. (#437) · 81d8d0b5
      Sam Yates authored
      * Replace improper use of brace initialization of vectors of classes with a deleted move constructed with a sequence of `emplace_back` invocations.
      81d8d0b5
    • Ben Cumming's avatar
      Fix event-generator bugs in model (#439) · c27757f9
      Ben Cumming authored
      There were two latent bugs in the event generation part of `model`.
      
      1. A segmentation fault when initializing the `event_generators` in the `model` constructor caused by using an index variable after it had been incremented.
      2. Events generated during the first epoch were not delivered on time.
      
      The first issue was simple to fix, by ensuring that the coutning variable is incremented at the end of the loop.
      
      The second issue required refactoring the event wrangling inside `model`. Events can be introduced into a model via three sources:
      
      1. Generated by spike exchange
      2. By calling the `model::inject_events()` interface
      3. `event_generator`s attached to cells.
      
      The refactoring was required to ensure that all three sources are handled correctly. There is further opportunities for refactoring the code to make it a bit cleaner, specifically putting the wrangling code in its own type that could be tested seperately, outside `model`, but that is beyond the scope of this fix. 
      c27757f9
    • Ben Cumming's avatar
      Make cell type copyable by default (#430) · 51d09f7d
      Ben Cumming authored and Sam Yates's avatar Sam Yates committed
      * Enable `cell` copy constructor, remove special tag type used to guard `cell` cloning.
      * Provide sane defaults for `recipe` methods.
      51d09f7d
  15. Dec 22, 2017
  16. Dec 21, 2017
    • Sam Yates's avatar
      Fix indirection in ion concentration write. (#425) · 17f7db98
      Sam Yates authored
      * Fix indirection in ion concentration write.
      * Remove second indirection in ion write assignment.
      * Extend ion write unit test to cover non-contiguous ion CV cases and verify correct ion concentration averaging.
      
      Fixes #424.
      17f7db98
  17. Dec 20, 2017
    • Ben Cumming's avatar
      Move miniapps path to 'example/' (#423) · f94f0eab
      Ben Cumming authored and Sam Yates's avatar Sam Yates committed
      * Rename `miniapps` subdirectory to `example`.
      * Have all example executables be built under `example` in the build directory.
      * Update Travis CI to run miniapp from new path.
      f94f0eab
    • Ben Cumming's avatar
      Add granule cell mechanisms (#421) · a80df6fa
      Ben Cumming authored and Sam Yates's avatar Sam Yates committed
      * Add three new mechanisms: `nax.mod`, `kdrmt.mod` and `kamt.mod`.
      * Add new built-in math operators to `modcc`: `min`, `max`, `abs` and `exprelr`. `exprelr` is defined as the reciprocal of the 'exprel' function, exprel(x)=x/(exp(x)-1), exprel(1)=1. This function occurs frequently in HH-style mechanisms, and having a built-in operator avoids the ad hoc `vtrap` functions found in NMODL files in the wild.
      * Split Arbor SIMD intrinsics support into AVX2- and AVX512-specific files.
      * Add unit tests for new maths operators for C++, SIMD and CUDA implementations.
      a80df6fa
  18. Dec 19, 2017
    • Sam Yates's avatar
      Reduce differences between `util::optional` and `std::optional`. (#420) · 80fe2f01
      Sam Yates authored
      Reduce differences between `util::optional` and `std::optional`.
      
      * Rename `util::nothing` to `util::nullopt`.
      * Replace `util::get()` by`util::optional::value()`.
      * Add correct move semantics to `util::optional::value()`.
      * Add `util::optional::value_or()` method.
      * Remove unused monadic functionality from `util::optional` and `util::uninitialized`.
      * Update code formatting to closer adhere to coding guidelines.
      * Add convenience ""_s string constructor for unit tests.
      * Update unit tests accordingly.
      
      Fixes #419.
      80fe2f01
  19. Dec 18, 2017
  20. Dec 16, 2017
    • Ben Cumming's avatar
      Implement cell-local event generators (#414) · 70d58166
      Ben Cumming authored
      Implement generic `event_generator`, and some common generators that should be useful to users out of the box:
      * poisson sequence                                                                                       
      * uniform regular sequence
      * from a user-prescribed sequence
      * from a `std::vector` of post synaptic events.
      
      Extend `recipe` API to provide an `recipe::event_generators(gid)` that returns a list of `event_generator`s attached to a cell with `gid`.
      
      Update the `model` class and `merge_events` method to support event generators.
      
      Fixes #401 
      70d58166
  21. Dec 11, 2017
    • Wouter Klijn's avatar
      410 rss cell bug (#411) · 1bd65e13
      Wouter Klijn authored
      Fix bug in `rss_cell_group`s with more than one cell with different `dt` or `start_time` values.
      Fixes #410.
      1bd65e13
  22. Dec 05, 2017
  23. Nov 30, 2017
    • Wouter Klijn's avatar
      Move miniapp sources to a miniapps directory (#408) · 3b5b0386
      Wouter Klijn authored
      Restructure the miniapp in such a way that we have to option to have multiple parallel mini-applications.
      
      Move the original miniapp directory to a miniapps directory.
      Output executable also in a nested miniapps directory.
      Update the Travis to point to the new executable location.
      3b5b0386
  24. Nov 29, 2017
    • Ben Cumming's avatar
      support ion species concentration updates (#398) · fa7d99b6
      Ben Cumming authored and Sam Yates's avatar Sam Yates committed
      * Add querying methods to modcc ion species type to simplify code generation.
      * Add `WriteBack` type that records per-mechanism ion usage metadata.
      * Add `write_back` implementation for C and CUDA printers that adds weighted concentration
        contributions to global concentration fields.
      * Extend `uses_ion` interface to provide information about which concentration fields are modified by mechanisms.
      * Update `update_ion_symbols` lambda that is responsible for adding metadata about interactions between mechanism fields and external ion species fields, creating a write-back when the mechanism field is a state variable or an indexed variable if it is a current/reversal potential, or else an error.
      * Add `test_ca.mod` mechanism that writes calcium ion concentration for testing purposes.
      * Add back-end callbacks that initialize concentration values.
      * Update `mechanism::uses_ion()` to return information regarding mechanism ion concentration updates.
      * Add `mechanism::write_back()` method.
      * Update stimulus mechanism specialization to use new mechanism interface.
      * Update `ion` type to calculate default concentration contributions in CVs where the concentration is only partially determined by mechanisms.
      * Update `fvm_multicell` to calculate the default ion concentration weights.
      * Add unit test for ion concentration weight determination.
      
      Fixes #373 
      fa7d99b6
  25. Nov 28, 2017
    • Sam Yates's avatar
      Tidy `modcc` driver, remove optimize flag. (#404) · 998ee724
      Sam Yates authored
      * Remove optimization option (use SIMD options for vectorization).
      * Remove arbor utility library dependencies from modcc (pending separation of utility lib from arbor lib source).
      * Split target (cpu, gpu) specification from vectorization architecture (avx2, avx512).
      * Remove `Options` singleton; replace with structure local to `modcc.cpp`.
      * Tidy `modcc` option parsing and main function; allow a single invocation of `modcc` to generate code for multiple backends.
      * Rename generated sources to include backend target in filename.
      * Always run a constant simplification pass on generated procedures.
      * Remove file i/o code from `Module` and `modcc` main function; move functionality to new functions in `io` namespace. (Note: in on-going mechanism revamp, other i/o utility code will reside in the `io` namespace and subdirectory.)
      * Remove classes `ConstantFolderVisitor` and `ExpressionClassifierVisitor` that are no longer used.
      * Modify CMakeLists.txt files, `backends/*/fvm.cpp` to reflect the new filenames of generated sources.
      * Small formatting changes in `modcc` source to reflect coding guidelines (incomplete).
      998ee724
    • Sam Yates's avatar
      Fix binary operator parentheses bug. (#400) · 67721f02
      Sam Yates authored
      Fixes #399.
      
      Update `test_printers.cpp`:
      * Fix compilation and scope management issues, and re-include in CMakeLists.txt.
      * Update to use `verbose_print` (run-time verbosity).
      * Apply expected output tests to `CPrinter` and `CUDAPrinter` outputs.
      
      Address binary operation rendering issue:
      * Move C-style expression rendering common to `CPrinter` and `CUDAPrinter` to a specialized `Visitor`, `CExprRenderer`.
      * Use operator associativity to determine need for parentheses around sub-expressions of a binary expression.
      67721f02
  26. Nov 20, 2017
    • Ben Cumming's avatar
      Fix GPU event delivery bugs (#394) · 8566655c
      Ben Cumming authored and Sam Yates's avatar Sam Yates committed
      * Properly iterate over all event queues in the case where a cell group has more than once cell (triggered in e.g. GPU miniapp).
      * Update GPU unit test to use the new `cell_group::advance()` interface.
      8566655c
    • Ben Cumming's avatar
      modcc now enforces derivatives only on state variables (#392) · 87a52776
      Ben Cumming authored and Sam Yates's avatar Sam Yates committed
      Derivatives should only appear on the left hand side of expressions that describe the time evolution of state variables. Without this check `modcc` segfaulted when processing a derivative expression of a non-state variable.
      
      * Specialize the semantic analysis of `DerivativeExpression` to enforce that derivatives are only applied to state variables.
      87a52776
  27. Nov 16, 2017
    • Ben Cumming's avatar
      Move event wrangling from cell_group to model (#390) · c76c0520
      Ben Cumming authored and Sam Yates's avatar Sam Yates committed
      * Remove `cell_group::enqueue_events` interface: `cell_group::advance` is given the events to deliver in the next epoch directly.
      * Implement event lane merging in `model` with stand-alone `merge_events` function.
      * Ensure event-delivery order is preserved across differing domain decompositions by performing a lexicographic sort over all of the `postsynaptic_spike_event` fields: fixes #385. 
                                                                                                               
      Fixes #378.
      c76c0520
    • Sam Yates's avatar
      Add custom streambuf for indented output. (#391) · 2fe61d04
      Sam Yates authored
      These classes aim to provide an alternative to `TextBuffer` in `modcc` printers.
      
      * Implement a streambuf wrapper `prefixbuf` that prepends a prefix string to each line.
      * Adds stream manipulators `setprefix`, `indent`, `popindent`, `settab` for manipulating the prefix in a `prefixbuf`.
      * Provide a wrapper stream `pfxstringstream` around `std::stringbuf` with `std::ostringstream` semantics.
      
      As implemented, a prefix string set with the `setprefix` is applied to the underlying streambuf, and is not a property of the stream. This behaviour may be surprising, so consider storing this prefix with the stream as a possible enhancement.
      2fe61d04