Extend the ring benchmark to have an optional number of synapses attached to each cell, instead of a fixed count of one synapse per cell.
This doesn't change the behavior of the model: only the first synapse is used for communication. The other synapses only effect is to
increase the per-cell computational overheads, to more effectively mimic real world performance.

noraabiakar authored 6 years ago and Benjamin Cumming committed 6 years ago

Dry-run mode: 
* An implementation of distributed_context that is used to mimic the performance of running an MPI distributed simulation with n ranks.
* Verifiable against an MPI run with the same parameters. 

Implementation: 
* Describe the model on a single domain (tile) and translate it to however many domains we want to mimic using arb::tile and arb::symmetric_recipe. This allows us to know the exact behavior of the entire system by only running the simulation on a single node.
* Mimic communication between domains using arb::dry_run_context

Example: 
* dryrun in example/ is a verifiable example of using dry-run mode with mc_cells

Other:
* Documentation of dry-run mode 
* unit test for dry_run_context 

Turns out that CMake thinks Clang and AppleClang are different things.

Make the execution context presented to users an opaque handle, moving all implementation of the gpu, thread and distributed contexts into the back end.

* move `execution_context` and `distributed_context` definitions to the back end
* create `execution_context` handle called `context` in the public API
* provide `make_context` helper functions that build different context configurations (default, user-specified local resources, with MPI)
* update documentation for all parts of the public API that touch contexts
* move `distributed_context` docs to the developer documentation (from the public API docs)

Benjamin Cumming authored 6 years ago and Sam Yates committed 6 years ago

* Add new ring benchmark to examples.
* Refactored common functionality for reading miniapp parameters from a json file to `aux` (used by both bench and ring).

Fixes #516.

noraabiakar authored 6 years ago and Sam Yates committed 6 years ago

* Replace distributed_contest with shared_ptr<distributed_context> in execution_context and pass around the shared pointer instead of a raw pointer.
* Fix construction of mpi_context
* Remove num_threads() from arb and arb::threading. Modify mpi_context so it also returns a shared_ptr. proc_allocation is initialized from execution context to determine available resources.
* Rename threading backend files. Delete useless files.
* Pass execution_context by const reference or value.
* Remove code duplication in thread_system constructors.

Reduce redundant functionality across event_generator, time_seq
and schedule by providing a low-heap overhead interface to schedule
and using that for time sequences in event_generator and specialized
cell groups.

* Have schedule return pair of pointers as view to generated times.
* Fix missing DEBUG/TRACE functionality.
* Use rate instead of mean_dt for Poisson schedule.
* Move merge_events() functionality to simulator.cpp.
* Migrate event_generator to event span interface.
* Migrate tourney_tree to event span interface.
* Only invoke tourney_tree merge if generators have events in the epoch.
* Use schedule for times in event_generator implementations.
* Replace seq_generator with explicit_generator that keeps a copy of events.
* Replace vector_backed_generator and poisson_generator with schedule_generator.
* Replace time_seq uses with schedule.
* Add default empty schedule.
* Move rounding error test for regular time sequence into schedule test.
* Update sampling API documentation for schedule.

noraabiakar authored 6 years ago and Benjamin Cumming committed 6 years ago

Use correct profiling and mpi flags.
Fix profiler doc

noraabiakar authored 6 years ago and Benjamin Cumming committed 6 years ago

Add initialize method to the profiler to set up the needed threading parameters given a simulation's task system.

noraabiakar authored 6 years ago and Benjamin Cumming committed 6 years ago

- Task system is no longer a single system private to the implementation of the threading backend and used everywhere. A separate task_system can be used (with a specified number of threads) for every simulation.
- arb::execution_context is the interface to task_system  and the previously defined distributed_context
- TBB and serial support has been removed. Cthreads is the only threading backend available. 

Sam Yates authored 6 years ago and Benjamin Cumming committed 6 years ago

All example code and validation tests no longer require access to private include directories. This provides the minimal requirement for an installable target

Note that it is still not possible to separately build mechanisms from NMODL with just the public includes, and there is not yet any package configuration file creation for use with CMake or pkg-config.

* Replace `hw::node_info` with `proc_allocation`, describing local resources for the purposes of domain decomposition.
* Group processor counting and gpu counting implementation under `node_info.cpp`.
* Remove `domain_decomposition` dependency from `cell_group_factory.hpp` so we can use the latter to test for backend support for a cell kind.
* Add `arb::cell_kind_implementation()` which performs the mapping from cell kind and backend kind to a `cell_group_ptr`-producing function (this will then become the site for custom cell group kind mapping support in future work).
* Move headers for aux library ...

Sam Yates authored 6 years ago and Benjamin Cumming committed 6 years ago

Migrate source/build to c++14                                                                                                                    (#522)

* Update `CMakeLists.txt` for C++14 option.
* Update to gcc 6 minimum.
* Update travis CI from gcc-5 to gcc-6
* Use `std::..._t` style type traits, replacing `util::` aliases.
* Use `std::cbegin`, `std::cend`, and `std::make_unique`, replacing `util::` versions.
* Remove `DEDUCED_RETURN_TYPE` macros.
* Remove redundant return type specifications.
* Use correct ADL for `begin` and `end` in (almost all) the range utilities.
* Remove redundant `mechinfo` ctor (aggregate initialization suffices).
* Use lambda capture initializers where appropriate.
* Use generic `std::equal_to`.
* Use variable templates for `math::infinity` and `math::pi`.
* Remove `enum_hash` workaround.
* Use `""s` string literals where we were using our own `""_s` construction.
* Use generic lambda for recursive lambda instead of `std::function` wrapper.
* Use generic lambda ...

Sam Yates authored 6 years ago and Benjamin Cumming committed 6 years ago

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<<`.

Sam Yates authored 6 years ago and Benjamin Cumming committed 6 years ago

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`.

Sam Yates authored 6 years ago and Benjamin Cumming committed 6 years ago

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.

Add a new cell type, and corresponding cell_group implementation, for benchmarking the simulator library architecture.

Add an benchmark_cell_group, where each cell in the group

generates a spike train prescribed by a time_seq
takes a prescribed time interval per cell to perform the cell_group::advance method.
With this cell type, one can easily build arbitrary networks with prescribed spiking and cell update overheads.
A miniapp that uses this cell type to build a benchmark model is implemented in example/bench.

Fixes #493
Fixes #501

Changes to libarbor
-------------------------

Time sequences were added in `src/time_sequence.hpp`:
- added new `time_seq` type that implements a type-erasure interface for the
  concept of a time sequence generator.
- added poisson, regular and vector-backed implementations of the time sequence
  concept.

Event generators:
- The poisson, regular and vector-backed implementations of the event generator
  concept were refactored to use the.

Cell groups:
- Removed the `dss_cell_group` and `rss_cell_group` and associated types.
- Added a generic spike source cell  that generates a sequence of spikes
  at time points specified by a `time_seq`. Using this approach, an
  additional `cell_group` specialization is not required for each type of
  sequence, and user-defined sequences can be used with minimal overhead.

Unit tests
------------

- Added unit tests for `time_seq`.
- Simplified `event_generator` unit tests, because much of the testing
  of the sequences was moved to the `time_seq` tests.
- Added unit tests for `spike_source_cell_group`.

Changes to miniapp
-------------------------

- simplified the miniapp by removing the command line options for using an input spike chain from file.
- updated the miniapp recipe to use `spike_source` cell group instead of `dss_cell_group`.

Benjamin Cumming authored 6 years ago and Sam Yates committed 6 years ago

Move from choosing the distributed communication model from a compile time choice (the old `arb::communication::communication_policy` type) to a run time decision.

* Add `arb::distributed_context` class that provides the required interface for distributed communication implementations, using type-erasure to provide value semantics.
* Add two implementations for the distributed context: `arb::mpi_context` and `arb::local_context`.
* Allow distribution over a user-supplied MPI communicator by providing it as an argument to `arb::mpi_context`.
* Add `mpi_error` exception type to wrap MPI errors.
* Move contents of the `arb::communication` namespace to the `arb` namespace.
* Add preprocessor for-each utility `ARB_PP_FOREACH`.
* Rewrite all examples and tests to use the new distributed context interface.
* Add documentation for distributed context class and semantics, and update documentation for load balancer and simulation classes accordingly.

Fixes #472

Benjamin Cumming authored 6 years ago and Sam Yates committed 6 years ago

Completes CUDA printing in modcc.
* Add CudaPrinter visitor, overriding CPrinter.
* Add `ostream` `operator<<` overloads for `arb::gpu::shared_state` and `device_view` for debugging.
* Fix GPU back-end bugs.

First commit of two for mechanism refactor work (refer to PR #484 and PR #483).

FVM/mechanism code:
* Refactor mechanism data structures to decouple backend-specific implementations and mechanism metadata.
* Add mechanism catalogue for managing mechanism metadata and concrete implementation prototypes.
* Add fingerprint-checking to mechanism metadata and implementations to confirm they come from the same NMODL source (fingerprint is not yet computed, but tests are in place).
* Split FVM discretization work out from FVM integrator code.
* Use abstract base class over backend-templated FVM integrator class `fvm_lowered_cell_impl` to allow separate compilation of `mc_cell_group` and to remove the dummy backend code.
* Add a new FVM-specific scalar type `fvm_index_type` that is an alias for `int` to replace
`fvm_size_type` in fvm layouts and mechanisms. This was chosen as an alternative
to making `unsigned` versions of all our SIMD implementation classes.
* Extend `cable1d_neuron` global data to encompass: mechanism catalogue; default ion concentrations and charges; global temperature (only for Nernst); initial membrane potential.

Modcc:
* Collect printer sources in modcc under `printer/`.
* Move common functionality across printers into `printer/printerutil.{hpp,cpp}`.
* Add string to file I/O implemented in routines read_all and write_all in `io/bulkio.hpp`.
* Implement indent-friendly source code generation via a `std::streambuf` filter `io::prefixbuf` defined in `io/prefixbuf.hpp`, together with manipulators and a corresponding std::ostream-derived wrapper.
* Rewrite printers to use new infrastructure: cpu target incorporates SIMD printing options; CUDA printer at this point produces only stubs for CUDA kernel wrappers.
* Modify SIMD printing command line options for modcc: `-s` enables explicit vectorization using the SIMD classes;  `-S <N>` allows a specific data width to be prescribed.
* Fix problem in `test_ca.mod` with uninitialized ion current.
* Add infrastructure support to allow future pre-computation of SIMD index conflict cases for (hopefully) faster scatters and updates.
* Simplify `IndexedVariable` expressions in the AST, making data source explicit via a `sourceKind` enum, and leaving the indexing method and index names up to the printers.
* Allow state variables in the AST to 'shadow' an ion concentration — these are assigned in the
generated `write_ions` method.

SIMD classes:
* Add `simd_cast` operation between SIMD value types of the same width, and with `std::array`. (Note: this was tested and used in an early development version of the code, but not in this version. It was still a lacuna in the original SIMD wrappers, so it has been left in.)
* Restructure SIMD gather/scatter API to use a `simd::indirect` expression,  which encapsulates a pointer and SIMD offset.
* Add `simd::index_constraint` scoped enum to describe knowledge of contention in indirect indices, so that we can branch on this to the appropriate implementation.
* Add SIMD concrete implementation routines `reduce_add` for horizontal reduction and `element0` for access to first lane scalar value.
* Add SIMD value method `sum()` that exposes implementation `reduce_add`.
* Add SIMD concrete implementation routine `compound_indexed_add` that provides the implementation for `indirect(p, simd_indices) += simd_value` construction.
* Fix SIMD `implbase` bug where some static methods were using the `implbase` fall-back functions instead of the derived class specialized implementations.
* Move SIMD mathematical functions into friend routines of `simd_impl` in order to resolve implicit conversions from scalars in mixed SIMD-scalar operations.
* Use a templated `tag` class to dispatch on SIMD concrete implementation types, to avoid problems with incomplete types in method signatures.
* Remove old SIMD intrinsics.

CMake infrastructure:
* Downcase some variables in `CMakeLists.txt` files to  distinguish them visually from CMake keywords and variables.
* Split arbor modcc vectorization option (now `ARB_VECTORIZE`) and target-architecture optimization (now `ARB_ARCH`).
* For `arbor` and `arbormech` targets, and in particular not the `modcc` target, use `ARB_ARCH` to generate corresponding target-appropriate binaries, including, for example, appropriate SIMD support.
* Extend `CompilerOptions.cmake` to map as best as able between the various target architecture names (we use the gcc names) and the correct option to pass to the compiler based on the compiler and platform.
* Add work-around for misidentification by CMake of XL C as Clang.
* As a temporary work-around, include `arbormech` library twice on link line to resolve circular arbor–arbormech dependencies.

Unit tests:
* Extend repertoire of generic sequence equality/near equality testing support  in `common.hpp`.
* Add warning suppression for icc for the malloc instrumentation code.
* SIMD unit tests for indirect expressions, compound indirect add, reduction.
* Make some exact tests into floating point 'near' tests when comparing computed areas and lengths in swc and fvm layout tests, to account for compiler (e.g. icc) performing semantically inequivalent floating point operation reordering or fusion at `-O3`.
* Split out some of the CUDA tests into separate .cpp/.cu files for  separate-compilation purposes.

Other:
* The `padded_allocator` has been modified to propagate alignment/padding on move and copy (these semantics make their use much easier and safer in the multicore mechanism instantiation code).
* Map/table searching utilities in `util/maputil.hpp`.
* Fixes for correct sequence type categorization and `begin/end` ADL.
* Fixes for type guards for range methods that take universal references.
* Removal of some redundant code in range utilities through the use of universal references.
* Add new range view `reverse_view` for ranges delineated by bidirectional iterators.
* Add single argument form of `make_span` to count up from zero, and associated helper `count_along` that gives a span that indexes a supplied container.
* Moved `prefixbuf` to `modcc` source.
* Make sequence positive and negative tests in algorithms generic.
* Add `private`-subverting helper code/macro to `tests/unit/common.hpp` to reduce the number of public testing-only interfaces in the library code.
* Add virtual destructors for virtual base classes.
* Add new arb::math:: functions: `next_pow2` for unsigned integral types, `round_up` to round a number away from zero to next largest magnitude multiple.
* New `index_into` implementation that supports bidirectional access (moved to `util::` namespace).
* Fix problem in `test_ca.mod` with uninitialized ion current.
* Rework dangerous `memory::array(Iter, Iter)` constructor to be less dangerous (and do the expected thing).
* Allow ranges to be constructed from other ranges if the iterators are compatible.

Ben Cumming authored 7 years ago and Sam Yates committed 7 years ago

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.

Ben Cumming authored 7 years ago and Sam Yates committed 7 years ago

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.

Ben Cumming authored 7 years ago and Sam Yates committed 7 years ago

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.

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).

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. 

Add an example miniapp that demonstrates how to use event generators in a C++ recipe.

Ben Cumming authored 7 years ago and Sam Yates committed 7 years ago

* Enable `cell` copy constructor, remove special tag type used to guard `cell` cloning.
* Provide sane defaults for `recipe` methods.

Ben Cumming authored 7 years ago and Sam Yates committed 7 years ago

* 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.