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

Use correct profiling and mpi flags.
Fix profiler doc

This small refactor simplifies the interface and implementation of the `tree` type.
* use `std::vector` instead of `memory::array` for internal storage in `arb::tree`
* return a `util::range` intstead of a view for `tree::children(int)`
* remove unused functionality for changing the root of a tree.

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. 

Fixes #139.

* Split colours and `pprintf(...)` into `io/pprintf.hpp` header.
* Remove generic `to_string()` function, replacing its very occasional usage with `pprintf`.
* Move block pretty printing into own .cpp file; this is the only place that the vector ostream printer was used.
* Remove `enum_hash`, as not needed with C++14.
* Move `is_in` utility function to `util.hpp`.
* Remove old SIMD printer backend code.

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

* Perform device-to-device copy when device_reference is assigned a device_reference.

Better error message on missing file.

* Don't call a missing file an 'internal compiler error'.

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

Cthreads classes:
- Notification queue : Manages tasks: tries or forces popping and pushing tasks.  
- Task system : manages the notifications queues; controls which queue to pop from/push to; controls spinning on queues if necessary; manages creating/joining threads. Is a singleton.
- Task group : manages synchronization on a group of tasks. 

Operation: 
- Each thread has an associated queue
- Task system _tries to_ push tasks in one of the available queues. If it is unable to acquire a lock on a queue, it tries the next in a round robin fashion. After it loops all queues if it still hasn't successfully pushed the task, it spins on a single queue until lock is acquired and task is pushed. 
- Task system _tries to_ pop a task from the calling thread's queue. If it is unable to acquire the lock, it tries to steal the task from another thread's queue, in a round robin loop. If it is still unable to pop a task, it spins on its the c...

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

Fixes #526.

Fixes issue #524.

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

Fixes #182.

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 for generic arithmetic tests.

Fixes #358.

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

Who broke the build? Sam did!

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

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.

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_CHA...

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

The built in profiler generates timings for state and current for individual multicore mechanisms.

Modcc generates and PE(advance_integrate_{state,current}_X) profiler calls (along with corresponding PL() for calls to multicore mechanism nrn_state and nrn_current API calls.

No timings are made for the gpu back end, which is not properly supported by the current profiling tools.

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

Changes have been made to the simd implementation of mechansim functions: 

- The node_index array (array of indices that specifies for each mechanism the CVs where it is present), is now partitioned into 4 arrays according to the constraint on each simd_vector in node_index:
    1. contiguous array: contains the indices of all simd_vectors in node_index where the elements in simd_vector are contiguous
    2. constant array: contains the indices of all simd_vectors in node_index where the elements in simd_vector are identical
    3. independent array: contains the indices of all simd_vectors in node_index where the elements in simd_vector are independent (no repetitions) but not contiguous 
    4. none array: contains the indices of all simd_vectors in node_index where the none of the above constraints apply

    When mechanism functions are executed, they loop over each of the 4 arrays separately. This allows for optimizations in every category. 

- The modcc...

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

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

Replace hard-coded index variable names in modcc cuda printer with ones derived from the external variable.

Uses `decode_indexed_variable`.

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

* Use `sys/types.h` instead of `endian.h` for greater portability.
* Avoid use of constructor for `std::vector` in unit tests that is only available from C++14.

* Update SIMD developer docs to reflect newly merged mechanism refactor work.

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.
* Exte...

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

Add two new documentation pages for the C++ API

* Add domain decomposition page that covers `domain_decomposition`, `node_info` and `partition_load_balance`.
* Add simulation page that describes `arb::simulation` API interface.
* Fix some small typos elsewhere in the docs.
* Use `std::move` when adding spike callbacks to `arb::simulation` (useful if callbacks are stateful).

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

Fixes issue #467 

* Add GPU synchronization points where required for Kepler to coordinate CPU access of managed memory.
* Use hand-rolled double precision atomic addition for Kelper targets.
* Replace `ARB_WITH_CUDA` build option with `ARB_GPU_MODEL` option that takes one of 'none', 'K20', 'K80' or 'P100', and set up source-code defines accoringly.
* Clean up of redundant compiler flags and defines no longer required now that the project uses separate compilation for CUDA sources.

Fix some typos in the SIMD documentation.

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

Put all the SIMD docs in a single topic, to simplify the documentation tree.

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

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.

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`.

fixes #446.