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 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. 

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

Add a micro-benchmark that illustrates scaling issues with event-setup on cell groups with many cells.

The benchmark also illustrates some alternative approaches that are significant optimizations over the current approach.

Fixes #357.

* Use ARB_ and arb_ as variable prefixes in place of NMC_ and nmc_.
* Replace references to 'NestMC' and 'NEST MC' to refer instead to Arbor.
* Use 'arbor' as the sim name in generated validation data.
* Reflow long-line paragraphs in `tests/ubench/README.md`.
* Change names of CUDA mechanism and CUDA kernel libraries to include arbor name.

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

Virtualization of the `cell_group` interface is necessary for support of other (i.e. non-multicompartment) cell models, including e.g. Poisson spike generators.

* Make `cell_group` an abstract base class; the previous `cell_group` class that is parameterized by the back-end FVM implementation is renamed `mc_cell_group` ('mc' stands for 'multi-compartment') and derives from the abstract `cell_group`.
* Remove template parameter `Cell` from `model` type: a `model` can in principle now manage multiple types of concrete objects derived from `cell_group`.
* Extend `model` constructor to take a hint about which back-end to use when constructing cell groups: `use_multicore` or `prefer_gpu`. This is a placeholder for a more sophisticated implementation once we have the requirements for a richer "ecosystem" of cell types.
* Simplified some generic types to remove template dependencies between front and back ends:
    * Define a global `using time_type=float` in `common_types.hpp`.
    * Define a concrete `sampler_function` type alias for the `std::function<...>` type used for samplers.
* Use a `null` back-end fallback for GPU if support is not there at compile time.

* Fix CMakeLists to handle build as a subproject

When several CMake generated projects are build together, it is common
practice to have a 'superproject' CMakeLists that uses
  add_subdir(proj1)
  add_subdir(proj2)
  ...
where each subproject is a self contained CMake based project
(Example proj1=HPX, proj2=nestmc, proj3=another, ...)

CMAKE_SOURCE_DIR always points to the top level directory which
is the superproject dir in this case, whereas PROJECT_SOURCE_DIR
always points to the root of the current project() in the CMakeLists
so one shouod use PROJECT_SOURCE_DIR as this gets the relative paths
correct.

* Add option to turn off auto generation from *.mod files

* Fix #134 : Change CMake WITH_OPTION to NMC_WITH_OPTION, compiler #define to NMC_HAVE_OPTION

1) The user may select an option by saying NMC_WITH_XXX

2) This may trigger CMake to use find_package(...) or setup some
other variables. CMake can then set variable NMC_HAVE_XXX and add a
what has actually been used.

3) Code should use #ifdef NMC_HAVE_XXX to check for a feature

Old CMake/define      New CMake                 Compiler #define
----------------      ---------                 ----------------
THREADING_MODEL       NMC_THREAD_MODEL
    WITH_TBB          NMC_WITH_TBB              NMC_HAVE_TBB
    WITH_OMP          NMC_WITH_OMP              NMC_HAVE_OMP
    WITH_SERIAL       NMC_WITH_SERiAL           NMC_HAVE_SERIAL

WITH_MPI              NMC_WITH_MPI              NMC_HAVE_MPI
WITH_CUDA             NMC_WITH_CUDA             NMC_HAVE_CUDA
WITH_GPU                                        NMC_HAVE_GPU
WITH_ASSERTIONS       NMC_WITH_ASSERTIONS       NMC_HAVE_ASSERTIONS
WITH_TRACE            NMC_WITH_TRACE            NMC_HAVE_TRACE
WITH_PROFILING        NMC_WITH_PROFILING        NMC_HAVE_PROFILING

Other user visible CMake vars
-----------------------------
VECTORIZE_TARGET            -> NMC_VECTORIZE_TARGET
USE_OPTIIZED_KERNELS        -> NMC_USE_OPTIIZED_KERNELS
BUILD_VALIDATION_DATA       -> NMC_BUILD_VALIDATION_DATA
BUILD_JULIA_VALIDATION_DATA -> NMC_BUILD_JULIA_VALIDATION_DATA
BUILD_NRN_VALIDATION_DATA   -> NMC_BUILD_NRN_VALIDATION_DATA
VALIDATION_DATA_DIR         -> NMC_VALIDATION_DATA_DIR

Variables such as NMC_THREADING_MODEL and NMC_VECTORIZE_TARGET now use
enumerated cmake values so you can toggle between them in ccmake gui.
SYSTEM_TYPE_CRAY/BGQ        -> NMC_SYSTEM_TYPE (Generic/Cray/BGQ)

* Use generator expression for modcc path

Some IDE's (like Xcode for example), override the CMake binary paths
and add /Debug or /Release etc so rules that have hard coded paths
to binaries will fail.

This PR is part of the gpu feature merge. The GPU implementation is not implemented here. Instead, we focus on refactoring of the original "multicore" back end so that it is ready for adding the GPU back end.

This is a big and messy change, for which I am sorry.

## build System

- A `WITH_CUDA` option has been added to the main CMakeLists. This finds the CUDA toolkit, and sets CUDA compiler flags, and will build unit tests for the gpu back end.
- The CMakeLists that generates mechanisms with modcc has been updated to generate CUDA mechanisms.
- the library is now named `libnestmc` instead of `libcellalgo`
- merge the external libraries that are optionally linked againts (tbb, libunwind, etc) into a single
  `EXTERNAL_LIBRARIES` list for ease of linking

## modcc

- the cprinter and cudaprinter have had small changes to generate mechanism files that are compatible with the refactored library.

## algorithms

- the indexes into algorithm was "rangified". An algorithm `index_into_iterator` takes two ranges as inputs to make a range that lazily generates the index of sub into super set.

## backends

- made a new path `src/backends/` for backend specific type and implementation code.
- currently:
  - complete support for the `multicore` and `gpu` backends
  - `gpu` back end is not optimized or validated
- the back end implementations are in `src/backends`
- a single `backend` class, `nest::mc::{multicore,gpu}::backend`, is provides all backend specific type and implementation details fro each backend
  - storage containers
  - Hines matrix assembly for FVM method
  - Hines matrix solver
  - mechanism "factory"

## lowered fvm cells

- removed `fvm_cell` because this can be modelled with an `fvm_multicell` with one cell.
- refactored to use backend type and implementation from `fvm_policy`
- use `std::vector` instead of containers in `nest::mc::memory::` where possible when building cells.

## memory library

Refactor the "memory" library, making it much simpler and better integrated into the rest of the application. However, it is still far from perfect. The `Coordinator` approach needs to be improved, most likely by putting target-specific wisdom into pointers (which could obviate the need for a `const_array_view` type.
1. renaming and moving
   - move from `vector/` to `src/memory`
   - move into the `nest::mc` namespace, i.e. all types and functions are now in `nest::mc::memory`
   - change from camel case nameing scheme to NestMC style naming.
2. simplification
   - remove the CRTP cruft that was used to make operator overloading work for operations like copying from one range into another, and filling a range with a constant value. These have been replaced with `memory::fill()` and `memory::copy()` helper functions. This simplified the code _a lot_, and makes code clearer in user land.
   
   ```
   // before
   vec(0, 5) = other;
   // now
   memory::copy(other, vec(0, 5));
   ```
   - add some wrappers in `src/memory/wrappers.hpp` that help with making views. These are particularly useful for passing `std::vector` through interfaces that expect a view.

## debug backtraces

Added stack traces for debugging.
- support for OSX and Linux via libunwind
- backtraces can be generated manually `nest::mc::util::backtrace().print()`
  - creates a new file and dumps trace into file
  - prints message to `stderr` with file name and instructions on how to analyse
- backtraces are also automatically generated when an assertion `EXPECTS` statement fails
- a python script in `scripts/print_backtrace` pretty prints the output with file name, line number and demangled symbols

## util simplification and consolidation

The `src/util.hpp` file was removed
- much of its contents were dead code and just removed
- useful components like `pprintf` and `make_unique` were moved into the `src/utils` path in standalone files
There was a lot of overlap between functionality provided in `src/memory/util.hpp` and existing functions/types in the `nest::mc::util` namespace. The `memory` implementations were removed, and their `nest::mc::util` counterparts used. There is still some work remaining, namely moving the rest of the `src/memory/util.hpp` into `src/util/...`

This is a big and unweildy update (the last one, we promise).
- added synapses
    - update to a version of modparser that generates net_receive and
      point process currents
    - added event_queue type for queueing events in a cell
    - added advance_to() method to FVM cell that supports event delivery
    - added synapse storage and modification to cell and fvm_cell types
    - added unit tests and NEURON validation test
- include support for const_views
    - moved to more recent bcumming/vector library with support for
      const_views
    - added const-safe const_view interace to fvm_cell and matrix types