Vasileios Karakasis authored 8 years ago and Sam Yates committed 8 years ago

* Update `README.md` to reflect the CMake options for vectorization.

Vasileios Karakasis authored 8 years ago and Sam Yates committed 8 years ago

Proposed patch to master branch:
* Qualify template in `indirect_view` to accommodate incorrect function template specialization determination (icpc ignores §14.8.2.4/9 rule on lvalue versus rvalue template arguments).
* Use parenthesis constructors for type parameter in `pointer_proxy`, as icpc has not adopted the corrected behaviour for DR#1467 [http://www.open-std.org/jtc1/sc22/wg21/docs/cwg_defects.html#1467].

`cell_tree::depth_from_root()` was incorrectly traversing only
the first branch from the tree root, leading to uninitialized
values in the returned depth array.

This leads to an incorrect maximum leaf node in `find_minimum_root()`,
which then returns `no_parent`. This gets passed to
`tree::change_root(size_t)`.

* Correct `cell_tree::depth_from_root()` implementation.
* Re-enable curiously disabled test case in `cell_tree.from_parent_index`
* Add unit tests for `cell_tree::depth_from_root`.

* Add perl program `cc-filter`, a general purpose by-line text filter with built-in default rules for filtering text containing C++ types and expressions.
* Add documentation for the tool to the scripts `README.md` file.
* Add demonstration table `filters/massif-strip-cxx` for using `cc-filter` with valgrind massif output.

Ben Cumming authored 8 years ago and Sam Yates committed 8 years ago

Fixes #189.

* Add memory usage meter to profiling infrastructure.
* Include GPU memory usage also, when GPU support is enabled.

meter_manager correctly detects first checkpoint, which is necessary to ensure that all the timers are synchronized.

  * An abstract `meter` class that defines interface for taking a reading, and returning the meter results as a json object.
  * A `time_meter` implementation of the `meter` that measures wall time.
  * To generate metering reports with global information, the global communication policy interfaces were extended to support `gather` and `barrier` operations. These are trivial for serial and dry run policies, and wrap the appropriate MPI calls for the MPI policy.
  * a `meter_manager` type that stores a list of meters was created
    * will also have memory and power meters soon.
  * a meter manager was added to the miniapp and now records startup, model initialization, time stepping and final file io times.

* Bug fix: crash on indirect test

* Simplify indirect overloads, add nomove/nocopy tests

* Stage events for next integration interval on lowered cell.
* Use explicit binning for event coalescence.
* Extend `event_queue` to allow checking top of queue against arbitrary predicates.
* Add `--bin-dt` and `--bin-regular` options to miniapp (disable binning with `--bin-dt 0`).
* Tidy up miniapp option settings class.

Integration in lowered cell over multiple steps is deferred until samplers can be set up with back-end polling.

Asynchronous integration itself is not yet implemented.

Ben Cumming authored 8 years ago and Sam Yates committed 8 years ago

Fixes #185.

Add a new back end GPU Hines matrix solver that uses a block-interleaved storage pattern to improve memory coalescing during the matrix solve.

  * Refactor the `src/backends` path into `src/backends/gpu` and `src/backends/multicore` paths that contain `gpu` and `multicore` implementations.
  * Refactor the matrix state and threshold detection members that were declared inline in the back end specifications to separate files.
  * Add a new interleaved matrix state back end.
  * Refactor all of the GPU kernels that were originally in the one back end header file into their own header files.
  * Write more comprehensive unit tests for the GPU matrix solver back end to test the `interleave` and `reverse_interleave` operations in isolation, as well as ensure that the flat and interleaved back ends produce identical results.
  * Add the GPU versions of the kinetic scheme validation tests.

* Implement `indirect_view` for indexed access via `transform_view`.
* Extend `transform_iterator` to permit non-const access to reference-returning functor results.
* Replace use of `indexed_view` with `indirect_view`.
* Fix missing cpu target for vectorized modcc outputs.

Ben Cumming authored 8 years ago and Sam Yates committed 8 years ago

Fixes #212.

* Update the main `CMakeLists.txt` file to select the cthread back end by default, and present the threading options in the order: cthread, tbb, serial.

Fixes #196.

Correct treatment of missing coefficients in `cnexp` solver.

* Extend `EXPECT_EXPR_EQ` functionality with wrapper that works with `Expression *` and `expression_ptr` arguments.
* Replace string comparison checks in `test_symdiff.cpp` with equivalents that use `EXPECT_EXPR_EQ`.
* Check explicitly for missing coefficient in `cnexp` solver, which should be treated equivalently to zero.

* Add class for managing state associated with binning event times across integration periods.
* Include support for no or fixed 'regular' binning.
* Add a gtest-assertion compatible test for comparing sequences of floating point numbers: `testing::seq_almost_eq` in `tests/unit/common.hpp`.
* Rename `cell_` in `cell_group` to `lowered_`, to clarify intent (i.e. lowered cell state is very different from a `cell` object, and maintains state for many cells).
* Reformat some comments for consistency.

Note that the `event_binner` class is not used in this commit for actual binning: the original logic is still in place.

Ben Cumming authored 8 years ago and Sam Yates committed 8 years ago

Fixes #152

* Remove OpenMP back end implementation.
* Remove CMake options for OpenMP.
* Simplify the threading model selection code in CMake.
* Remove Extrae benchmarking scripts, which require OpenMP.

Includes a fix to the readme which applies to any external modcc, and a way to keep from rebuilding locally an external modcc.

The requirements for event types for use in event_queue were restrictive and a bit 'special'.

  * Allow event times of any time which is well ordered by operator>.
  * Allow any event type with a public time member containing the time value.
  * Provide customization point event_time() via ADL for extracting the time value for event types that do not have a time member.
  * Simplify interface: push(begin, end) was only ever used in the unit test; add empty() const method.
  * Add unit test for more flexible functionality.

Differing classes had their own time_type and other classes were parameterized on it in ways that were compatibile, but only by chance. 

With these changes, modifying the time type used in spike will propagate through to all dependent classes.

  * Rename generic spike<I, T> as basic_spike<I, T>. 
  * Use spike = basic_spike<cell_member_type, float> as the common spike type.
  * Replace instances of spike_type aliases with just spike.
  * time_type aliases are defined in terms of spike::time_type.
  * Remove time_type parameterization in connection.
  * Remove time_type parameterization in communicator.
  * Remove time_type parameterization in exporter classes.

Ben Cumming authored 8 years ago and Sam Yates committed 8 years ago

fixes #197

* Add functions that can find thread affinity and the number of available cores on linux systems via `sched_getaffinity`.
* On other systems they default to "unknown affinity" and return 0 to indicate that the number of cores is unknown.
* Set the default number of threads according to the new functions above if no environment variable explicitly setting the number of threads is set.
* Validate environment variable value against regex and range check; terminate if improper.
* Terminate if no number of threads is provided and the library is unable to determine a sensible number automatically.

Basic features:

* Compile with -t avx512
* Automatically set up by CMake if USE_OPTIMIZED_KERNELS is on and VECTORIZE_TARGET is set to KNL 
* Generic SIMD printer that contacts a SIMD backend for emitting the actual SIMD intrinsics

Note: compilation for the avx512 target requires the Intel compiler. 

Ben Cumming authored 8 years ago and Sam Yates committed 8 years ago

* Add an additional exchange at the end of the time stepping loop to ensure that any spikes still in spike buffers are exchanged and saved to disk.
* Remove the parallel sort from the cthread back end to fix compilation errors with CUDA and cthreads.
* Fix `nvcc` warning concerning initialization of `std::size_t` variable with literal `-1`.

Fixes #183

Use a device kernel for net_receive state updates.
Note: very naive, but gives about a 30% speed up on the 1000 cell miniapp test. All the fun optimization will end up under issue #184.

This also incorporates PR #192, so this PR will be amended if that one is rejected.

When NMC_WITH_CUDA is off, still allow the generation
of CUDA mechanisms with modcc by exposing the
`build_all_gpu_mods` target; this can be performed
independently of the presence (or otherwise) of a
CUDA development environment.

This eases development of GPU-related modcc tasks,
as preliminary work can be performed and checked on
machines without a CUDA environment.

Using latexmk simplifies the makefile structure and avoids many of the problems with redundant pdflatex invocation.

Rewrite docs/model/makefile and docs/model/images/makefile to use latexmk for building and cleaning.
Remove generated report.bbl from repo.

Fixes #166

Debackwardsate math::signum().
Unit tests in test_math.cpp for same.

Ben Cumming authored 8 years ago and Sam Yates committed 8 years ago

The storage of matrix data, and the operations on matrices (i.e. matrix assembly and matrix solution), have not been implemented in a consistent manner.

The main problem was that matrix assembly was managed by a `matrix_assembler` type provided by the back end, which had views on information that it required to perform assembly. Specifically, the views were on properties like `face_conductance`, model state like `voltage` and `current`, and on the underlying matrix storage `d`, `u` and `p`.

This was not a good solution because 
  * there was a hidden dependence of the assembly on model data. e.g. if the voltage storage was reallocated, the reference in the `matrix_assembler` would become stale.
  * if we want back end specific optimizations that require a different data layout to that used elsewhere in the back end, this layout should be shared with the solver, but there is no obvious mechanism for doing that.

This patch addresses this by making a `matrix_state` type in the back end.
  * stores the matrix state opaquely, allowing back-end specific optimizations
  * provides interface for performing operations on the state, namely `assemble`, `solve` and `get_solution`.
  * stores fields such as `face_conductance` and `cv_capacitance` that were stored in the `fvm_multicell`, despite being used only in matrix assembly.
  * takes `voltage` and `current` as parameters to the `assemble` interface, removing the hidden reference to model state.

The actual data layout has not been changed in this PR. Instead, the interface has been refactored and hidden references removed so that it is now possible to implement back-end specific optimizations cleanly.

Fix morphology section ctor bug.
Add morphology pools for miniapp from which morphologies are drawn in the recipe.
Add command-line options to expose above.
Add option --report-compartments to (slowly) check the min, mean, and max number of compartments in the generated cells across the simulation.
Use morphology::add_section to do all the heavy lifting; no need to make section_geometry objects by hand, unless you really, really want to.

This PR is a prelude to closer integration of the random morphology generation with the miniapp, with the first step being support for recipes that create cells from morphologies generated off-line. It aims to use nest::mc::morphology as the flat morphology-only representation that can be used to construct nest::mc::cell objects and which can exist as a target for SWC conversion and random morphology generation.

Simplify swc io implementation:
Avoid throwing exceptions in istream parsing and swc_record constructors — only throw when explicitly checking consistency, or when parsing a full sequence of records.
Allow direct access to record members.
Separate parsing considerations from canonicalization (renumbering, sorting) of a sequence of records.
Move lmorpho morphology classes into src/
Add invariant check procedure for morphology.
Make cells via swc -> morphology -> cell building, rather than direct swc -> cell.
Allow option to use 'natural' discretization in morphology to determine number of compartments in built cell.
Update test_swcio.cpp to accommodate new API.

Ben Cumming authored 8 years ago and Sam Yates committed 8 years ago

This patch removes the many small `cudaMemcpy` calls for single values, except for those from calling `net_receive` in event delivery.

The small copies during initialization were from when the upper diagonal and time invariant component of the diagonal were computed on the host. There were many small reads/writes to device memory accessing the `p` and `u` vectors.

* Remove many small device copies in matrix setup by copying required data to host, computing, and then copying back in one copy.
* Add `constexpr` test `is_debug_mode()` for having been compiled in debug mode (tests `NDEBUG`).
* Only perform `is_physical_solution` test if `is_debug_mode()` is true. (The `is_physical_solution` test triggers a single copy from device to host on each time step to test whether the voltage has exceeded some "reasonable" physical bounds.)

Ben Cumming authored 8 years ago and Sam Yates committed 8 years ago

Fixes #125

* Add `cuda_atomic_add` and `cuda_atomic_sub` wrappers for atomic addition.
* Choose native atomic add for Pascal and later architectures.
* Choose CAS workaround for devices earlier than Pascal.
* Add unit test for wrappers.
* Change default CUDA architecture target to `sm_60` in `CMakeLists.txt`.

Vasileios Karakasis authored 8 years ago and Sam Yates committed 8 years ago

* Add missing `<string>` header to `modcc/msparse.hpp`

Ben Cumming authored 8 years ago and Sam Yates committed 8 years ago

Moves spike detection to the back end, which is required to have fast spike detection on the gpu.

Fixes #106.

Backend:
* Move spike detection into the backend.
* Add a `threshold_watcher` type to each backend that is initialized with a reference to the field that it is to watch, along with indexes and thresholds for each variable in the field that is being watched. This class presents a simple host-side interface:
   * `test(t)` tests for crossings at time `t`.
   *  `crossings()` returns all threshold crossings.
   * `clear_crossings()` resets (clears) the collected crossing events.
* Implement the multicore back end detector directly from the original code.
* Implement a `gpu_stack` for use with the gpu back end, that lets threads in a kernel conditionally push back into a flat array.

Miniapp:
* Run a single-step dummy run of model before starting the profiler, when profiling is enabled.
* Initialize the spike output callback functions _after_ the dummy run so that spikes from the dummy step are not output.

`cell_group`:
* Pass responsibility for spike detection to the lowered cells (`fvm_multicell`) and associated back ends.

`memory`:
* Add a new allocator for CUDA managed memory.
* Implement `managed_ptr` and `make_managed_ptr`, which are managed memory equivalents of `std::unique_ptr` and `std::make_unique_ptr`.

Tests:
* Improve host-side spike detection unit tests.
* Add device-side spike detection unit tests.
* Add unit tests for `gpu_stack`.

Building:
* Surpress CMP0023 CMake warning.

* Ignore dendrite branches with negative radii arising from correlated child diameter distribution.
* Fix fencepost errors in morphology discretization.
* Rename `tip.p` to `tip.point`.

Adds a stand-alone program for the generation of random morphologies form a L-system description. The algorithm is that of Burke (1992), with some of the extensions provided by Ascoli et al. (2001).

Two sets of L-system parameters have been included, corresponding to alpha motoneurons and Purkinje cells, but there is certainly something wrong with the data for the latter, and more correct numbers will probably need to be synthesized from existing Purkinje cell morphological information.

Documentation for `lmorpho` is incomplete, but the command line help (`--help`) goes some way to explain the usage. In order to get output, one must specify `--swc` or `--pvec` (or both) to emit SWC files or the structural parent vectors. Coarser discretization can be obtained with the `--segment` option.

Some minor modifications have been included in other parts of the source repo:
* Added copy constructor for `TextBuffer` in `modcc/textbuffer.hpp`, required to keep cl...

fix #164

Disambiguate e symbol in statements like the following
  for (auto& e: e->terms())
This caused GCC 5 to give an error.

Build images.dir when building report.pdf
Add outputs to .gitignore

Incorporate symbolic GE code from prototype (with some simplifications) in msparse.hpp, symge.hpp and symge.cpp, together with unit tests.

Add two kinetic scheme test cases for validation: test_kin1 (simple exponential scheme) and test_kinlva (combination of exponential gate and a three-species kinetic scheme, modelling a low voltage-activated Calcium channel from Wang, X. J. et al., J. Neurophys. 1991).

Adapt numeric HH validation data generation to LVA Ca channel, with explicit stopping at stimulus discontinuities.

Add two new validation tests based on above: kinetic.kin1_numeric_ref and kinetic.kinlva_numeric_ref (multicore backend only).

Introduce a BlockRewriterBase visitor base class, as an aid for visitors that transform/rewrite procedure bodies; refactor KineticRewriter over this class.

Introduce common error_stack mixin class for common functionality across Module and the various procedure rewriters.

Implement visitors and public-facin...

fix bug introduced when global policy was refactored.

The reproducible problem is now green on two separate systems