- Jun 30, 2016
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Benjamin Cumming authored
* change `probe_sort` enum to scoped enum - renamed to `probeKind` - refactored out of class - updated coding guidelines wiki with enum rules * refactor `std::pair` into structs with meaningfull name types in `cell.hpp` - not just probes: stimulii and detectors too. * add profiling region around sampling in `cell_group` * change output data format for traces to json * remove white space at end of lines (looking at you Sam)
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Ben Cumming authored
Feature/probes
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Ben Cumming authored
Fix linking of MPI libraries for tests and validation.
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- Jun 28, 2016
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Sam Yates authored
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Sam Yates authored
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Benjamin Cumming authored
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Benjamin Cumming authored
- profiler generates one report per MPI rank - estimates the thread imbalance per rank - generates a json file with profiling stats for each rank - works with/without MPI - works with/without TBB Conflicts: miniapp/miniapp.cpp
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Benjamin Cumming authored
- move definition of `global_policy` to header file src/communication/global_policy.hpp - the `#ifdef WITH_MPI` guards go there so that - they don't pollute user code - they are available throughout the application - small cleanup of a couple of style points in the mpi code
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Benjamin Cumming authored
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Sam Yates authored
* Make global_policy methods static * Move global_policy init/finalize into static methods * Make miniapp use only global_policy methods for setup, rank, etc.
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- Jun 27, 2016
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Sam Yates authored
* First implementation of simple current/voltage probe interface * Sample a specific collection of voltage or current values at independent dt (current implementation chooses to provide at most one sample per simulation dt per request.) * Miniapp uses samplers to write soma and dendrite membrane potentials from first three cells. * Also: fix noncompliant use of nullptr -> bool conversion in test_optional.cpp
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Sam Yates authored
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Benjamin Cumming authored
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Benjamin Cumming authored
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- Jun 24, 2016
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Sam Yates authored
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Ben Cumming authored
Feature/spike handling
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Sam Yates authored
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Sam Yates authored
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Benjamin Cumming authored
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Benjamin Cumming authored
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Sam Yates authored
* Add WITH_MPI CMake option to enable MPI code in application * Use find_package(MPI) and set up flags, etc. for MPI * Extra defines to disable the inclusion of C++ MPI headers for MPICH and OpenMPI. * Fix signed/unsigned compare warning in algorithms.hpp
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Sam Yates authored
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Benjamin Cumming authored
Added MPI support to the miniapp - added ring model and all-to-all model - started refactoring general model setup steps into a model class in miniapp - optional -DWITH_MPI to turn on MPI support
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- Jun 23, 2016
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Ben Cumming authored
Low-level algorithms for manipulating cell trees.
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Vasileios Karakasis authored
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Benjamin Cumming authored
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Ben Cumming authored
Feature/optional review
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- Jun 22, 2016
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Benjamin Cumming authored
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- Jun 17, 2016
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Sam Yates authored
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Vasileios Karakasis authored
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- Jun 16, 2016
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Sam Yates authored
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Benjamin Cumming authored
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Benjamin Cumming authored
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- Jun 15, 2016
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Benjamin Cumming authored
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Benjamin Cumming authored
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Vasileios Karakasis authored
At this low level a cell tree is just a sequence of parent indices, where each parent index is the parent of the current index in the sequence. There four basic algorithms: 1. child_count(parent_index): Computes the number of children for each node in parent_index Time: O(N), Space: O(1) 2. branches(parent_index): Returns a set of the branching nodes in parent_index, last branch index equals the parent_index's size. Time: O(N), Space: O(N) 3. expand_branches(branch_index): Takes a branch_index (result from branches()) and expands it at the size of the original tree with all the nodes inside a branch having the same number. Time: O(parent_index), Space: O(1) 4. make_parent_index(parent_index, branch_index): Return a compacted tree (single node per branch) from parent_index and its corresponding branch_index. Time: O(N), Space: O(N) There is another utility function as well: find_branch(branch_index, nid): Returns the id of the branch where nid belongs to. Time: O(N), Space: O(1)
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Ben Cumming authored
merge to my fork
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- Jun 11, 2016
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Ben Cumming authored
Remove redundant #ifdef'ed code
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Sam Yates authored
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Ben Cumming authored
Address clang compiler warnings
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