-
Notifications
You must be signed in to change notification settings - Fork 59
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Part 1 of the big GPU merge #45
Commits on Sep 8, 2016
-
* add CMake option and target for CUDA * add some workarounds for CUDA compiler bugs
Configuration menu - View commit details
-
Copy full SHA for b38f78b - Browse repository at this point
Copy the full SHA b38f78bView commit details
Commits on Sep 9, 2016
-
WIP towards basic GPU implementation
* created a gpu multicell target type * missing CUDA specific kernels * basic cell state (voltage, current, etc) is on gpu * moved the vector library into main source tree * have not yet deleted external dependency
Configuration menu - View commit details
-
Copy full SHA for 7e54957 - Browse repository at this point
Copy the full SHA 7e54957View commit details
Commits on Sep 29, 2016
-
Configuration menu - View commit details
-
Copy full SHA for b7bd5dd - Browse repository at this point
Copy the full SHA b7bd5ddView commit details -
Configuration menu - View commit details
-
Copy full SHA for 3edad46 - Browse repository at this point
Copy the full SHA 3edad46View commit details -
Configuration menu - View commit details
-
Copy full SHA for 1388d20 - Browse repository at this point
Copy the full SHA 1388d20View commit details
Commits on Sep 30, 2016
-
Configuration menu - View commit details
-
Copy full SHA for 8e6d97f - Browse repository at this point
Copy the full SHA 8e6d97fView commit details -
Configuration menu - View commit details
-
Copy full SHA for 4ee9930 - Browse repository at this point
Copy the full SHA 4ee9930View commit details -
Configuration menu - View commit details
-
Copy full SHA for 4c0864b - Browse repository at this point
Copy the full SHA 4c0864bView commit details
Commits on Oct 4, 2016
-
* more simplifications of the memory library * clean up of policy based matrix gpu/multicore implementation
Configuration menu - View commit details
-
Copy full SHA for d1a5b6e - Browse repository at this point
Copy the full SHA d1a5b6eView commit details
Commits on Oct 6, 2016
-
Configuration menu - View commit details
-
Copy full SHA for 36ebcc7 - Browse repository at this point
Copy the full SHA 36ebcc7View commit details -
Configuration menu - View commit details
-
Copy full SHA for 851f38c - Browse repository at this point
Copy the full SHA 851f38cView commit details
Commits on Oct 9, 2016
-
Configuration menu - View commit details
-
Copy full SHA for 4a1777f - Browse repository at this point
Copy the full SHA 4a1777fView commit details
Commits on Oct 10, 2016
-
snapshot of code before attempting to merge the multicore and gpu implementation of the FVM into a single code base. The gpu version of the miniapp doesn't compile, but fixing this is better done as part of merging. * fixed bug in multicore fvm_multicell where solutions wasn't copied from rhs to voltage vector after linear system solution * add check for ion channel CV indexes to unit tests - this fails due to CV bug that is in issue 20 * small fixes towards gpu support
Configuration menu - View commit details
-
Copy full SHA for 2c6f5a3 - Browse repository at this point
Copy the full SHA 2c6f5a3View commit details
Commits on Oct 13, 2016
-
Configuration menu - View commit details
-
Copy full SHA for c742fd5 - Browse repository at this point
Copy the full SHA c742fd5View commit details -
Configuration menu - View commit details
-
Copy full SHA for 039d5a9 - Browse repository at this point
Copy the full SHA 039d5a9View commit details
Commits on Oct 15, 2016
-
Configuration menu - View commit details
-
Copy full SHA for 121dade - Browse repository at this point
Copy the full SHA 121dadeView commit details
Commits on Oct 22, 2016
-
Support for units syntax within state block.
Vasileios Karakasis committedOct 22, 2016 Configuration menu - View commit details
-
Copy full SHA for b6aec69 - Browse repository at this point
Copy the full SHA b6aec69View commit details
Commits on Oct 24, 2016
-
Configuration menu - View commit details
-
Copy full SHA for 44c8ac0 - Browse repository at this point
Copy the full SHA 44c8ac0View commit details
Commits on Oct 25, 2016
-
Configuration menu - View commit details
-
Copy full SHA for 78f60f5 - Browse repository at this point
Copy the full SHA 78f60f5View commit details -
Configuration menu - View commit details
-
Copy full SHA for 5c09594 - Browse repository at this point
Copy the full SHA 5c09594View commit details -
Configuration menu - View commit details
-
Copy full SHA for 3830c9a - Browse repository at this point
Copy the full SHA 3830c9aView commit details -
Configuration menu - View commit details
-
Copy full SHA for 2db99a2 - Browse repository at this point
Copy the full SHA 2db99a2View commit details -
Configuration menu - View commit details
-
Copy full SHA for 65ed2fe - Browse repository at this point
Copy the full SHA 65ed2feView commit details -
Configuration menu - View commit details
-
Copy full SHA for 7f1216d - Browse repository at this point
Copy the full SHA 7f1216dView commit details
Commits on Oct 26, 2016
-
Configuration menu - View commit details
-
Copy full SHA for de992ad - Browse repository at this point
Copy the full SHA de992adView commit details -
Configuration menu - View commit details
-
Copy full SHA for b5bae5b - Browse repository at this point
Copy the full SHA b5bae5bView commit details -
Configuration menu - View commit details
-
Copy full SHA for 06ef117 - Browse repository at this point
Copy the full SHA 06ef117View commit details -
Merge branch 'master' into bugfix/modcc/state-block-units
Vasileios Karakasis committedOct 26, 2016 Configuration menu - View commit details
-
Copy full SHA for 18a9226 - Browse repository at this point
Copy the full SHA 18a9226View commit details -
Adds unit tests for the STATE block.
Vasileios Karakasis committedOct 26, 2016 Configuration menu - View commit details
-
Copy full SHA for 05e4770 - Browse repository at this point
Copy the full SHA 05e4770View commit details
Commits on Oct 27, 2016
-
Configuration menu - View commit details
-
Copy full SHA for b9b1e57 - Browse repository at this point
Copy the full SHA b9b1e57View commit details -
Address deprecated use of 'symbol' warning.
Julia 0.5 deprecates use of `symbol` instead of `Symbol`. This patch just substitutes the correct call.
Configuration menu - View commit details
-
Copy full SHA for dbca304 - Browse repository at this point
Copy the full SHA dbca304View commit details -
Configuration menu - View commit details
-
Copy full SHA for ff14704 - Browse repository at this point
Copy the full SHA ff14704View commit details -
Vasileios Karakasis committed
Oct 27, 2016 Configuration menu - View commit details
-
Copy full SHA for 9e0b874 - Browse repository at this point
Copy the full SHA 9e0b874View commit details -
Merge pull request #35 from vkarak/bugfix/modcc/state-block-units
modcc: Support for units syntax within a state block.
Configuration menu - View commit details
-
Copy full SHA for f1eac25 - Browse repository at this point
Copy the full SHA f1eac25View commit details -
Configuration menu - View commit details
-
Copy full SHA for 5174b69 - Browse repository at this point
Copy the full SHA 5174b69View commit details -
* Tests for `math::pi`, `math::lerp`, `math::area_frustrum` and `math::volume_frustrum` * Fix `math:pi<long double>()`.
Configuration menu - View commit details
-
Copy full SHA for a39c9a3 - Browse repository at this point
Copy the full SHA a39c9a3View commit details -
Extend range, view functionality.
* New `filter` view: lazily selects based on predicate. * Generic `front` and `back` for sequences. * New rangeutil STL wrappers `stable_sort_by`, `all_of`, `any_of`. * Consolidate common utility unit testing structures into `tests/unit/common.hpp`
Configuration menu - View commit details
-
Copy full SHA for 63c507b - Browse repository at this point
Copy the full SHA 63c507bView commit details -
Add
ball_and_squiggle
model; fixball_and_taper
.* Make `test_common_cells.hpp` and `ball_and_taper.py` agree. * Add `ball_and_squiggle` model that has a tapering undulating profile.
Configuration menu - View commit details
-
Copy full SHA for 830428a - Browse repository at this point
Copy the full SHA 830428aView commit details
Commits on Oct 28, 2016
-
Address PR#46 review comments.
* Add documentation of template parameters for `filter_iterator`. * Document use of `uninitalized<F>` for holding functional objects in `filter_iterator` and `transform_iterator`
Configuration menu - View commit details
-
Copy full SHA for cee495c - Browse repository at this point
Copy the full SHA cee495cView commit details -
Merge pull request #46 from halfflat/feature/more-range-utils
More range functionality, unit tests.
Configuration menu - View commit details
-
Copy full SHA for c97135d - Browse repository at this point
Copy the full SHA c97135dView commit details -
Merge pull request #47 from halfflat/feature/new-test-model
Feature/new test model
Configuration menu - View commit details
-
Copy full SHA for 5ade8d0 - Browse repository at this point
Copy the full SHA 5ade8d0View commit details -
Consolidate validation test code (issue #41)
* Simplify trace analysis and reporting code in `trace_analysis.hpp` * Consolidate convergence test run procedures into new class `convergence_test_runner`.
Configuration menu - View commit details
-
Copy full SHA for 1b929ff - Browse repository at this point
Copy the full SHA 1b929ffView commit details -
New compartment info structure for FVM.
* Make `algorithm::sum`, `algorithm::mean` more generic, allowing use with array types. * Add `div_compartment` compartment representation, that holds geometric information for each half of a compartment that will then be used in calculating control volumes. * Add three compartmentalisation schemes/policies that discretize a segment into `div_compartment` objects: * `div_compartment_by_ends` divides based only on the segment end points and radii. * `div_compartment_sampler` forms frusta by sampling the segment radius at each compartment boundary * `div_compartment_integrator` computes the compartment areas and volumes exactly by summing all frustra in the intersection of the segment and the compartmnet span.
Configuration menu - View commit details
-
Copy full SHA for f189d73 - Browse repository at this point
Copy the full SHA f189d73View commit details -
Merge pull request #48 from halfflat/feature/consolidate-validation-t…
…ests Consolidate validation tests (issue #41)
Configuration menu - View commit details
-
Copy full SHA for 550da10 - Browse repository at this point
Copy the full SHA 550da10View commit details -
Merge pull request #49 from halfflat/feature/divided-compartments
Feature/divided compartments
Configuration menu - View commit details
-
Copy full SHA for a03af27 - Browse repository at this point
Copy the full SHA a03af27View commit details
Commits on Oct 30, 2016
-
* Use divided compartments to determine FVM coefficients. * Pick correct control volume in FVM from sgement position (avoids off-by-half error.) * Add colour override functionality to tsplot: `--colour` option. * Add const accessor for cell soma. * Source formatting, comments in `math.hpp` * Fix `range_view`: was using incorrectly named type trait. * Add unit test for `range_view`. * Allow points of discontinuity to be omitted from L-infinity norm calculations. * Add `-d, --min-dt` option to `validate.exe` to control time step in validation convergence tests. * Add validation test: confirm divided compartment policy does not effect results on simple frustrum dendrites. * Change default max compartments on validation tests to 100 (ad hoc observed convergence limit at dt circa 0.001 ms; finder spatial division would required much finer dt.) * Make NEURON validation data generation scripts use CVODE by default, and with `secondorder=2` when non-zero `dt` is given.
Configuration menu - View commit details
-
Copy full SHA for e7a8fb6 - Browse repository at this point
Copy the full SHA e7a8fb6View commit details
Commits on Oct 31, 2016
-
Remove division policy type parameter.
* Use only `div_compartment_integrator` for compartmentalization in `fvm_multicell`. The policy will later be moved to a backend policy class. * For now, disable validation tests that test different division policies (see above). * Tweak comments and remove redundant `using`, following comments on PR#54.
Configuration menu - View commit details
-
Copy full SHA for 5aeea90 - Browse repository at this point
Copy the full SHA 5aeea90View commit details -
Merge pull request #54 from halfflat/feature/complex-compartments
Complex compartments
Configuration menu - View commit details
-
Copy full SHA for e8d3285 - Browse repository at this point
Copy the full SHA e8d3285View commit details
Commits on Nov 2, 2016
-
Configuration menu - View commit details
-
Copy full SHA for b39a93e - Browse repository at this point
Copy the full SHA b39a93eView commit details
Commits on Nov 4, 2016
-
* first version of openmp threading back end * adding openmp parallel sort implementation * OpenMP sort working * Support for units syntax within state block. * Add soma-less cable cell to test cells. Also: * Ensure intrinsic and passive properties properly set on test cells. * Change bulk resistivity default. * Align defaults with values used in most of the NEURON validation scripts. * Use consistent 100 Ω·m bulk resistivity across both NEURON test models and basic validation cells. * OpenMP back end working * Add Extrae+paraver support, needs to fix compilation warnings * Reorganize validation data generation * Move generation and data to top-level validation directory. * Make BUILD_VALIDATION_DATA and VALIDATION_DATA_DIR cache vars. * Add helper CMake functions for data generation. Note `validation/ref/numeric/foo.sh` is just a placeholder. * Bugfix: hh_soma.jl * Use consistent scaling for y[1] scalar voltage in hh_soma.jl * Also: add more reserved target names to CMakeLists.txt helper function. * Refactor convergence tests; add numeric soma ref. * Amend data directory path in validation tests. * Enmodulate `hh_soma.jl` * Add HH channel reference data generations script. * Switch `validate_soma.cpp` to numeric reference data. * Consolidate common code in `validate_ball_and_stick.cpp` * Add (nearly) Rallpack1 validation test (see below). * Gentle failure on absence of reference data in `validate_ball_and_stick.cpp` Can't yet override mechanism default parameter values, so the cable cell model added to `test_common_cells.hpp` lets the default stand; validation script will have to use the default membrane conductance rather than that given by Rallpack1. * Add Rallpack1 validation, plus bugfix, clean * Implement Rallpack1 validation test (with a workaround for inability to set membrane conductance). * Fix bug in L≠1 case in PassiveCable.jl (this may still be wrong). * Fix bug in peak delta computation in trace analysis when both traces have no local maxima. * Gentle failure on missing `numeric_soma.json` * Allow multiple `-s` selection operations for `tsplot`, acting disjunctively. * Remove errant test file. * file's cleanup * Remove tabs * Use correct routine in numeric_rallpack1.jl x0.3 * Configure-time test for julia * `math::infinity<>()` wrapper for infinity * Use name `i_e` for Stim current density * Use `math::infinity<>()` for infinite value * Adds unit tests for the STATE block. * Add "lib" to search prefixes for libtbb * Fix quoting error in library search. * Add "lib" to prefixes when system is "Linux". * Address deprecated use of 'symbol' warning. Julia 0.5 deprecates use of `symbol` instead of `Symbol`. This patch just substitutes the correct call. * Address deprecated use of 'symbol' warning. Julia 0.5 deprecates use of `symbol` instead of `Symbol`. This patch just substitutes the correct call. * Addresses PR comments. * Unit tests for math.hpp * Tests for `math::pi`, `math::lerp`, `math::area_frustrum` and `math::volume_frustrum` * Fix `math:pi<long double>()`. * Extend range, view functionality. * New `filter` view: lazily selects based on predicate. * Generic `front` and `back` for sequences. * New rangeutil STL wrappers `stable_sort_by`, `all_of`, `any_of`. * Consolidate common utility unit testing structures into `tests/unit/common.hpp` * Add `ball_and_squiggle` model; fix `ball_and_taper`. * Make `test_common_cells.hpp` and `ball_and_taper.py` agree. * Add `ball_and_squiggle` model that has a tapering undulating profile. * Address PR#46 review comments. * Add documentation of template parameters for `filter_iterator`. * Document use of `uninitalized<F>` for holding functional objects in `filter_iterator` and `transform_iterator` * Consolidate validation test code (issue #41) * Simplify trace analysis and reporting code in `trace_analysis.hpp` * Consolidate convergence test run procedures into new class `convergence_test_runner`. * New compartment info structure for FVM. * Make `algorithm::sum`, `algorithm::mean` more generic, allowing use with array types. * Add `div_compartment` compartment representation, that holds geometric information for each half of a compartment that will then be used in calculating control volumes. * Add three compartmentalisation schemes/policies that discretize a segment into `div_compartment` objects: * `div_compartment_by_ends` divides based only on the segment end points and radii. * `div_compartment_sampler` forms frusta by sampling the segment radius at each compartment boundary * `div_compartment_integrator` computes the compartment areas and volumes exactly by summing all frustra in the intersection of the segment and the compartmnet span. * Extrae linked at execution time * cleaning project * Complex compartments * Use divided compartments to determine FVM coefficients. * Pick correct control volume in FVM from sgement position (avoids off-by-half error.) * Add colour override functionality to tsplot: `--colour` option. * Add const accessor for cell soma. * Source formatting, comments in `math.hpp` * Fix `range_view`: was using incorrectly named type trait. * Add unit test for `range_view`. * Allow points of discontinuity to be omitted from L-infinity norm calculations. * Add `-d, --min-dt` option to `validate.exe` to control time step in validation convergence tests. * Add validation test: confirm divided compartment policy does not effect results on simple frustrum dendrites. * Change default max compartments on validation tests to 100 (ad hoc observed convergence limit at dt circa 0.001 ms; finder spatial division would required much finer dt.) * Make NEURON validation data generation scripts use CVODE by default, and with `secondorder=2` when non-zero `dt` is given. * Remove division policy type parameter. * Use only `div_compartment_integrator` for compartmentalization in `fvm_multicell`. The policy will later be moved to a backend policy class. * For now, disable validation tests that test different division policies (see above). * Tweak comments and remove redundant `using`, following comments on PR#54. * Minor twicks and corrections
Configuration menu - View commit details
-
Copy full SHA for 0ded25a - Browse repository at this point
Copy the full SHA 0ded25aView commit details -
Configuration menu - View commit details
-
Copy full SHA for cd4d9ae - Browse repository at this point
Copy the full SHA cd4d9aeView commit details
Commits on Nov 9, 2016
-
Configuration menu - View commit details
-
Copy full SHA for e74720b - Browse repository at this point
Copy the full SHA e74720bView commit details
Commits on Nov 10, 2016
-
Configuration menu - View commit details
-
Copy full SHA for b11990f - Browse repository at this point
Copy the full SHA b11990fView commit details
Commits on Nov 11, 2016
-
Configuration menu - View commit details
-
Copy full SHA for bb14d18 - Browse repository at this point
Copy the full SHA bb14d18View commit details -
Configuration menu - View commit details
-
Copy full SHA for 1584bf3 - Browse repository at this point
Copy the full SHA 1584bf3View commit details -
Configuration menu - View commit details
-
Copy full SHA for 46427e6 - Browse repository at this point
Copy the full SHA 46427e6View commit details
Commits on Nov 14, 2016
-
* streamline CMake * list of external libaries to link against CMake is concatenated in `EXTERNAL_LIBRARIES` variable * UNWIND_STACK is enabled by default if the libunwind package can be found * stack trace printer * optionally prints with color * takes the executable to perform address translation as command line argument * added documentation to c++, in particular some comments in fvm_multicell.hpp to explain some steps in more detail.
Configuration menu - View commit details
-
Copy full SHA for 7751058 - Browse repository at this point
Copy the full SHA 7751058View commit details -
Configuration menu - View commit details
-
Copy full SHA for 2b2b310 - Browse repository at this point
Copy the full SHA 2b2b310View commit details -
Configuration menu - View commit details
-
Copy full SHA for 5825543 - Browse repository at this point
Copy the full SHA 5825543View commit details -
Configuration menu - View commit details
-
Copy full SHA for faf1a41 - Browse repository at this point
Copy the full SHA faf1a41View commit details -
Sam Yates committed
Nov 14, 2016 Configuration menu - View commit details
-
Copy full SHA for 6cf11d3 - Browse repository at this point
Copy the full SHA 6cf11d3View commit details