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Created a bash script for running our unit and regression tests. | {
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"Apparently actions that don't run using either push or pull request won't show up unless they are in the default branch. This is a sad oversight by the GitHub team and the issue has been documented by many complaints found here: https://github.community/t/workflow-files-only-picked-up-from-master/16129/29 and http... | 2022-04-27T21:46:30 | 2022-05-03T05:29:51 | 2022-05-03T05:29:47 | CONTRIBUTOR | null | {
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} | null | As per a request by @stiber, there should be a manual action that publishes the gh-pages with the click of a button. I plan to use a similar format to the gh-pages action that already exists. The reason there needs to be a separate one though is because the gh-pages action re-generates the doxygen files. This new action will only publish the gh-pages and won't worry about new doxygen changes. | {
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} | null | This pull request holds new changes to the structure of Graphitti's documentation files as well as adding new documentation for the GitHub actions workflows (doxygen, gh-pages, and plantUML). I am asking @stiber to look over the structural changes and additions. I would also ask @jardiamj to look over the actions documentation to see if there is anything I missed, either forgot to include or shouldn't be there in the first place. | {
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} | null | At the moment we have two (soon to be 3) GitHub Action workflows. One for automating tests, another for updating the Doxygen and GitHub pages files, and the last for automating the creation of UML diagrams from plantUML files. Very little of this is documented yet, and as per @stiber request in PR #311 this documentation needs to be added and updated. This issue will also require some larger reorganization of the current documentation structure as well. | {
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} | null | At the moment, we have a GitHub action that automatically runs the unit and regression tests when we submit a PR against the master branch. For testing locally, the unit tests can be run by executing `build/tests` but for the regression tests you have to manually run Graphitti with the config files described in [Test Config File Parameters](https://github.com/UWB-Biocomputing/Graphitti/blob/master/docs/Testing/TestConfigFileParameters/testConfigFileParameters.md), and then compare the output files against the [known Good Output files](https://github.com/UWB-Biocomputing/Graphitti/tree/master/Testing/RegressionTesting/GoodOutput). We should have a script to run these tests locally. | {
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"@jardiamj, I'd like to resolve why the gh-pages and master branches are different. Changes to the MD files in master don't seem to be reflected in the gh-pages branch.",
"This is because the GitHub action that does the deployment to gh-pages only runs on the 1st of each month. It seems sensible to have an action... | 2022-04-14T17:41:42 | 2022-04-15T20:29:55 | 2022-04-15T20:29:37 | CONTRIBUTOR | null | {
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Merging this PR with master separates documentation changes done in PR #281. | {
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Bumped log4cplus to version 2.0.7 so that Graphitti compiles with glibc >= 2.34.
Previous log4cplus version 2.0.2 wouldn't compile with glibc >= 2.34 due to a bug in its embedded catch2 library. This is fixed in version 2.0.7 so I am upgrading it. | {
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} | null | The compilation failure comes from log4cplus 2.0.2, caused by the catch2 version bundled with it. These are the error messages that I get:
```
error: size of array ‘altStackMem’ is not an integral constant-expression
6285 | static char altStackMem[SIGSTKSZ];
| ^~~~~~~~
```
And
```
error: size of array ‘altStackMem’ is not an integral constant-expression
6336 | char FatalConditionHandler::altStackMem[SIGSTKSZ] = {};
```
The log4cplus bug was fixed in v2.0.7 as per this issue in GitHub: [log4cplus-2.0.6 tests fail to compile](https://github.com/log4cplus/log4cplus/issues/519)
Resolution: log4cplug should be updated. | {
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"@NewBobCon @jardiamj Can you two get together to work out whether this should just put the output images in the gh-pages branch, rather than master, so that GitHub isn't tracking the images? Also, please document (probably should be a new branch/pull request) the following:\r\n\r\n1. How does the PlantUML conversi... | 2022-03-17T05:37:51 | 2022-04-19T23:40:51 | 2022-04-19T23:37:30 | CONTRIBUTOR | null | {
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The GitHub action is set to run on push and pull requests but the diagrams will only be generated for the files that were modified in the last commit. What this means is, that you would need all the files you want rendered to have been touched in your last commit before you push or open a pull request. I tried looking for a better solution such as using `github.pull_request.base.sha` but that didn't work on my test.
Link to markdown page: [Sequence Diagrams](https://github.com/UWB-Biocomputing/Graphitti/blob/cfd29236c8d6ec60f703ca9ba3e6c431d1114dbf/docs/Developer/sequenceDiagrams.md) | {
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"Opened by accident. I am still testing it on my own fork.",
"I've got an undergrad who is interested in process automation. Maybe you can hand all of this documentation automation off to him."
] | 2022-03-17T01:23:00 | 2022-03-22T20:15:59 | 2022-03-17T01:52:10 | CONTRIBUTOR | null | {
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"I will go ahead and turn those methods into ones that return a pointer, then we can figure out what we want to use as device pointers. My first thought was to encapsulate the pointers into a template class that uses RAII for allocating memory in the GPU at least for structures with a fixed size.\r\n\r\nI don't kno... | 2022-02-15T19:25:51 | 2024-01-17T20:16:44 | null | CONTRIBUTOR | null | {
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} | null | What's below is just an example (actually, a start of a thread that one can pull on to find a long string of examples). OK, it's true: the CUDA memory allocation functions are really C functions (hence, they use "malloc" in their names). So, rather than taking a variable by reference if that variable is to be changed, they take a pointer to that variable (and they can't return a value for that variable because the return value is an error code). But, that's no reason that our C++ code should preserve that C style. So, what we need to do is the following:
1. Create a new type that is a GPU address type. The type name should make it clear that it is such a type; it should not look like a C++ (CPU) pointer. If we decide that we want it to be a GPU address of a thing (like the GPU address of an array of ints, versus the GPU address of a struct), then we might decide that this should be a template. This would prevent C++ code from mixing up addresses of different kinds of things. See #137, #136.
2. If a C++ method allocates GPU memory and needs to provide the address of that allocated memory to a calling method, it should return that address.
3. If a C++ method needs to modify more than one GPU address, or it needs to return something other than such an address, then the GPU address(es) should be passed by reference.
4. Only at the location in the code where we need to call the CUDA function should we do things like take the (CPU) address of a GPU address variable, cast to `void*` or `void**`, etc.
https://github.com/UWB-Biocomputing/Graphitti/blob/6b0763fa64e40750593fe87bfbac852d2c58bd2c/Simulator/Core/GPUModel.cu#L112 | null | {
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"Once the code base passes this, it can be added as a second automatic test script on GitHub.",
"Here's an example YML file for automating this in GitHub:\r\n\r\n```\r\nname: Basic compile, code checks, and test run\r\n\r\non:\r\n push:\r\n branches: [ master ]\r\n pull_request:\r\n branches: [ master ]\r... | 2022-01-26T17:52:37 | 2022-05-23T00:50:02 | 2022-05-18T01:57:53 | CONTRIBUTOR | null | {
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} | null | Use `clang-format` and `clang-tidy`. Starting points:
For `clang-format`:
```sh
# Generate new .clang-format based on LLVM style
clang-format -style=llvm -dump-config >> .clang-format
for i in *.cpp; do
echo "*** formatting suggestions for $i"
clang-format "$i" | diff --unchanged-line-format="" --old-line-format=":%.3dn OLD: %L" --new-line-format=": NEW: %L" "$i" -
done
```
For `clang-tidy`:
```sh
clang-tidy *.cpp -- -std=c++11
```
Using the `.clang-tidy` format file
```
# Configuration options for clang-tidy
# Modified from Yusuf Pisan's starter code
#
# usage: clang-tidy *.cpp -- -std=c++11
#
#
---
# See https://clang.llvm.org/extra/clang-tidy/#using-clang-tidy for all possible checks
Checks: '*,-fuchsia-*,-cppcoreguidelines-pro-bounds-array-to-pointer-decay,-google-build-using-namespace,-hicpp-no-array-decay,-modernize-use-trailing-return-type,-hicpp-braces-around-statements,-cppcoreguidelines-pro-bounds-pointer-arithmetic,-llvm-header-guard,-google-global-names-in-headers,-cppcoreguidelines-special-member-functions,-hicpp-special-member-functions,-cppcoreguidelines-owning-memory,-cppcoreguidelines-pro-bounds-constant-array-index'
# Only defined in the newer clang-tidy not the old CSS Lab machines
# WarningsAsErrors: '*'
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# Based on LLVM style in https://llvm.org/docs/CodingStandards.html#the-low-level-issues
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- { key: readability-identifier-naming.VariableCase, value: camelBack }
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- { key: readability-identifier-naming.GlobalConstantCase, value: UPPER_CASE }
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- { key: readability-identifier-naming.PrivateMethodCase, value: camelBack }
- { key: readability-identifier-naming.PublicMemberCase, value: CamelCase }
...
``` | {
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"Also I should add that the C++ standard has now been raised to 17 in my particular build, and I changed the minimum CMake requirement to `3.21` in preparation for CMakePresets, but since that isnt integrated yet you are free to change the minimum back.",
"Closed due to age."
] | 2022-01-26T01:09:35 | 2024-12-20T22:14:51 | 2024-12-20T22:14:51 | NONE | null | {
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} | null | # PLEASE DO NOT TRY TO ACTUALLY MERGE THIS INTO MASTER YET FOR THE LOVE OF GOD : ) <3
I'm just posting my fork's current work in trying to get Windows supported for Graphitti.
Some main changes so far, at the time of writing:
- As of #302 , I removed all `using namespace std;` usages as a temporary fix to the old Windows SDK C++17 breaking change - I expect that in a future iteration, we should just attempt to remove using `windows.h` in `Timer.h` and see if we can move forth with reintroducing `using namespace std;`.
- Moved some constructor assignments into the respective initializer lists instead.
- changed plain `enum`s to `enum class`es for stronger type checking.
- Changed `USE_GPU` to `__CUDACC__` because _I'm pretty sure_ the latter macro is a way to discern between CUDA/Non-CUDA applications already provided by NVIDIA.
This build currently doesn't compile on Windows because of the third task point in #302 - for those interested in trying this build out, generate the windows .lib of `log4cplus` with MSVC and link it manually : ). I'm 90% sure none of the changes I introduced so far have affected the Linux build though.
Not implemented in yet is:
- #303 (experimental, will only move forward if there is a general consensus for me to try)
- #304 (same as ^) | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/305 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/305/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/305/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/305/events | https://github.com/UWB-Biocomputing/Graphitti/issues/305 | 1,114,249,837 | I_kwDOEEdqD85Cahpt | 305 | Document top-level program flow | {
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"I was literally working on something like this yesterday, coincidentally! I was planning on trying to demonstrate the program flow of graphitti in a sequence diagram - it may take me awhile, but I'll use that whiteboard info, @VivekGandhi54 's knowledge, and the source code to guide the diagram. ",
"Update: I ju... | 2022-01-25T18:55:32 | 2022-04-19T23:37:30 | 2022-04-19T23:37:30 | CONTRIBUTOR | null | {
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} | null | The whiteboard image below is an old summary of the top-level simulator execution sequence. We need to produce an up-to-date version of this, possibly as a UML sequence diagram but maybe not. We also need to incorporate into this information regarding when each kind of class gets instantiated, when each kind of class reads its parameters, and when each kind of class initializes itself.
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/304 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/304/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/304/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/304/events | https://github.com/UWB-Biocomputing/Graphitti/issues/304 | 1,111,036,568 | I_kwDOEEdqD85CORKY | 304 | Feature Suggestion: The Usage of `vcpkg` | {
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"So, my worries are that C++ packages may not be maintained for proper interoperability with this. We'd need to be careful, to ensure that this will reliably be able to retrieve a compatible version of the code we use.\r\n\r\nRegarding `paramcontainer` and `TinyXPath`, they work so I don't think this is a super hig... | 2022-01-21T23:06:57 | 2025-01-23T23:14:34 | null | NONE | null | {
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} | null | # What is `vcpkg` ?
[`vcpkg`](https://vcpkg.io/en/index.html) is a C++ package manager, available on a majority of popular platforms (including Windows, Linux, and Mac).
# What convenience would it bring to Graphitti ?
Automatic compilation of the correct platform-specific version of a given library, easing burden of cross-platform users of the project. For example, in relation to #302, `log4cplus` does not automatically build for Windows despite the included repo indicating `MSVC` support.
# Does `vcpkg` support each library we currently manually include in Graphitti ?
Unfortunately no :( But a good chunk of them are!
The packages that _are_ inside `vcpkg`:
- [`cereal`](https://vcpkg.info/port/cereal)
- [`log4cplus`](https://vcpkg.info/port/log4cplus)
- [`gtest`](https://vcpkg.info/port/gtest)
- [`hdf5`](https://vcpkg.info/port/hdf5)
And the packages that _are not_ inside `vcpkg`:
- `paramcontainer` (this is really old btw)
- `tinyxpath` (this is also really old)
# What would this look like in Graphitti ?
A `vcpkg.json` file would list Graphitti's project dependencies that can be resolved by `vcpkg`. the `vcpkg.cmake` toolchain can be readily included in the `CMAKE_TOOLCHAIN_FILE` variable, or if we are using `Cmake(User)Presets` as in #303, then we can include the toolchain there.
Furthermore, the `ThirdParty` directory could have a slight refactor to better illustrate which dependencies are built by `vcpkg` and which ones are built by us ourselves. An example file directory would look like:
```bash
../Graphitti/
|->...
|-> /ThirdParty/
||-->/vcpkg/ # this is not what the actual install tree looks like, but just short-handing it for simplicity
|||--->log4cplus
|||--->cereal
|||--->gtest
||-->/manual/
|||--->/paramcontainer/
|||--->/TinyXPath/
|||--->CMakeLists.txt
|->vcpkg.json
|->CMakeLists.txt
|->CMake(User)Presets.json # assuming we implement #303
|->...
```
# What are some other things to consider ?
`vcpkg` is another dependency that the user must install themselves (unless we wrap that up in a bash script) - it's not too much trouble to install though. And it can be reused for other projects, not just Graphitti.
One thing to investigate though is how `vcpkg` will affect CI testing in Graphitti - we ideally do not want to include the built `vcpkg` packages into the main git repo.
Lastly, from this point, we could look to _upgrade_ the functionality of the libraries that were not found in `vcpkg` - Preliminarily, `paramcontainer` could be replaced by any modern argument parsing C++ library like [`cxxopts`](https://vcpkg.info/port/cxxopts), and `TinyXPath` could be replaced by a more modern XPath parser like [`pugixml`](https://vcpkg.info/port/pugixml). Of course, there's an overhead to _replacing_ these older libraries with the new ones, but I believe that these open up opportunities to not only modernize Graphitti but also provide new first issues for first-time contributors. | null | {
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"This is certainly interesting. The cross-OS possibility isn't a high priority (and, if it builds on Linux for CPU, it will likely build on MacOS), and the generators/compilers is even lower, but the CPU/GPU, debug/release/performance measurement conditional compilation stuff is interesting. This has to be weighed ... | 2022-01-21T22:07:42 | 2025-01-23T23:14:53 | null | NONE | null | {
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} | null | # What are `CMake(User)Presets` ?
A feature supported in `CMake 3.19` and onwards that allows projects to save a set of configurations in a `JSON` file to ease the transition between different build types (e.g. Windows/Linux, CPU/GPU, Debug/Release, etc...). Not only can it be called from the command line (via `cmake --preset "<preset-name>"`) and the `cmake-gui`, but `CMake(User)Presets` is readily supported on popular IDEs like Visual Studio (Code). Here is an example snippet to demonstrate:
On my setup (Windows, Visual Studio 2022), this particular `CMake` project has support for the `CMakeUserPresets.json` file, and detects a subset of configurations for me to choose (those that are supported by my system). If I were to change the environment, such as tapping into my `WSL` distro, the IDE readily changes the subset of available configurations:
For some more examples of how these configurations look, please look at the [official documentation](https://cmake.org/cmake/help/latest/manual/cmake-presets.7.html).
# Main Benefits for Graphitti Developers
- A project-wide set of configurations that are, for the most part readily set; no more needing to manually changing environment variables inside the `CMakeLists.txt` to change between CPU and GPU modes. Primarily the only variables that may need manual tuning are those that require user-specific paths, such as an installation directory.
- more cleanly specify the default build directory with `binaryDir`
- Cross-xxx support: building a particular configuration of independent factors is simply the composition of those factors. The primary configuration presets we could feasibly see in Graphitti are as follows:
- `CPU`/`GPU`
- `Windows`/`Linux`(/`Apple`?)
- `Debug`/`Release`
- Generators (`MSVC` versus `Ninja` versus `Makefiles` versus `Xcode`...)
- Specific Compilers (`cl` versus `gcc` versus `clang`....)
Creating a CPU+Windows+Debug configuration is simply the union of the three individual configurations presets. In other words, we can write 6 individual configurations that handles the specifics of each, and then create configurations that simply inherit from the original 6.
# What would this immediately affect in Graphitti currently ?
- Inside `CMakeLists.txt`:
- Any use of `set(...)` can instead be stored inside the `cacheVariable` `JSON` node of a configuration preset.
- _COULD_ get rid of the `DEBUG_MODE` check, if we use `CMAKE_BUILD_TYPE` in a configuration preset instead
- _COULD_ also move out the `add_compile_definitions(...)` into `CMAKE_CXX/CUDA_FLAGS`, but this is not as important
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"Actually, Mac already works. It seems clang is very close to g++, in that respect.\n\nNote that Graphitti is a 32-bit program, as all GPUs (as far as I know) are 32-bit hardware.",
"We should replace `Timer` with more modern timing calls (this is for performance measurement, I assume). There may be another issue... | 2022-01-21T20:59:24 | 2025-01-22T18:56:39 | null | NONE | null | {
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} | null | Graphitti should be able to run on any 64-bit device - primarily _Windows_, but I do not see why not on Apple as well. The primary development and testing environments will be Windows and Linux though.
Here are some current points:
- [x] The usage of `__invoke` in `Generic FunctionNode.h` is Linux specific; the standard library call is `std::invoke` and is only available in `C++17` _and beyond_. Thus, this would create an explicit need to raise the standard required by the project to `C++17`. This opens up a number of other modernization opportunities, but we should be careful that raising the standard does not produce any _heavy_ breaking changes (afaik, they shouldn't, at worst just a lot of warnings).
- [x] Immediately, when raising the standard, [there seems to be an issue raised that is prevalent in the Windows SDK that prevents us from compiling](https://developercommunity.visualstudio.com/t/byte-ambiguous-symbol-build-error-after-enabling-s/822269). I am pretty sure this is because the `Timer` class uses stuff from `windows.h` for some reason, but the workaround temporarily, especially if we want to keep using `Timer`, is to get rid of any `using namespace std;` calls around the project; this workaround allows us to bypass this issue in the Windows SDK. _this change also does not introduce any breaking changes into Graphitti on the Linux version_.
- [ ] Current issue is that the `log4cplus.lib` file is not being found on the Windows build, presumably because the `CMakeLists.txt` file may not be building the Windows version automatically (it _should_ be the case that the 3p module _automagically_ builds for the right platform). Building this current version seems to have no issues in compiling _on Linux_. So either some time needs to be spent in looking at the right places for `log4cplus` to be built from source properly per platform (which I currently can't tell if its the issue of the 3p module itself or us as the users), or using a package manager (like `vcpkg`) to take care of that stuff for us. | null | {
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} | null | Right now, this is a macro and static function defined in [Book.h](https://github.com/UWB-Biocomputing/Graphitti/blob/master/Simulator/Utils/Book.h). There must be a better way. Should probably be connected to coming up with an exception handling scheme, as indicated in #2 . | null | {
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https://github.com/UWB-Biocomputing/Graphitti/blob/da271b09a16aa0c32cb233eebac4bbeebaf97444/docs/index.md?plain=1#L55 | {
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"Looks good. In future, remember to set the project and link PR to associated issue(s)",
"Oh, @king-shak , once this is merges, you are go for the changes on Workbench!",
"Thankyou @king-shak "
] | 2021-12-09T04:00:28 | 2022-01-10T02:45:58 | 2021-12-20T01:37:14 | CONTRIBUTOR | null | {
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} | null | Changed Runtime file locations in all files. Tested multiple small, medium , large GPU and CPU *.xml files and also tested their diffs before and after making the required changes.
Also changed the .gitignore file. In terms of changing file locations , there is need to commit the .gitignore file first and then the required changes.
There is a need for .md files in the /build/Output folder, because git will not push an empty directory to a commit. | {
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"> * The log files (such as `build/Output/Debug/edges.txt`) need to be excluded from commits to GitHub by editing `.gitignore`.\r\n> * Similarly, simulation outputs should be ignored (I believe all contents of the `Results` directory).\r\n> * Was doxygen re-run? I'm not asking for that to happen; I'm just wondering... | 2021-12-08T03:22:06 | 2022-01-10T02:42:47 | 2021-12-09T04:31:47 | CONTRIBUTOR | null | {
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} | null | # Background
As of now in Workbench, when you start a simulation you are presented with a dialog (see below) that contains a record of everything that Workbench has done to run the simulation (just a vertically scrollable area with text) and a button labeled "Analyze" in the lower-right hand corner. To check whether the sim is done, you have to press this button, enter your credentials for the machine, and check whether it retrieved all the output and log files from the sim. If it didn't, you have to wait and try again later. This is obviously not very convenient, as the user doesn't know how long they should be waiting for.
Ideally, in the future, we want to completely re-do this dialog so that it has a progress bar instead, clearly indicating the simulator's progress. To do this, Graphitti needs to log it's progress using log4cplus as it goes about running the simulation so that Workbench is able to read its progress and update its progress bar.
# Proposed Log Structure
Here is the proposed structure for the log file:
* First, at the beginning of every line in the log shall be a timestamp, including the year, month, day, and second.
* One message should be logged when the sim is starting up and hasn't yet gotten to actually the simulation.
* There should be a message at the beginning of each epoch, specifying which epoch it is.
* Lastly, there will be one message at the end once the final epoch has run and the sim is writing results.
Here is an example for a simulation with 3 epochs:
```
[YYYY:MM:DD:SS] Starting up...
[YYYY:MM:DD:SS] Epoch 1/3...
[YYYY:MM:DD:SS] Epoch 2/3...
[YYYY:MM:DD:SS] Epoch 3/3...
[YYYY:MM:DD:SS] Writing results...
```
# Important Notes
**Please do note** that this design doesn't need to be followed strictly, it can be adapted. This is just a suggestion.
Also, this should be done with someone from the Workbench team, to ensure whatever log structure is implemented is sufficient for Workbench (the corresponding issue in Workbench is [here](https://github.com/UWB-Biocomputing/WorkBench/issues/119)). | null | {
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```
...
<EdgesParams name = "Edges Parameters" class="AllSTDPSynapses">
...
<STDPgap name="STDP Gap">2e-3</STDPgap>
...
</EdgesParams>
...
```
It should be something like this:
```
...
<EdgesParams name = "Edges Parameters" class="AllSTDPSynapses">
...
<STDPgap name="STDP Gap">
<val>2e-3</val>
</STDPgap>
...
</EdgesParams>
...
```
i.e., it needs to be nested one level deeper. This is necessary for Workbench so it can properly display and write the value of this parameter.
Once this issue is solved, the template files in Workbench need to be updated. | null | {
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"Output for GPU simulations run on Graphitti currently (as of 12/2/2021) match exactly (pass a diff) that of the same GPU simulation run on the version 1 release of BrainGrid, up to a point. After a large number of epochs, there seems to be a difference.\r\n \r\nThe simulation that I observed this on was test-mediu... | 2021-12-02T20:21:15 | 2021-12-02T20:29:51 | null | CONTRIBUTOR | null | {
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"I had asked you about this before, but we decided to implement it in `parseCommandLine()` using `ParamContainer`, which is only called after other stuff is printed. I can change it so that the -v arg is checked at the start of `main`.",
"Good point. Maybe we can look into parsing tinted commands line early in th... | 2021-12-02T19:42:18 | 2021-12-05T23:59:41 | null | CONTRIBUTOR | null | {
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"I think maybe the best thing would be to make the current `ConnStatic` a new, `ConnRandom`, connection class and then create a new `ConnStatic` class that starts with no edges — basically, a class built to support deserialization."
] | 2021-12-02T19:22:18 | 2025-01-19T00:34:19 | null | CONTRIBUTOR | null | {
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https://github.com/UWB-Biocomputing/Graphitti/blob/da271b09a16aa0c32cb233eebac4bbeebaf97444/Simulator/Connections/Neuro/ConnStatic.cpp#L131-L139
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"I think that the `probedNeuronList_` could be renamed `probedVertexList_` and kept at the top level. Actually, I believe that this is going to be/is being moved to the `Recorder` classes, right, @kimjamesuw?"
] | 2021-11-27T04:34:02 | 2022-07-31T16:58:32 | null | CONTRIBUTOR | null | {
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```
BGSIZE numCallerVertices_
...
vector<int> callerVertexList_; ///< Caller vertex list.
vector<int> psapVertexList_; ///< PSAP vertex list.
vector<int> responderVertexList_; ///< Responder vertex list.
```
The Neuron specific class members are being used in the implementation of printParameters() for printing to the logging file. It seems to me that, since these parameters are model specific, the printParameters() method could be an abstract method to be implemented by the model specific sub-classes, the same way we are doing it with loadParameters().
layout.h Neuro specific class members:
```
vector<int> probedNeuronList_;
...
BGSIZE numEndogenouslyActiveNeurons_;
...
vector<int> endogenouslyActiveNeuronList_; ///< Endogenously active neurons list.
vector<int> inhibitoryNeuronLayout_; ///< Inhibitory neurons list.
```
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"I'm not clear about what it would mean to deploy to an orphan branch. My understanding was that GitHub pages wiki only works in master. Regarding how often to do this, we had thought that this would be done quarterly, but if it's automated then it could be done monthly. But I think it would be a waste to do it wit... | 2021-11-25T05:12:07 | 2022-04-07T19:08:14 | 2021-12-30T01:46:38 | CONTRIBUTOR | null | {
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Closes #253
This Github Action auto-generates the project's Doxygen documentation and deploys it to an orphan gh-pages branch.
The idea is that we can set the docs directory in gh-pages branch as the root for our documentation page: https://uwb-biocomputing.github.io/Graphitti/
Does it make sense to have it executing on every push and pull requests to the master branch? | {
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} | null | Many changes that were necessary to fix problems with the GPU sim (most notably the problems where certain kernels were not executing at all and where the output varied greatly from what was expected & observed from BrainGrid)
Changes include mostly changes to the CMakeLists.txt files, the most important of which were setting the libraries where CUDA source code resides to be STATIC upon creation, and setting CUDA_SEPERABLE_COMPILATION to ON for those same libraries. This solved several CUDA related compilation, linking, and runtime problems. Also, the method of passing flags to nvcc was changed (as our old flags were not actually making it to the nvcc compiler) and some of the flags used were changed. Subdirectory CMakeLists files not made by a third party were consolidated into the top level one. The top level CMakeLists.txt file was reorganized, and comments were added. Several other small changes.
Some small changes to other simulator files such as AllSynapsesDeviceFuncs.h and AllSynapsesDeviceFuncs_d.cu to solve compilation problems.
Tested all 12 basic test config simulations, which now match 100% to the output of BrainGrid (v1 release)'s output from the same GPU sims. Spot tested a few of those same 12 simulations on CPU against previously gathered results to make sure that output for the CPU was not affected by these changes. No differences were found. | {
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"FYI, the CMakeLists.txt within the RNG folder explicitly defines it as a shared library. This was a fix to an older issue where the simulator would come across a linking error when running a GPU sim. Just want to make sure that it doesn't break again.",
"Ah yes I did run across that today. I was wondering why th... | 2021-11-20T22:50:06 | 2021-11-22T18:39:32 | 2021-11-22T18:39:32 | CONTRIBUTOR | null | {
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"> Thanks Professor Stiber for adding all the information in spikeRecording.md!\r\n\r\nNo problem. This pull request isn't ready to close yet. I don't think we can disconnect this from resolving #240; I intend this to at least be where we work together on the re-engineering. I'll do the encapsulating and perhaps wh... | 2021-11-19T01:15:12 | 2022-05-10T22:22:24 | 2022-05-10T17:36:56 | CONTRIBUTOR | null | {
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See documentation in docs/Developer/spikeRecording.md in this branch for on-the-fly notes regarding the current state of planning for this redesign. It seems like the approach to be used involves encapsulating the spike recording data structures within a new class that provides a clean interface to the recorders for their need, a clean interface to the CPU side vertex and edge classes, and the ability to allocate and copy the "raw" data structures on the GPU side. | {
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"Addressed through introducing event buffer changes in #334 "
] | 2021-11-15T21:06:37 | 2022-05-10T17:41:49 | 2022-05-10T17:41:48 | CONTRIBUTOR | null | {
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Right now, extracting spike information for recording in XML or HDF5 is very complex. If we want to simplify the Recorder classes, then we need to have an interface to the spike history information that is straightforward, like a one or two-dimensional array. Morerover, the documentation of the spike history data structures in the vertex classes (inherited from AllSpikingNeurons) is very poor — basically not possible to understand without puzzling through the code (which is what documentation is supposed to obviate). Need to go through AllSpikingNeurons, figure out and document what is going on, and then determine if the current approach can be simplified within AllSpikingNeurons.
If that is not the case, then we should create a wrapper object around the spike history info that presents a simple interface, consistent with either a 2D array, vertex, VectorMatrix, or the like, so that Recorders can access and copy out spike information with code consistent with other variables to record. | {
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"Assuming the test passes, all looks good. However, I'd like to test these changes with Workbench first before approving - please don't merge till then."
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```XML
<RecorderParams class="XmlGrowthRecorder" name="RecorderParams">
<probedNListFileName name="prbNListFileName" type="InputFile">../configfiles/NList/probedNList_900.xml</probedNListFileName>
<resultFileName name="resultFileName">../Output/Results/test-medium-connected-long-out.xml</resultFileName>
</RecorderParams>
```
This should have another level (see `LayoutParams` as an example):
```XML
<RecorderParams class="XmlGrowthRecorder" name="Recorder Parameters">
<RecorderFiles name="Recorder Files">
<probedNListFileName name="Probed Neurons" type="InputFile">../configfiles/NList/probedNList_900.xml</probedNListFileName>
<resultFileName name="Result File">../Output/Results/test-medium-connected-long-out.xml</resultFileName>
</RecorderFiles>
</RecorderParams>
```
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"Should this be computed within the simulator at all? Perhaps it should be computed in Matlab _ex post facto_.",
"I think it's OK to just remove this code. We can compute it after the fact. This code can be preserved in the release we make before the Recorders go through major modification."
] | 2021-11-08T19:02:18 | 2023-04-12T17:57:30 | 2023-04-12T17:57:30 | CONTRIBUTOR | null | {
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https://github.com/UWB-Biocomputing/Graphitti/blob/eccbec4bf65666580bd4b7f36589666ebd0fde2d/Simulator/Recorders/Hdf5Recorder.cpp#L286-L291 | {
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https://github.com/UWB-Biocomputing/Graphitti/blob/eccbec4bf65666580bd4b7f36589666ebd0fde2d/Simulator/Recorders/Hdf5Recorder.cpp#L279-L284 | {
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"I think this will be irrelevant when Recorders are re-engineered"
] | 2021-11-08T18:52:55 | 2025-02-07T06:57:38 | 2025-02-07T06:57:37 | CONTRIBUTOR | null | {
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"Actually, a (maybe sorted, maybe that doesn't matter) vector of ints is better; we can just iterate through that and indirectly access the listed neurons.",
"After some thought, I think that it's better to make our code simpler and just always record from all vertices. We have run simulations with 10,000 vertice... | 2021-11-08T18:45:44 | 2025-03-10T06:39:03 | 2025-03-10T06:39:03 | CONTRIBUTOR | null | {
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https://github.com/UWB-Biocomputing/Graphitti/blob/eccbec4bf65666580bd4b7f36589666ebd0fde2d/Simulator/Recorders/Hdf5Recorder.cpp#L262 | {
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"After reengineering the Recorder subsystem, this line of code will be removed."
] | 2021-11-08T18:27:14 | 2025-02-06T02:31:34 | 2025-02-06T02:31:34 | CONTRIBUTOR | null | {
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} | null | As part of #240, things that are common to all recorders, such as loading the output filename parameter (and, in fact, registering the `loadParameters()` method with `OperationManager`) should be in the top-level class (and, for consistency with other subsystems, we should remove the "I" from `IRecorder`). This should likely be part of an overall review of the subclass members once we have a clear idea of the new, generic recorder architecture. | {
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"Good point; I'll put it in the fall 2021 project. Whoever does it should output a FATAL log output to console and then, for now, `exit()`. We can decide on exceptions later and just search for all of the exits.",
"All factories' `invokeCreateFunction` were removed in #352 since this added unnecessary complexity.... | 2021-11-06T23:04:30 | 2024-06-05T19:38:05 | 2024-06-05T19:38:05 | COLLABORATOR | null | {
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This also happens when the name string is uninitialized. Variables that couldn't be initialized by `ParameterManager` should also throw FATAL errors (see issue #217 , which, given our now longer regression test times, should probably be a higher priority). | {
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"I think there are some config files that didn't get updated. Seems like these are the ones in the `Testing/RegressionTesting/configfiles` directory.",
"Oh those files don't exist on this branch, oops. I'll rebase with master, edit those, and push changes soon.",
"I'm not a 100% sure on what I did, because the ... | 2021-11-06T20:58:04 | 2021-11-07T00:35:49 | 2021-11-07T00:22:30 | COLLABORATOR | null | {
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Renames:
`NoiseRNGParams` to `NoiseRNGSeed`
`InitRNGParams` to `InitRNGSeed` | {
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"The parameter loading still doesn't happen inside `IRecorder::loadParameters()` (No real reason for `IRecorder` to remain an interface class and do this in all derived classes).\r\nIt doesn't change much, but might be important/nice for things like issue #216 and #240",
"> The parameter loading still doesn't hap... | 2021-11-05T00:05:49 | 2021-11-10T21:34:02 | 2021-11-10T21:33:57 | CONTRIBUTOR | null | {
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"We should see if we can do this through CMake. We already have a `DEBUG_MODE` flag that disables -O3 optimization."
] | 2021-10-27T23:47:08 | 2022-01-21T20:53:58 | null | CONTRIBUTOR | null | {
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"We should also make sure to update documentation describing how to build Graphitti, plus add a wiki page that summarizes the differences among the arch levels and specifically calls out the conditional sections of code and what the specific differences are there — ideally with some performance notes (after all, co... | 2021-10-26T03:51:18 | 2024-07-16T01:17:27 | null | NONE | null | {
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This may have the drawback in having to add define macros for compiling specific sections of code, depending on whether or not the device supports a certain feature, to maintain full backwards compatibility with AT LEAST CC 3.5. | null | {
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"It failed checks because the config files used for regression testing are here: `Testing/RegressionTesting/configfiles/`\r\nThese need to be updated too."
] | 2021-10-22T02:28:29 | 2021-11-01T05:21:06 | 2021-11-01T05:21:00 | CONTRIBUTOR | null | {
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SimInfoParams/OutputParams/resultFileName
Move it down to:
ModelParams/RecorderParams/resultFileName | {
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} | null | In preparation for true out-of-source build, we should reorganize the runtime files and directories so that they are all under one directory and could be copied to an installation target directory. From what I can see, this implies:
- In the code, lines that include something like `../RuntimeFiles/...` become `RuntimeFiles/...`
- In the code, are there any lines that include something like `../Output/...`, or is that in the config files?
- Need to move RuntimeFiles directory in the repo to under the build directory in the repo and verify that it pushes to GitHub.
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"Yes, and here is the code to add a badge ([](https://zenodo.org/badge/latestdoi/273115663)) to README.md:\r\n```\r\n[](https://zenodo.org/badge/latestdoi/273115663)\r\n```"
] | 2021-10-12T19:16:43 | 2021-10-14T18:42:21 | 2021-10-14T18:42:21 | CONTRIBUTOR | null | {
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Note that this was set up for BrainGrid. | {
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"Actually, this needs to be at the top level, so maybe it can't be linked in with the other documentation."
] | 2021-10-07T17:07:28 | 2024-02-24T00:26:14 | null | CONTRIBUTOR | null | {
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This is very old. | null | {
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"@stiber , should actions run and verify a subset of these?\r\nRunning all would take a substantial amount of time. I got actions to continue and run all the tests even if a previous one had failed on the `github-actions-testing` branch\r\n\r\ntest-small.xml\r\ntest-small-connected.xml\r\ntest-small-long.xml\r\ntes... | 2021-10-07T16:51:47 | 2021-10-16T00:16:06 | 2021-10-16T00:16:06 | COLLABORATOR | null | {
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I'm guessing that these should also be compared to the BrainGrid output once? | {
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} | null | Changes to testing config files and inhibitory neuron lists used. Created a set of testing config files with standardized parameters and incremental changes. Added long (10 epoch) versions of small, medium, and large tests. Test config file set consists of:
test-small.xml
test-small-connected.xml
test-small-long.xml
test-small-connected-long.xml
test-medium.xml
test-medium-connected.xml
test-medium-long.xml
test-medium-connected-long.xml
test-large.xml
test-large-connected.xml
test-large-long.xml
test-large-connected-long.xml
Names for some existing large test config files were changed to make more sense. test-large-short config files had short removed from their name, and the existing test-large-long config files were renamed to very long (600 epochs), as test-large-long is included in this testing set (only 10 epochs).
New inhibitory neuron lists for a ratio of 0.1 inhibitory neurons on 10x10 and 30x30 simulations added to have a standard ratio between all tests listed above.
closes #247 | {
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} | null | Tests small, small-connected, medium, medium-connected, large short, and maybe others, need to have their changing parameters looked at and standardized so that there are logical incremental changes between them.
Unnecessary changes between them should be removed.
Large-short should have a large-short-connected made to match the others in the set.
Long versions of the standard test config files should be made.
Names should be changed if they don't make sense | {
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} | null | Many parameters can be cross-validated against each other (for instance, that vertex IDs should not be larger than the number of vertices minus 1). Also, there are only some combinations of C++ classes (vertices, edges, etc.) that make sense.
To do this, we need to think thought how to specify these constraints so that they can be tested by the `ParameterManager`. A constraint file? Extra parameters passed in when a client class loads its parameters? Need some thought/research regarding the architecture/design pattern for this. | null | {
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- Any significant performance hit (likely not)
- That we actually check the return value in case it fails (which signals a bug that shouldn't have gotten through testing) | null | {
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Can be tied into issues #51/#50 | {
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**GITHUB WORKFLOW**
// start here for new issues
1. Create a new issue
2. Add issue to Projects/_Current Project_/To do
// start here for existing issues
3. Assign the issue to yourself
4. Create a new feature branch
5. Add a comment to the issue including a link to the feature branch
6. Move issue to the 'In progress' column in Projects
7. Make changes to the feature branch (commit/push)
8. Create a pull request and assign it to yourself
9. Link pull request to issue
10. Check that pull request passes automated tests
11. Run manual tests on pull request
10. Request review on the pull request
11. Reviewer moves issue to 'Review in progress' in Projects
12. Reviewer approves the pull request
13. Reviewer moves issue to 'Reviewer approved' in Projects
14. Merge feature branch with main branch
15. Issue automatically moved to 'Done' in Projects
16. Delete feature branch | {
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"This umbrella issue needs to be broken down into actionable tasks.",
"Some questions to answer related to this:\r\n\r\n- When does the recorder method that periodically captures data to the output get called?\r\n- Who calls it?\r\n- Right now, how does recorder know which variables to capture?\r\n- For capturing... | 2021-08-21T17:35:05 | 2025-03-23T10:15:35 | null | CONTRIBUTOR | null | {
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} | null | Right now, the Recorder classes are implemented specially for each model. However, the fundamental operation of a recorder is as follows:
1. A set of variables is specified for recording. Each variable has a name and dimensions (it may be the case that one of the dimensions is unknown ahead of time, for example, for the list of spike times produced by neurons — we know how many neurons, but we don't know how many spikes each neuron will produce).
2. Each variable has a temporal resolution. Some variables need to be recorded (can update) every time step; some will not update more often than once per epoch.
3. In addition, as set of constants may be specified. These are values that do not change during the simulation, such as neuron types, vertex locations, etc.
4. The recorder has an output format, which is captured by the subclass, currently XML or HDF5.
Can we do something like the ParameterManager, where we register variables with a recorder object, providing whatever information is needed at that time (variable name as a string, variable update interval, variable dimensions)? The recorder would have a method that is periodically called to buffer/output variable contents. Using the above scheme, perhaps we would no longer need to provide a list of vertices to attach recorders to, since recording would be at a variable basis and so could be completely generic (we could record edge variables, for instance). | null | {
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"I think `allVerticesDevice.summationMap_` should be a GPU-side pointer, while the other is a CPU-side pointer. Have these gotten mixed up?",
"Yup, here is where the mixup happens. I'm not sure what the point of this line of code is, maybe it's supposed to be doing a deep copy?\r\n\r\nAllIFNeurons_d.cu, ln 62-63:... | 2021-08-05T14:36:17 | 2022-11-16T20:25:43 | 2022-11-16T20:25:42 | COLLABORATOR | null | {
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1. In a GPU simulation, the `summationMap_` is first allocated (AllVertices.cpp, ln 42).
2. This pointer is then set to a second `allVerticesDevice.summationMap_` (AllIFNeurons_d.cu, ln 63).
3. Consequently, the original `summationMap_` is never deleted, and causes a memory leak.
4. After the sim, `allVerticesDevice.summationMap_` is deleted (AllIFNeurons_d.cu, ln 112).
5. When `AllVertices` tries to delete `summationMap_`, it points to the same thing (which was already deleted). So, it causes a segmentation fault (AllVertices.cpp, ln 34). | {
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"@stiber The small and large tests are outputting identical results. All four of those tests are 2 epochs. The two medium tests are 20 epochs, and they start showing differences in spikes and radii after connections start forming. For test-medium this begins on epoch 14, and for test-medium-connected it starts on e... | 2021-08-05T03:14:38 | 2021-11-23T17:56:49 | 2021-11-22T18:39:32 | CONTRIBUTOR | null | {
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- [x] test-small
- [x] test-small-connected
- [x] test-medium
- [x] test-medium-connected
- [x] test-large-short
- [x] test-large-short-connected | {
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"This is something we would need to look at in detail. Since it impinges upon GPU performance, it will require a validated GPU version of Graphitti and careful performance analysis. Some preliminary notes:\r\n\r\n- Generally, we design the CPU-side data structures with the GPU-side ones in mind. In effect, we desig... | 2021-08-03T13:56:27 | 2023-04-18T20:14:25 | 2023-04-18T20:14:25 | COLLABORATOR | null | {
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(See: `GPUModel::copySynapseIndexMapHostToDevice`)
Should the data be placed in a non-contiguous manner? GPU efficiency is a possible argument against this.
The data from the edgeIndexMap is `cudaMemcpy`-ed on and off the GPU, and it only copies `totalEdgeCount_` edges. As the edges are placed contiguously, this is no issue.
As `totalEdgeCount_` may change, this space on the GPU is freed and re-allocated each time. Is GPU memory more expensive, or should this change to accommodate the maximum number of edges?
Line 271 of `GPUModel.cu`: ` if (totalSynapseCount == 0) return;`
Is this a bug? It clearly just leaves behind dirty data. The same line was in `AllEdges::createEdgeIndexMap`, and caused seg faults with `test-tiny.xml` (See: b0ef10699617b64528d52b7ba18f35cb619ec629, issue #222). | {
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"The 911 models have changed so much that his code is no longer relevant. therefore, I am closing this PR and deleting the branch."
] | 2021-08-03T13:22:44 | 2023-09-27T15:51:11 | 2023-09-27T15:50:54 | COLLABORATOR | null | {
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Just want to push everything into master to start working on a clean branch as this one is ~100 commits behind. | {
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"It looks like some commits from my regression testing branch made their way into this PR. Still learning the finer points of git.",
"For Hdf5Recorder:\r\n- Reverted `burstinessHist_` and `spikesHistory_` arrays to original lengths \r\n- Added back a term in the calculation of idx1 and idx2 that was removed in b8... | 2021-07-29T17:54:34 | 2021-08-09T16:54:05 | 2021-08-09T16:54:02 | CONTRIBUTOR | null | {
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Incremental HDF5 file writing from BrainGrid was already implemented in d4dc1240a9fb1f8332466846f6012b2a93f1e887. I verified that it was writing readable files using the `h5dump --header` command. I also checked the output file of a simulation in progress and saw that the file size increases after every epoch. | {
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"Seems like the hdf5 recorder doesn't account for simulations with multiple epochs.\r\nThese changes should fix it:\r\n\r\n`Hdf5Recorder.cpp`, lines 172:175:\r\n```\r\n// allocate and initialize data memories\r\nburstinessHist_ = new int[static_cast<int>(Simulator::getInstance().getEpochDuration() * Simulator::getI... | 2021-07-29T07:35:19 | 2021-08-09T16:54:02 | 2021-08-09T16:54:02 | CONTRIBUTOR | null | {
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` assert(idx1 >= 0 && idx1 < simulator.getEpochDuration());`
Some notes:
- The problem is that `idx1` is >= `simulator.getEpochDuration()` on a simulation with more than 1 epoch.
- This assertion is to prevent `burstinessHist_[idx1]++` on the next line from writing outside of bounds, since `burstinessHist_` has a length of `simulator.getEpochDuration()`.
- Two lines down, `spikesHistory_[idx2]++` is similarly at risk of writing out of bounds, but doesn't have its own assertion.
- Removing this assertion predictably causes a segmentation fault.
- Removing the assertion and arbitrarily making both `burstinessHist_` and `spikesHistory_` twice as long allows `test-small` to complete and write to a .h5 file successfully.
So the solution would be to either initialize these two arrays to a larger, hopefully non-arbitrary value OR figure out why `idx1` and `idx2` are being calculated as values too large for their arrays to hold them. If `idx1` and `idx2` are being calculated correctly, then the array needs to be bigger to fit them.
Also:
- This assertion does not exist in `XMLRecorder`
- `burtsinessHist_` and `spikesHistory_` are of type `VectorMatrix` in `XMLRecorder`, so dynamic resizing means writing out of bounds is not an issue.
Another solution might be to change these two arrays to both be a `VectorMatrix` in `HDF5Recorder`, but that might not be possible due to the H5 write method wanting an array as an output buffer. | {
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"Reverted changes to `EdgeIndexMap` because CUDA wanted normal C++ arrays",
"`test-small.xml` and `test-medium.xml` create the exact same output as `master`. Valarrays seem to be about as fast as arrays, with `-O3`. Times for `test-medium`:\r\n\r\nWith valarrays (valarray-switch):\r\n```\r\nreal 17m12.246s\r\n... | 2021-07-28T01:45:19 | 2022-05-10T22:17:19 | 2021-08-03T03:12:00 | COLLABORATOR | null | {
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I didn't touch the GPU code (other than to edit the references to the member variables) or anything in Utils.
Might be easier to review this commit-by-commit. I realize that the commit messages aren't the most helpful, but I went from directory to directory. | {
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"Changes:\r\n\r\n- Explicitly declared RNG as a shared library in Cmake, which fixes the GPU linking error.\r\n- Renamed \"MersenneTwister.h\" -> \"MTRand.h\".\r\n- Cleaned up some bad code in `MTRand` and `Norm`.\r\n- Created `RNGFactory`, which creates instances of `MTRand` or `Norm`.\r\n- Created Norm re-seeding... | 2021-07-26T04:12:55 | 2021-08-03T03:14:39 | 2021-08-03T03:10:09 | COLLABORATOR | null | {
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"Same as #222 "
] | 2021-07-23T20:37:49 | 2021-07-23T21:17:13 | 2021-07-23T21:17:13 | CONTRIBUTOR | null | {
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```
.../AllSpikingSynapses.cpp:263: virtual void AllSpikingSynapses::preSpikeHit(uint32_t): Assertion `false' failed.
```
This doesn't seem to happen with any of the other test files. Likely related to 034298ca07f8adfe162ab6a24a9757446f5727af. | {
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"If it executes in `parseCommandLine`, then this gets printed to the terminal first, which may be undesirable:\r\n```\r\n[TRACE][2021-07-22 22:28:43] Instantiating Simulator\r\n[TRACE][2021-07-22 22:28:43] Parsing command line\r\n```",
"> If it executes in `parseCommandLine`, then this gets printed to the termina... | 2021-07-22T16:38:20 | 2021-07-26T18:48:29 | 2021-07-26T18:47:54 | COLLABORATOR | null | {
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https://github.com/UWB-Biocomputing/Graphitti/blob/master/build/README.md | null | {
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"A check for epsilon having a value of 0 is done to avoid division by 0. It currently just writes a warning to the log, but this could change to a console warning or a termination of the simulator if need be"
] | 2021-07-21T02:46:27 | 2021-07-21T17:39:25 | 2021-07-21T17:39:21 | CONTRIBUTOR | null | {
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"Accomplished this using a cmake-generated `config.h` file.\r\nUnsure about the specific message it should output, or the length of the commit ID (short 7 hex chars vs full 40 hex chars).",
"After some thought, let's output the full commit ID (40 digits). Workbench can always deal with the UI issue to substitute ... | 2021-07-19T18:19:34 | 2021-07-26T18:47:54 | 2021-07-26T18:47:54 | CONTRIBUTOR | null | {
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} | null | The basic idea here is to be able to run, say, `graphitti -v` and have graphitti output the commit ID from which it was built and quit (not running a simulation). An off-the-cuff idea how this might be accomplished would be to have CMake run `git` to get the repo's commit ID, then have it add a `-DCOMMIT=<that ID>` to the g++ command line (or the `CFLAGS`) in the Makefile it generates. That macro definition could be used in the code to accomplish this.
This is something that will be desirable for Workbench interoperability. | {
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} | null | This should pre-date the multithreaded simulator (where this would make sense). Is there another reason, or is code that crept into the earlier codebase as prep work for multithreading?
https://github.com/UWB-Biocomputing/Graphitti/blob/a6121fd76be715f125c6513d1cfa297b500f2d51/Simulator/Vertices/Neuro/AllLIFNeurons.cpp#L50 | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/224 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/224/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/224/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/224/events | https://github.com/UWB-Biocomputing/Graphitti/issues/224 | 947,869,999 | MDU6SXNzdWU5NDc4Njk5OTk= | 224 | Synapse parameter loading is still not correct | {
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} | [
{
"id": 2144423149,
"node_id": "MDU6TGFiZWwyMTQ0NDIzMTQ5",
"url": "https://api.github.com/repos/UWB-Biocomputing/Graphitti/labels/bug",
"name": "bug",
"color": "d73a4a",
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"description": "Something isn't working"
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{
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"node_id": "MDU6TGFiZWwyM... | open | false | null | [] | null | [] | 2021-07-19T17:26:16 | 2022-01-21T20:50:09 | null | CONTRIBUTOR | null | {
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} | null | It seems that the DS Synapse parameters are not being loaded, but are hard coded.
Should also check other synapse classes; we need to get rid of hard-coded parameters.
| null | {
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