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Created a bash script for running our unit and regression tests. | {
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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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```
error: size of array ‘altStackMem’ is not an integral constant-expression
6285 | static char altStackMem[SIGSTKSZ];
| ^~~~~~... | {
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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... | {
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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, ... | 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 --unch... | {
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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... | {
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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 r... | {
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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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[`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 burd... | 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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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 ... | null | {
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Here are some current points:
- [x] The usage of `__invoke` in `Generic FunctionNode.h` is Linux specific; the st... | null | {
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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 "
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Also changed the .gitignore file. In terms of changing file locations , there is need to commit the .gitignore file first and then the r... | {
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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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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... | 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... | 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> psapVertexLi... | null | {
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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 se... | {
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Changes include mostly changes to the CMakeLists.txt files, the most important of which we... | {
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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 i... | {
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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... | {
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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/Resul... | {
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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."
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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 issu... | {
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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",
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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."
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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."
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SimInfoParams/OutputParams/resultFileName
Move it down to:
ModelParams/RecorderParams/resultFileName | {
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- In the code, lines that include something like `../RuntimeFiles/...` become `Runti... | {
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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 outpu... | {
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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.x... | {
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Unnecessary changes between them should be removed.
Large-short should have a large-short-connected ... | {
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To do this, we need to think thought how to specify these constraints so t... | 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 fe... | {
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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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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... | 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... | {
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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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"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 ... | {
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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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} | null | HDF5 output works fine on `test-tiny-hdf5.xml`, but when I made a version of `test-small` that uses the `HDF5GrowthRecorder`, it fails an assertion at line 268 of `HDF5Recorder`:
` assert(idx1 >= 0 && idx1 < simulator.getEpochDuration());`
Some notes:
- The problem is that `idx1` is >= `simulator.getEpochDuration(... | {
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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 director... | {
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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 ... | {
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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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https://github.com/UWB-Biocomputing/Graphitti/blob/a6121fd76be715f125c6513d1cfa297b500f2d51/Simulator/Vertices/Neuro/AllLIFNeurons.... | {
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Should also check other synapse classes; we need to get rid of hard-coded parameters.
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