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Closes #722
Closes #719
Closes #574
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This expands the set of variables recorded by including additional ones, providing a wider range... | null | {
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https://... | null | {
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Closes #734
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Add source, target and weighted connections for STDP simulations from graphml files. Create NeuralEdgeProperties struct for ... | {
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Closes #648
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Closes #786 #806
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#### Description
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#### Checklist (Mandatory for new features)
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Closes #783
Closes #773
Closes #319
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#### Description
This PR replaces and continues work from #794
Continues from work on #794:
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Closes #791
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Move neuronTypeToString to AllVertices and rename to vertexTypeToString (utility function).
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<!-- Please provide a brief overview of the changes implemented -->
#### Description
Removed the probed neuron/vertex list from all config files, as this code no longer exists.
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#### Checklist (Mandatory for new features)
- [ ] Added Documentation
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Closes #648
Closes #734
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#### Description
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"@stiber based on the edge state not being updated until after we know that we need to transfer the call to the vertex, I think it's reasonable for all of the current advanceEdges implementation to be moved into integrateVertexInput. Lets discuss this PR at our 1:1 later this week."
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Closes #806
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On debugging we found the follwing two root causes:
1. The `summationPoints_` v... | {
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"@stiber this should be a quick review, but it is ready when you get a chance. I'll then set up a PR to merge this into Shared Development."
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Closes #786
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#### Description
It looks like the 911 file wasn't moved when the Cpu and Gpu testing subfolders were created. Moved small 911 test into Cpu s... | {
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CloudBees' repo for the PlantUML github-action is no longer available.
Investigation is needed. | null | {
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PlantUML link is more than just a broken link, and may require an alternative repo. Should be opened as its' own issue.
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Closes #
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"Well, on the bright side, this problem will go away in the not-too-distant future, since this recorder class is a hack and the 911 simulations will switch over to using the standard recorder classes. See #719 ",
"@stiber ahhh okay. That makes sense. Is that why the 911Edges.h doesn't have the Cereal serializatio... | 2025-02-26T04:58:49 | 2025-03-06T22:52:04 | null | CONTRIBUTOR | null | {
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https://github.com/UWB-Biocomputing/Graphitti/blob/212fb1df8950cf5cd040ef2a0bf0f80b32e8af64/Simulator/Recorders/NG911/Xml911Recorder.cpp#L35-L40
Not sure why this is or if/why its needed. | null | {
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#### Description
Adding VertexType to Recorders
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#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [x] Added Unit Tests
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#### Description
The GraphManager class needs to be modified to support different property structs for specific application domains. This enhancement will involve templating the class and adding inheritance to the VertexProperty.
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"@stiber this PR is to merge my PoseyDevelopment branch into SharedDevelopment. This will merge PRs 777 and 789 into SharedDevelopment. Per the above commits, it is now up-to-date with SharedDevelopment. I took a quick look through the file changes and it looks like it only contains the changes from the two PRs so ... | 2025-02-18T05:16:51 | 2025-02-19T19:45:52 | 2025-02-19T19:45:52 | CONTRIBUTOR | null | {
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Closes #745 #785
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Merge includes two PRs. PR 777 which moved the vertex integration logic that lived in the Edges class into the Vertices... | {
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#### Description
Code to copy the weights back from the GPU after each epoch.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [ ] Added Unit Tests
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As a part of the onboarding task add Padmanabh Patil to the Contributors list of Graphitti.
#### Files
Contributors.txt | null | {
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Closes #783
Closes #773
<!-- Please provide a brief overview of the changes implemented -->
#### Description
CMAKE build types cleaned up in cmakelists
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# Build Type Configuration
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2. Move it to `AllVertices`
3. Should this be a utility function or a method?
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"@stiber this is ready for review. We can discuss at our 1:1 this Thursday."
] | 2025-02-04T23:11:34 | 2025-03-06T08:53:57 | 2025-02-18T03:51:24 | CONTRIBUTOR | null | {
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Closes #785
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Focus was on refactoring the GPUModel class to not refer to anything neuro-related. This was mostly renaming variables and m... | {
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"Repo for CloudBees/plantuml-github-action no longer exists: https://github.com/cloudbees/plantuml-github-action\n\nNeed to verify if this action is still being utilized in the repo.",
"[Introducing GitFlow](https://uwb-biocomputing.github.io/Graphitti/Developer/GitFlowDiagram.html)\nLink already fixed in current... | 2025-02-03T23:06:11 | 2025-02-26T05:30:08 | 2025-02-26T05:30:08 | NONE | null | {
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1.2 Installation
1.2.2.1 [Fork and clone Graphitt](https://uwb-biocomputing.github.io/Graphitti/User/installation.html)
Contribute to Graphitti - Correct link location.
1.2.3
h5c++ link no longer works
2. Developer Documentation
[PlantUML Action](https://uwb-biocomputing.github.io/Graphitti/Developer/... | {
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Closes #443
Closes #444
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#### Description
Documetnation links updated from relative to absolute.
<!-- Please check the boxes as applicable -->
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"Nope, no reason to not include this. Will need to ensure there is a good output file. I note that it is already running in the GitHub action, so this is likely an oversight.",
"I can confirm that there is already a test-small-911-out.xml file in the GoodOutput directory. It would need to be moved into the GoodOu... | 2025-02-01T04:20:04 | 2025-03-07T04:10:46 | 2025-03-07T04:10:45 | CONTRIBUTOR | null | {
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There is a "test-small-911.xml" in Testing/RegressionTesting/configFiles. It doesn't look like this is being run when we run the CPU regression tests.
I suspect it's... | {
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"Completed and pushed into SharedDevelopment"
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https://github.com/UWB-Biocomputing/Graphitti/blob/291506208498bfaa2d5d13372c069dabe290c86c/Simulator/Core/GPUModel.h#L126-L130 | {
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https://github.com/UWB-Biocomputing/Graphitti/blob/291506208498bfaa2d5d13372c069dabe290c86c/Simulator/Vertices/Neuro/AllIFNeurons.h#L86-L87
overridden methods should be marked `override` | null | {
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The cache variable TARGET_ARCH can be passed in on the command line to change the cuda architecture used.
e.g. when running the GPU simulation on target architecture 70:
`cmake -D ENABLE_CUDA=YES -D TARGET_ARCH=70 ..`
The quickstart guide also need... | null | {
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Closes #644
<!-- Please provide a brief overview of the changes implemented -->
#### Description
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
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Closes #768
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Changes in comments
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"This may only be \"easily\" working for CPU simulations, because weights currently aren't copied back for GPU simulations."
] | 2025-01-30T00:56:42 | 2025-01-30T01:10:08 | null | CONTRIBUTOR | null | {
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- source vertex
- destination vertex
- edge weight
@priyadhanu14 is hacking code to do this for growth simulations. | null | {
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Closes #732
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#### Description
Replaced all enums with C++ enum classes and added streaming operator<< functions where needed.
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"@stiber ran the GPU unit and regression tests as well and they all passed so I think this change is ready for a review.",
"Nick, did you want to request a review from me? That's done under \"reviewers\", not \"assignees\"...",
"@stiber yes, that was my intention. Sorry about that. I will switch that around.",
... | 2025-01-26T10:10:05 | 2025-02-03T23:32:49 | 2025-02-03T23:32:39 | CONTRIBUTOR | null | {
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Closes #745
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The summation point logic was being done in the neuron edges for the CPU model while the GPU model had a calcSummationPoint ... | {
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Closes #404
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#### Description
Created new conditional compilation switch for testing.
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https://github.com/UWB-Biocomputing/Graphitti/blob/617ada45a934d47e1a5e5cbe602a8ea35fa34d3d/CMakeLists.txt#L11
Moreover, this information should be added to the student Quickstart to make it clear how to compile and build for the GPU. | null | {
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"I wanted to provide a complete update regarding the segmentation fault issue in GGraphitti. After investigation, I discovered that two shared libraries were each including AllSynapsesDeviceFunc.cpp (and its corresponding header). This file declares a device variable\r\n\r\n`extern __device__ enumClassSynapses clas... | 2025-01-17T02:00:51 | 2025-01-25T00:32:09 | 2025-01-25T00:31:48 | NONE | null | {
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#### Description
I was unable to run ggraphitti with the old CMakeLists configuration. I was able to compile and link, but when the program loaded there was a seg fault. I investigated and there is an external variable, classSynapses_d, that is defined in AllSynapsesDeviceFuncs_d.cpp. Under the old CMak... | {
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This PR adds Andrew Madison to the Contributors.md file.
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#### Description
Renamed folder from Graph Generation to GraphGeneration for accessibility. No changes to code or documentation.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
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Closes #
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#### Description
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
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* tR_1.0--fE_0.90_10000.xml
* tR_1.0--fE_0.98_10000.xml
* tR_1.9--fE_0.90_10000.xml
* tR_1.9--fE_0.98_10000.xml
* fE_0.90_10000.graphml
* fE_0.98_10000.graphml
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* tR_0.1*
* fE_0.80*
* full_*
* half_*
* any other duplicate file... | {
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"No need to publish this into the repo."
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"Hi @d-kamath how does this describe things? If you select \"View file\" from the `...` menu for the Markdown file, GitHub will render all of the Mermaid diagrams.",
"The failed checks have me worried.",
"I have merged my PR #755. Please pull the remote `SharedDevelopment` branch into `issue-752-add-per-user-de... | 2025-01-15T19:34:01 | 2025-01-20T18:45:00 | 2025-01-20T18:42:53 | CONTRIBUTOR | null | {
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Closes #752
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#### Description
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"Wrong base branch; should merge into SharedDevelopment."
] | 2025-01-15T19:27:00 | 2025-01-15T19:34:47 | 2025-01-15T19:34:46 | CONTRIBUTOR | null | {
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Closes #752
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#### Description
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"We need to merge PR #755 to fix the regression test. Additionally, we should consider adding the following configuration to avoid running regression tests on documentation files:\r\n```\r\npaths-ignore:\r\n - '**.md'\r\n - '**.yml'\r\n``` "
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"When you create a pull request to merge branch A into branch B on GitHub, the version of the action that will run is the one from the base branch of the pull request, which in this case is branch B[1][8]. This is because GitHub Actions uses the workflow definition from the base branch when processing pull requests... | 2025-01-14T01:17:15 | 2025-01-15T01:11:41 | 2025-01-15T01:11:41 | CONTRIBUTOR | null | {
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```
on:
pull_request:
types: [opened, synchronize, reopened]
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- Rename "development" to "Sha... | {
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Closes #754
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#### Description
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"Naming convention for per-user development branch: \"Username-Dev\"\r\n\r\nHotfix branch naming convention: \"hotfix-issue-#-short-desc\"\r\nNote that this is a branch off of \"master\".\r\nStill would have a PR, with naming based on branch, as usual. Assumption is that there are no commits to or releases on \"mas... | 2025-01-10T17:38:27 | 2025-01-10T18:34:29 | null | CONTRIBUTOR | null | {
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This PR adds Andrew Madison to the Contributors.txt file.
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This PR adds Andrew Madison to the Contributors.md file.
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https://github.com/UWB-Biocomputing/Graphitti/blob/d22f59d90a1e5a097d4f26151d6a6e7dc8b11e22/Simulator/Vertices/Neuro/AllLIFNeurons_d.cpp#L148-L176 | null | {
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- tR_1.0--fE_0.90_10000.xml
- tR_1.0--fE_0.98_10000.xml
- tR_1.9--fE_0.90_10000.xml
- tR_1.9--fE_0.98_10000.xml
Remove any duplicates of those files. Examples include:
- files that start with full_ and half_
- tR_0.1--*
- fE_0.80* | {
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"After some reading and testing, this implementation will not work. Below is the logical flow of the change.\n\n1. Start by changing Call.type from string to char[].\n2. Call.type is passed to the InputManager.registerProperty method through the EventMemberPtr argument.\n3. Therefore, EventMemberPtr needs to suppor... | 2025-01-02T02:30:31 | 2025-02-27T23:44:20 | null | CONTRIBUTOR | null | {
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Lets change the type to a char array. The size of the array is TBH, but we will try starting ... | null | {
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"@stiber I spent some time thinking about the calcSummationPoint logic issue and outlined my thoughts above. I believe we had worked up to bullet 2 in our last meeting, but didn't really discuss whether that required bullet 3 or not.\r\n\r\nLet me know if the above makes sense or if there is anything that I am miss... | 2024-12-30T04:40:34 | 2025-02-19T19:53:35 | 2025-02-19T19:53:33 | CONTRIBUTOR | null | {
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This should be pulled out into a calcSummationPoint method that the CPUModel.cpp implements. This method would then get... | {
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"Some cleanup needed in the two `index.md` files."
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Closes #207
<!-- Please provide a brief overview of the changes implemented -->
#### Description
This PR has been recreated to incorporate the updates originally made by silvercube227 in [PR-545](https://github.com/UWB-Bi... | null | {
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#### Description
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#### Checklist (Mandatory for new features)
- [ ] Added Documentation
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"Would be good to put a complete list of tests to be retained, with proposed modifications, if any, in test config file names or content."
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* small, small-connected-stdp, small-connected-long
* The small-connected-long graph should run for enough epochs that non-endogenously active neurons show spiking activity
* We can probably use less epochs if we set the startRadius... | null | {
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"So, do we really want to do this? Let's discuss it at a lab meeting; I think there are arguments either way, but maybe not; maybe this was just something different than before. After all, if we don't output a variable, then we know 100% what's in it. OTOH, if we regis... | 2024-11-19T03:04:27 | 2025-01-31T04:32:47 | 2025-01-31T04:32:47 | CONTRIBUTOR | null | {
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XML Recorder should produce an empty output for variables with no values. Tested and now the output is as in the below image... | {
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"Actually, this needs to copy to the GPU and work in a GPU-side `switch` statement. It may or may not work this way, depending on whether we can rely on the \"data footprint\" on the GPU matching up well with the CPU implementation of this language feature."
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https://github.com/UWB-Biocomputing/Graphitti/blob/b507ae9a4ccc6377c36fde9413af726366734b07/Simulator/Edges/Neuro/AllNeuroEdges.h#L42-L48
See https://en.cppreference.com/w/cpp/language/enum for more information about this language feature. | null | {
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Closes #
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#### Description
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#### Checklist (Mandatory for new features)
- [ ] Added Documentation
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