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This makes the codebase harder to extend, test, and maintain as new components and GPU resources are added.
Although OperationManager is used elsewhere to dispatch operations, it is designed for parallel, decoupled callbacks, not ordered, interdependent execution. Therefore, introducing a new ChainManager class to manage sequenced GPU operations would improve modularity and clarity.
Proposed Tasks:
Design a base GPUOperation interface for chainable GPU tasks
Implement reusable operation steps for memory allocation, data transfer, and cleanup
Allow composition of these steps into ordered execution chains
Replace hardcoded sequences in GPUModel with ChainManager-based chains | null | {
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Closes #722
Closes #719
Closes #574
<!-- Please provide a brief overview of the changes implemented -->
#### Description
This expands the set of variables recorded by including additional ones, providing a wider range of the data captured. Additionally, it removes the dependency on XML911Recorder by using the recorders instead.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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} | null | Not only is this awkward from the point of view of GPU code, it also makes it difficult to record these variables (without adding custom code to the Recorder classes for every struct we make a vector of). So, we should stick to data members that are vectors (actually `RecorderableVector`) of primitive types.
https://github.com/UWB-Biocomputing/Graphitti/blob/004f58ccb6e19bf41ae2f1fe9d2eea53e7879144/Simulator/Connections/NG911/Connections911.h#L60-L65 | null | {
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Closes #734
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Add source, target and weighted connections for STDP simulations from graphml files. Create NeuralEdgeProperties struct for connections data and implement Connstatic code. Update documentation for GraphManager class and update test-tiny.graphml for STDP testing.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [x] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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Closes #648
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#### Description
Created new personal development branch (KaurSainiDevelopment) to merge conflicting updates into SharedDevelopment. 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 VertexProperties.
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- [x] Added Documentation
- [x] Added Unit Tests
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- [x] GPU Test: `test-large-long.xml` Passed
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- [ ] Added Unit Tests
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"@stiber changes are mostly the same as the two PRs that we reviewed. Had a merge conflict with a change Diva made to fix a seg fault that I resolved, but it doesn't look like it's in the list of changes. One weird thing I noticed was that Raiju is causing some of the GPU regression tests to fail while Otachi is no... | 2025-03-07T05:20:51 | 2025-03-13T23:50:55 | 2025-03-13T23:46:37 | CONTRIBUTOR | null | {
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Closes #786 #806
<!-- Please provide a brief overview of the changes implemented -->
#### Description
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/813 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/813/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/813/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/813/events | https://github.com/UWB-Biocomputing/Graphitti/pull/813 | 2,901,786,846 | PR_kwDOEEdqD86NtmMP | 813 | [ISSUE-783][ISSUE-773][ISSUE-319] Validation Mode and Cleanup | {
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Closes #783
Closes #773
Closes #319
<!-- Please provide a brief overview of the changes implemented -->
#### Description
This PR replaces and continues work from #794
Continues from work on #794:
CMAKE build types cleaned up in cmakelists
```
# Build Type Configuration
#
# CMake support for different build types controlling optimization, debugging and profiling:
#
# - Debug : No optimizations (`-O0`), includes debug symbols (`-g`).
# - Release : Optimized build (`-O3`), removes debug symbols.
# - RelWithDebInfo: Optimized (`-O2`) but keeps debug symbols (`-g`) for profiling.
# - Profiling : Custom build type (defined in this project) that enables:
# - CPU profiling via `-pg` (GPROF)
# - CUDA profiling via `-lineinfo` (for Nsight Compute)
#
# Selecting a Build Type:
# - By default, CMake does NOT set a build type for single-config generators.
# - If no build type is specified, this script defaults to "Release" for performance.
# - You can explicitly set the build type when configuring CMake:
#
# cmake -S . -B build -DCMAKE_BUILD_TYPE=Debug # Debug mode
# cmake -S . -B build -DCMAKE_BUILD_TYPE=Release # Release mode
# cmake -S . -B build -DCMAKE_BUILD_TYPE=Profiling # Profiling mode
#
# If you don't want to pass in the build type flag, you can edit this file and add...
# set(CMAKE_BUILD_TYPE "Debug") or whichever build type you want
# -----------------------------------------------------------------------------
```
Additionally, added a new conditional flag to change the target architecture for cuda compilation.
```
#CONDITIONAL FLAG to change target architecture for the GPU simulator from the default
#
#You can pass this flag when running cmake from the command line like this, setting TARGET_ARCH \
# to your desired architecture: \
#
#cmake -D ENABLE_CUDA=YES -D TARGET_ARCH=70 ..
#
#"YES" / GPU choice only available if CUDA library is installed and the GPU is CUDA capable.
#If no TARGET_ARCH is passed in then it will default to 37 which is the kepler architecture
```
Quickstart guide, StudentSetup, and codingConventions documentation was updated.
Added support for nvtx profiling tools. The profiling build option will enable this if the nvtx libraries are present.
About the comment in #794 about the build.sh file added to the .gitignore [here](https://github.com/UWB-Biocomputing/Graphitti/pull/794#discussion_r1956908137): I have created a build.sh file with the intention in mind to create a simple build script with machine specific build and compile flags that eliminate the need to retype every conditional flag every time I do a cmake. Others who wish to run graphitti on their own machine can follow similarly, but since it is changed regularly to test different build and compile options it shouldn't be tracked by git. For example in my build.sh:
```
set -e # Exit immediately if a command exits with a non-zero status
# You can allow a build type to be specified as an argument; default is 'Release'
BUILD_TYPE="${1:-Release}"
# Print result (for debugging)
echo "BUILD_TYPE: $BUILD_TYPE"
# Where to build (you can customize this directory)
BUILD_DIR="build"
# Clean up previous build artifacts if desired
# Invoke CMake with the desired flags
cmake -S . -B "${BUILD_DIR}" \
-DENABLE_CUDA=YES \
-DTARGET_ARCH=75 \
-DCMAKE_BUILD_TYPE="${BUILD_TYPE}"
# Now build. The "--build" command is cross-platform.
cmake --build "${BUILD_DIR}" -- -j$(nproc)
```
Implements the validation mode outlined in #319
There is a new conditional flag to turn on the validation mode
```
#CONDITIONAL FLAG to turn on the validation mode
if(NOT VALIDATION_MODE)
set(VALIDATION_MODE NO)
endif()
```
When validation mode is enabled, the MTRand on the host generates noise for each vertex every time the simulation advances. This noise is then copied to the randNoise_d buffer for use in the GPU’s advanceVertices kernel. As long as cgraphitti is also run in validation mode, the generated noise will match, ensuring that each vertex receives noise from MTRand in every advanceNeuron call, regardless of whether it is refractory or firing.
Noise is generated in reverse order, from the highest to lowest vertex, because advanceVertices processes neurons in that sequence. While it may be worth investigating whether advanceVertices should instead process vertices in their natural order, the validation mode remains functional after accounting for this behavior.
Validation mode collects and logs data on noise, Vm, summation points, and Inoise during each vertex update, saving the information to vertices.txt in the Debug output folder. However, this process is slow. The next step in validating the GPU and CPU algorithms is to analyze the exported data to identify the cause of slight deviations in simulation results.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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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).
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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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.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
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- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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Closes #648
Closes #734
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Add in STDP ability to have connections with source, destination and weight. Update Global.h with NeuroEdgeProperties struct and ConnStatic code.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [x] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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Closes #805
<!-- Please provide a brief overview of the changes implemented -->
#### Description
This pull request addresses a segmentation fault observed during the STDP simulation after deserializing a large, GPU-based growth simulation.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
The simulation was tested using the following commands:
GPU-based simulation:
ggraphitti -g 1 -c ../configfiles/tR_1.0--fE_0.90_10000.xml -s Output/Results/tR_1.0--fE_0.90_10000_serialized.xml
CPU-based simulation:
cgraphitti -c ../configfiles/stdp_fE_0.90_10000.xml -d ./Output/Results/tR_1.0--fE_0.90_10000_serialized.xml
Both commands were successfully executed without encountering the segmentation fault after the proposed fixes were applied
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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."
] | 2025-03-03T04:00:41 | 2025-03-07T04:41:48 | 2025-03-07T04:41:40 | CONTRIBUTOR | null | {
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Closes #806
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Since advanceEdges doesn't update the edge state until after we know that we can transfer the call, we move all of the advanceEdges logic into integrateVertexInputs.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [ ] GPU Test: `test-medium-connected.xml` Passed
- [ ] GPU Test: `test-large-long.xml` Passed
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} | null | A segmentation fault is observed during the STDP simulation after deserializing a large, GPU-based growth simulation. This crash has been identified by @varndorfer and she traced to an inconsistent state of the `summationPoints_` variable.
On debugging we found the follwing two root causes:
1. The `summationPoints_` variable under the class `AllSpikingNeurons` was intentionally left uninitialized on the CPU side. This design decision was made to prevent accidental or incorrect usage of this variable within GPU-specific code. However, with the introduction of serialization and deserialization functionalities, this uninitialized state becomes problematic. During deserialization, the saved state of `summationPoints_` needs to be loaded onto the CPU, and subsequently transferred to the GPU. Without proper initialization, the CPU memory location is undefined, leading to potential errors.
2. Corresponding to the intentional un-initialization, there was no need for a mechanism to synchronize the `summationPoints_` data between the CPU and GPU. Now, this lack of synchronization is revealed as a critical flaw. Deserialization involves loading data onto the CPU, but without a transfer or synchronization step, the GPU is unable to populate the deserialized `summationPoints_` values. This disparity results in the GPU accessing incorrect memory locations during STDP execution, leading to the segmentation fault. | {
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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."
] | 2025-02-28T01:00:42 | 2025-03-07T04:03:39 | 2025-03-07T04:03:27 | CONTRIBUTOR | null | {
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} | null | <!-- Link to the issue and use the appropriate closing keyword (e.g., Closes, Resolves) -->
Closes #786
<!-- Please provide a brief overview of the changes implemented -->
#### 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 subfolder since it was generated with Cpu code. This required corresponding update to github actions. Then updated RunTests so that it would build the appropriate list of tests based on the current processing unit.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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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.
<!-- Link to the issue and use the appropriate closing keyword (e.g., Closes, Resolves) -->
Closes #
<!-- Please provide a brief overview of the changes implemented -->
#### Description
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#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [ ] Added Unit Tests
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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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} | null | Looks like we are using the vertexType::EXC (which is a neuro vertex type) in the 911 recorder.
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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<!-- Please provide a brief overview of the changes implemented -->
#### Description
Adding VertexType to Recorders
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [x] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/799 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/799/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/799/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/799/events | https://github.com/UWB-Biocomputing/Graphitti/pull/799 | 2,861,837,124 | PR_kwDOEEdqD86LrCV2 | 799 | [ISSUE-648] Templatize GraphManager Class and Add Inheritance to VertexProperty | {
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<!-- Please provide a brief overview of the changes implemented -->
#### 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.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [x] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
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- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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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
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#### Description
Merge includes two PRs. PR 777 which moved the vertex integration logic that lived in the Edges class into the Vertices class and PR 789 which cleaned up neuro-specific references in the GPU and CPU models.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
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- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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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
<!-- Ensure all boxes are checked before submitting the PR -->
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As a part of the onboarding task add Padmanabh Patil to the Contributors list of Graphitti.
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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
```
# Build Type Configuration
#
# CMake support for different build types controlling optimization, debugging and profiling:
#
# - Debug : No optimizations (`-O0`), includes debug symbols (`-g`).
# - Release : Optimized build (`-O3`), removes debug symbols.
# - RelWithDebInfo: Optimized (`-O2`) but keeps debug symbols (`-g`) for profiling.
# - Profiling : Custom build type (defined in this project) that enables:
# - CPU profiling via `-pg` (GPROF)
# - CUDA profiling via `-lineinfo` (for Nsight Compute)
#
# Selecting a Build Type:
# - By default, CMake does NOT set a build type for single-config generators.
# - If no build type is specified, this script defaults to "Release" for performance.
# - You can explicitly set the build type when configuring CMake:
#
# cmake -S . -B build -DCMAKE_BUILD_TYPE=Debug # Debug mode
# cmake -S . -B build -DCMAKE_BUILD_TYPE=Release # Release mode
# cmake -S . -B build -DCMAKE_BUILD_TYPE=Profiling # Profiling mode
#
# If you don't want to pass in the build type flag, you can edit this file and add...
# set(CMAKE_BUILD_TYPE "Debug") or whichever build type you want
# -----------------------------------------------------------------------------
```
Additionally, added a new conditional flag to change the target architecture for cuda compilation.
```
#CONDITIONAL FLAG to change target architecture for the GPU simulator from the default
#
#You can pass this flag when running cmake from the command line like this, setting TARGET_ARCH \
# to your desired architecture: \
#
#cmake -D ENABLE_CUDA=YES -D TARGET_ARCH=70 ..
#
#"YES" / GPU choice only available if CUDA library is installed and the GPU is CUDA capable.
#If no TARGET_ARCH is passed in then it will default to 37 which is the kepler architecture
```
Quickstart guide, StudentSetup, and codingConventions documentation was updated.
Added support for nvtx profiling tools. The profiling build option will enable this if the nvtx libraries are present.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
<!--
PR Guidelines
1. Ensure that your changes are merged into the `development` branch. Only merge into the `master` branch if explicitly instructed.
- On GitHub, at the top of the PR page, change the base branch from `master` to `development`.
2. Assign the PR to yourself and apply the appropriate labels.
3. Only add a reviewer after submitting the PR and confirming that all GitHub Actions have passed.
Thank you for your contribution!
-->
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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 | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | null | <!-- Link to the issue and use the appropriate closing keyword (e.g., Closes, Resolves) -->
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 methods.
The one except to this being the AllSpikingSynapsesDeviceProperties and AllSpikingNeuronsDeviceProperties types being changed to AllEdgesDeviceProperties and AllVerticesDeviceProperties respectively. The required a refactor of the device properties. The AllEdgesDeviceProperties now lives in AllEdges.h instead of AllNeuroEdges.h. AllNeuroEdgesDeviceProperties inherits from this and adds the PSR property. The summation points properties were moved from AllVertices.h to AllSpikingNeurons.h since it's not a general vertex property.
The change to AllSTDPSynapses.cpp was a bug exposed after moving the summation points property out of AllSpikingNeurons.h. It should have been removed when we added integrateVertexInputs.
The other except was after removing the dynamic cast in the GPUModel::updateHistory() method. This is a private method in GPUModel that called clearNeuronSpikeCounts. This method was renamed to clearVertexHistory and pulled up from AllSpikingNeurons.h to AllVertices.h.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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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 | {
"total": 0,
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} | null | Documentation:
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/GHActions.html#plantuml-action)
Link to CloudBees github-action broken
[Introducing GitFlow](https://uwb-biocomputing.github.io/Graphitti/Developer/GitFlowDiagram.html)
Contributing link broken.
3. Testing
3.1 Unit Tests
[docs/Testing/GoogleTest](../docs/testing/GoogleTestsTutorial.md)
File no longer exists.
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Closes #443
Closes #444
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Documetnation links updated from relative to absolute.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [x] Updated Documentation
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
N/A - documentation only changes
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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 because it needs to manually be added to the TEST_FILES in RunTests.sh
@stiber is there a reason NOT to add the test-small-911.xml to TEST_FILES so that it is run with the other CPU tests? We might have to do an if else so that we only add it when the processing unit is CPU. | {
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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 needs to be updated for this change. | null | {
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} | null | If no events are recorded for a given element, then no output is produced by the recorders (ex: `XMLRecorder::saveSimData()`). This can be confusing for new users, for example, when you run a short Neuro simulation, only the endogenously active neurons will output spiking activity. New users may think there is something wrong with their configuration or the simulation because they are missing output for most of the neurons.
We should add documentation to clearly explain that elements will only display in the output if an event is recorded for that element.
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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
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [ ] GPU Test: `test-medium-connected.xml` Passed
- [ ] GPU Test: `test-large-long.xml` Passed
<!--
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1. Ensure that your changes are merged into the `development` branch. Only merge into the `master` branch if explicitly instructed.
- On GitHub, at the top of the PR page, change the base branch from `master` to `development`.
2. Assign the PR to yourself and apply the appropriate labels.
3. Only add a reviewer after submitting the PR and confirming that all GitHub Actions have passed.
Thank you for your contribution!
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Closes #768
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#### Description
Changes in comments
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#### Checklist (Mandatory for new features)
- [Check] Added Documentation
- [ ] Added Unit Tests
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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
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Replaced all enums with C++ enum classes and added streaming operator<< functions where needed.
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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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
<!-- Please provide a brief overview of the changes implemented -->
#### Description
The summation point logic was being done in the neuron edges for the CPU model while the GPU model had a calcSummationPoint method that handled the GPU-side summation point logic. The feature branch refactors this by introducing a integrateVertexInputs method to AllVertices for both CPU and GPU. The neuron implementation of AllVertices can then implement the summation point logic in this method. This refactor also allows models types other than neuron (such as 911) to define how they want to integration their vertex inputs since not all model types will use summation point logic.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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} | null | <!-- Link to the issue and use the appropriate closing keyword (e.g., Closes, Resolves) -->
Closes #404
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Created new conditional compilation switch for testing.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
<!--
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3. Only add a reviewer after submitting the PR and confirming that all GitHub Actions have passed.
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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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} | null | Right now, this is tied too deeply into the `ConnGrowth` class, due to historical reasons and the fact that `ConnGrowth` needs to update the edge weights. But it perhaps makes sense for the edges to own their weights. Moreover, for other connections classes, such as `ConnStatic` and STDP simulations, the edges update their own weights. Also, I think that the different apparent weight matrix data actually holds different values: one may be just area of overlap during a growth simulation, while the other has signed and scaled down actual weight values.
There is of course an intersection with the GPU implementation, and the GPU implementation needs to mirror the CPU implementation (including any modifications). This should also take into account the ability to copy such information back and forth between the host and device. | 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 CMakeLists configuration, this file was included in multiple libraries, two of which were linked together. I am not sure how this works.
I changed the source files for the three libraries, edges, vertices, and connections, to only include the necessary sources for each library. In addition to this change, I made the libraries static. This solved the problem I had, and now ggraphitti loads and runs correctly.
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed | {
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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
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
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Closes #
<!-- Please provide a brief overview of the changes implemented -->
#### Description
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [ ] GPU Test: `test-medium-connected.xml` Passed
- [ ] GPU Test: `test-large-long.xml` Passed
<!--
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} | null | Keep the canonical STDP config files known to exhibit bursting behavior:
* 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
Remove:
* tR_0.1*
* fE_0.80*
* full_*
* half_*
* any other duplicate files
Add:
* STDP config file to run after the canonical growth simulations (stdp_fE_0.90_10000.xml)
Also commented out the lines that need serialFileAccessTest in CMakeLists.txt. These test files should be re-added by issue-754
<!-- Link to the issue and use the appropriate closing keyword (e.g., Closes, Resolves) -->
Closes #747
<!-- Please provide a brief overview of the changes implemented -->
#### Description
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
<!--
PR Guidelines
1. Ensure that your changes are merged into the `development` branch. Only merge into the `master` branch if explicitly instructed.
- On GitHub, at the top of the PR page, change the base branch from `master` to `development`.
2. Assign the PR to yourself and apply the appropriate labels.
3. Only add a reviewer after submitting the PR and confirming that all GitHub Actions have passed.
Thank you for your contribution!
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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
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Rewrite of GitFlow documentation to describe shared/personal development branches. All Mermaid diagrams now included using the GitHub Mermaid code block facility (which renders the diagrams within the GitHub Markdown renderer, without needing to go out to Mermaid for image rendering).
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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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<!-- Link to the issue and use the appropriate closing keyword (e.g., Closes, Resolves) -->
Closes #756
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Changed the two testing actions to trigger on type of PR activity, rather than only the master and development base branches.
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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]
```
- Rename "development" to "SharedDevelopment"
This will need to be a hotfix, to merge into both "master" and "SharedDevelopment". See next comment for (lengthy, of course) LLM explanation. | {
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Closes #754
<!-- Please provide a brief overview of the changes implemented -->
#### Description
The `serialFileAccessTest` was removed during the cleanup of serialization unit tests. However, the CMake file still had the test linked, which caused a build failure. To resolve this, we are restoring the unit test and ensuring the CMake configuration is updated accordingly.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [x] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [ ] GPU Test: `test-medium-connected.xml` Passed
- [ ] GPU Test: `test-large-long.xml` Passed
<!--
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1. Ensure that your changes are merged into the `development` branch. Only merge into the `master` branch if explicitly instructed.
- On GitHub, at the top of the PR page, change the base branch from `master` to `development`.
2. Assign the PR to yourself and apply the appropriate labels.
3. Only add a reviewer after submitting the PR and confirming that all GitHub Actions have passed.
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} | null | Right now, it looks like all of the CUDA files get added to a STATIC library and to a bunch of SHARED libraries. They are also individually deleted from libraries (but maybe not all; maybe just the ones under each subdirectory) explicitly. Instead, we might make all libraries STATIC and only include the relevant CUDA files in each library. Or, alternatively, we might make a single STATIC library with all CUDA files, putting none in with the various subsystems.
This needs to be figure out by someone who really understands CMake.
https://github.com/UWB-Biocomputing/Graphitti/blob/7a50b56ad048c1bdb610d5b6e1351a3e1640ea1a/CMakeLists.txt#L162-L191 | 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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As a part of the onboarding task add Andrew Madison to the Contributors list of Graphitti.
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"Closed by #763 "
] | 2025-01-03T23:07:30 | 2025-01-20T23:33:43 | 2025-01-20T23:33:42 | CONTRIBUTOR | 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 with size 4.
This will require an update to the InputManager. We plan to leave the type in the input files as string and pull out the first 4 characters for our char array member. | 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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} | null | The GPUModel.cpp has a calcSummationPoint method that implements the GPU version of the summation point logic. On the CPU side, this logic is embedded in the AllSpikingSynapses::advanceEdge method.
This should be pulled out into a calcSummationPoint method that the CPUModel.cpp implements. This method would then get called in the CPUModel::advance method after advancing the edges, similar to to how the GPUModel::advance method behaves.
Some other related changes that could be made:
- Since CPUModel and GPUModel would both be implementing a calcSummationPoint method, this could be added as a virtual method in Model.h for a derived type of model to implement.
- The name "calcSummationPoint" would not be an appropriate name for an NG911 model. Therefore, if we make change 1, we should rename "calcSummationPoint". I propose this method is named "updateVertexState".
- In addition, we wouldn't expect the NG911 model to have the same implementation logic as a neuron model for updateVertexState. I see two ways to resolve this issue:
1. The first is that we could consider changing the current "CPUModel" and "GPUModel" classes to "NeuronCPUModel" and "NeuronGPUModel" respectively. This would allow us to define different logic for updating the vertex state in a NG911 model while keeping the changes relatively minimal. I estimate that at least the Simulator.cpp class and the Model classes would need to be changed (assuming we can get the derived type information from what is currently in the config files).
2. The second is that we could add a updateVertexState method to the AllVertices class and call updateVertexState as a AllVertices method instead of a Model method. This would allow vertex-related stuff to live in a more appropriate place.
The last point can be summarized as such:
- Make Model be extensible for neuron and NG911 models
- Pros: Implementation would mostly look like it currently does for the area we are trying to update.
- Cons: Model type would contain vertex-related logic. Vertices are already extensible for neuron and NG911 models. Introduces new model types which may require changes to config files.
- Add current calcSummationPoint logic into AllVertices
- Pros: Cleaner separation of model and vertex logic. No need to add new derived model types.
- Cons: Less files being touched, but are touched more (e.g. the summation point kernel would need to be moved from the GPUModel.cpp into the AllVertices_d.cpp).
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"Some cleanup needed in the two `index.md` files."
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Closes #207
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#### Description
This PR has been recreated to incorporate the updates originally made by silvercube227 in [PR-545](https://github.com/UWB-Biocomputing/Graphitti/pull/545). The previous PR had become stale and could not be merged due to changes in the merge base.
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- [x] Added Documentation
- [ ] Added Unit Tests
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- [ ] GPU Test: `test-medium-connected.xml` Passed
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Closes #404
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Added Conditional compilation switch- testing
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [x] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [ ] GPU Test: `test-large-long.xml` Passed
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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."
] | 2024-12-02T19:19:27 | 2024-12-03T21:11:41 | null | CONTRIBUTOR | null | {
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} | null | * Use only the tests with the small graph `configfiles/graphs/test-small.graphml`
* 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 value to 0.499 (currently it's at 0.49)
* keep 911 test
* Add a readme file detailing each of the tests and what they cover | null | {
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Closes #
<!-- Please provide a brief overview of the changes implemented -->
#### Description
Added Unit tests for Event Buffer class.
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [x] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
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- [ ] GPU Test: `test-large-long.xml` Passed
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"Are any changes needed to `Hdf5Recorder`?",
"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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Closes #680
<!-- Please provide a brief overview of the changes implemented -->
#### Description
XML Recorder should produce an empty output for variables with no values. Tested and now the output is as in the below image:
<img width="383" alt="image" src="https://github.com/user-attachments/assets/2351fad9-e380-4e03-84fe-43abccf4a061">
<!-- Please check the boxes as applicable -->
#### Checklist (Mandatory for new features)
- [ ] Added Documentation
- [ ] Added Unit Tests
<!-- Ensure all boxes are checked before submitting the PR -->
#### Testing (Mandatory for all changes)
- [x] GPU Test: `test-medium-connected.xml` Passed
- [x] GPU Test: `test-large-long.xml` Passed
<!--
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1. Ensure that your changes are merged into the `development` branch. Only merge into the `master` branch if explicitly instructed.
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3. Only add a reviewer after submitting the PR and confirming that all GitHub Actions have passed.
Thank you for your contribution!
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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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#### Checklist (Mandatory for new features)
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- [ ] Added Unit Tests
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