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This PR addresses a bug related to the event buffer implementation. The issue stemmed from an additional slot in the event buffer, leading to inconsistencies between CPU and GPU implementations. This inconsistency caused unexpected behavior during GPU simulation.
Changes Made:
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This PR addresses the compatibility issue with the `registerSpikeHistoryVariables` function in `AllSpikingNeurons.h`. The function was previously declared under CPU-specific code, causing compilation errors when accessed from GPU code. To resolve this issue, I've moved the function declaration to both C... | {
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This pull request updates the CUDA_STANDARD in `CMakeLists.txt` from 11 to 17 to leverage C++17 features like `std::variant` for GPU programming.
To ensure correctness, the GPU simulation was run for a set of 12 configurations (ranging from small to large) before and after the update on commit [f632... | {
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In the context of neural network simulations, The redesigned Recorder subsystem is currently unable to register the number of neurons, which is represented by the variable numVertices. This variable is a primitive type and is located within the Layout class of our simulation framework. | null | {
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We can refactor code in the All911Vertices class from vector<vector<uint64_t>> to Vector<EventBuffer>
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"This issue is resolved by pull request #631 "
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1) Add sequential diagram for Recorder workflow
2) Add Recorder Class Diagram
3) Update... | {
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"As far as I know, cereal serialization does not support classes inheriting directly from standard library containers. Since it's crucial to provide a `serialize` function for all base classes and we cannot add a `serialize` function to a standard library class.\r\n\r\nTo resolve this, I modified the `RecordableVec... | 2024-03-10T08:13:17 | 2024-04-22T19:11:03 | 2024-04-18T17:08:35 | CONTRIBUTOR | null | {
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1. Added Recorder::UpdateType to enable recording of both Dynamical and Constant variables
2. Added RecordableVector template to record standard library vector variant
3. Used RecordableBase interface as the base class of Matrix for recording VectorMatrix variables. Instead of creating a separate cons... | {
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Should also include current import of actual caller da... | null | {
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Reminder that these changes should also be merged to development | {
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Note that these changes must be merged in both Master and development branches | {
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"Commits not merged in this release \r\ncbd304b\r\n42d22d9\r\n92a6b63\r\nfb5e256\r\n"
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Left Recorder and serialization behind. | {
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"I ran this simulation and noticed that `idx2` was negative when the simulation failed. This was a wrap-around due to an overflow of the `int` data type meant to hold the value. Still, even without this, it would fail the second condition of the assertion (`idx2 < (simulator.getEpochDuration() * 100)`).\r\n\r\nFor ... | 2024-02-15T19:27:52 | 2024-04-15T16:53:57 | 2024-04-15T16:53:57 | COLLABORATOR | null | {
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This issue is seen in `version 0.9.1` of the Graphitti, whereas `version 0.9` does not display this problem.
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"Actually, for a hotfix, merging the hotfix into master and then hotfix into development has the same effect, with one fewer merge commit.",
"Actually, it may be better to cherry pick the merge commit from hotfix to master into development; this seems to avoid replaying (and, potentially, having to resolve confli... | 2024-02-15T19:17:53 | 2025-01-17T18:38:11 | 2025-01-17T18:38:10 | CONTRIBUTOR | null | {
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- Fix capitalization of branches; change feature branch names to match our naming convention (can use ellipses to not include full branch names in diagram)
- First diagram shouldn't show development branch being closed off.
- Second diagram: feature A merge into development should... | {
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Changed the plantuml generation reference from the old (and deleted) repo to the forked repo in UWB-Biocomputing. | {
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"Seems like you can get this information from https://github.com/UWB-Biocomputing/Graphitti/network/dependencies"
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Comment updated. | {
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"OK, please make sure to read [our contributing guide](https://github.com/UWB-Biocomputing/Graphitti/blob/fc673110eb6d18a636ee5519e02691698c07c3c1/CONTRIBUTING.md)"
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Closes #586
Hot fix to update sequence diagrams so that they are to date with the master branch. | {
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1. Appended Method on 1-D vector :
- Given a one-dimensional vector and the number of vertices ( k = the number of vertices), the Recorder breaks the vector into pieces. For each epoch, the Rec... | null | {
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### Task:
Update the CMAKELists.txt file | {
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Implemented serialize functions for all Neuro-related classes in `Layout` and `AllVertices`, along with their utility classes.
Classes Targeted:
1. Layout, FixedLayout, DynamicLayout
2. AllVertices, AllSpikingNeurons, AllIFNeurons, AllLIFNeurons, AllIZHNeurons
3. EventBuffer, Recordable, Recordabl... | {
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- [x] #692
- [x] #697
- [x] #703
- [x] #706
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"So, based on conversation, there seems to not be a best practice. Instead, to be risk averse, we need to catalog what other folks' stuff we're using that we are happy with, fork those repos, and use our own version. We could, if we want, schedule periodic checks of our forks against the originals to see if there a... | 2024-01-22T23:54:17 | 2024-02-06T19:09:44 | 2024-02-06T19:09:44 | CONTRIBUTOR | null | {
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"Ben, don't worry about the failed PlantUML failure; it seems that it is being triggered as a side effect of changing the base branch from master (i.e., that it was originally master). However, ple... | 2024-01-19T16:26:07 | 2024-12-20T21:32:31 | 2024-12-20T21:32:26 | CONTRIBUTOR | null | {
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"I don't think it needs to be repeated. I think that there is a way to also merge the hot fix branch into development. Since this is documentation, it would be hard to break development (though not impossible). One approach might be to create a feature branch from development, merge the hotfix branch into that, the... | 2024-01-16T20:18:08 | 2024-01-30T19:33:27 | 2024-01-30T19:33:27 | CONTRIBUTOR | null | {
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"Observations from comparing \"topLevelFlow.puml\", \"graphitti.puml\", and code:\r\n\r\nExecutive Summary: \"graphitti.puml\" is more updated and detailed, although \"topLevelFlow.puml\" has 'ParameterManager' and 'OperationManager' logic.\r\nDetails:\r\n\r\n- \"topLevelFlow.puml\" starts the diagram with the Core... | 2024-01-16T20:13:18 | 2024-01-30T19:10:11 | 2024-01-30T19:10:11 | CONTRIBUTOR | null | {
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Specifically (professor Stiber's words):
- There are two top-level .puml files: topLevelFlow.puml and graphitti.puml. Need to compare them, produce a single, correct version, and get that version lin... | {
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1. Implemented `serialize` functions for all Neuro-related classes in `Connections` and `AllEdges`, along with their utility classes.
2. Replaced existing `load` and `save` methods with a single `serialize` method.
3. Removed version number tracking from derived classes, retaining it only in the base c... | {
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"Looks good so far.",
"Closing due to age."
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- Revisited the changes made by Andrew Andrzej
- Added assertion to Global.h and Global.cpp
- Added conditional compilation switch for testing incorporating a testing flag during compilation to perform assertions in various places in the code. (CMakeLists.txt) | {
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- Added Python GUI using PyQT5 (handles input errors)
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This fixes a bug in checking for available space in the queue. When NG911 vertices pull messages from their incoming edges a check is done to ensure that there is space in the queue, this change ensures that the check doesn't fail. | {
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primary event. This produces tight clusters that are too dissimilar to the real call arrival.
Instead, adding the cumulative sum of secondary points' time intervals to the primary event's time produces... | {
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> Dear all,
>
> This is to alert you to the availability of exciting new resources for the model description language NeuroML and a recently posted bioRxiv preprint on the ecosystem of NeuroML-compliant tools for data-driven modelling of neurons and circuits.
>
> In... | null | {
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Closes #502
This pull request introduces a Recordable template for the EventBuffer class, incorporates a RecordableBase interface for the Recordable template, and adjusts the XmlRecorder code accordingly. The C++17 std::variant feature is utilized in the Recorder module to manage a list of different data types fo... | {
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Sub-Tasks
- [x] #572
- [x] #571
- [x] #592
- [x] #581 | {
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Fixes #566
This PR adds a regression test for a small 911 simulation with a verified good output. In addition, it updates the location of the Seattle PD PSAP in its `graphml` file so it appears in the center of the graph when using the visualization tool.
The `graphml` file for this test was adapted... | {
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} | null | The current `test-small-911.xml` config file was developed for a previous implementation and thus no longer works. We must create configuration files for a small 911 simulation (config, graphml, and inputs file) and verify that the outputs are as expected.
This `small 911` simulation should be added to the regressio... | {
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This pull request updates the `inUse` member variable within the `AllEdges` class, shifting from `std::vector<std::unique_ptr<bool>>` to `std::vector<unsigned char>`. The decision to utilize `unsigned char` for storing Boolean values is driven by a focus on significantly enhancing serialization. Th... | {
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- Added gitflowdiagram.md file under docs/Developer
- Updated CONTRIBUTING.md to support new file (gitflowdiagram.md)
- Updated CONTRIBUTING.md's broken links and numbering (pull requests, github issues, duplicate steps #s)
- Updated index.md in docs/Developer to support new file (gitflowdiagram.md)
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Adding GitFlow documentation to CONTRIBUTING.md; our version of the diagram with Gitgraph using Mermaid.js
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Made all the class members of All911Vertices private. The Xml911Recorder class was made a friend of All911Vertices because it needs access to some of its internal data structures. Some accessors were also implemented for values needed by the All911Edges class. | {
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This PR adds the recording of queue length and utilization histories for the NG911 PSAP and Responder nodes.
These histories are recorded on a per-time-step basis.
In addition, I changed the average on-scene time used in the cluster point process script and the Seattle PD real data, to 20 minutes. T... | {
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Closes #491
This PR implements the logic for the emergency responder nodes. That includes estimation of the driving and on-site time, and the discrete event queueing model associated with it.
It also fixes a bug found in the `CircularBuffer` class, where it was reporting the wrong size (off by one) w... | {
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"I note that there are file paths written \"Windows style\", using back slashes as separators. These are wrapped in calls to `os.path.normpath()`. Is that common practice in Python? In most languages, the backslash in strings is used as an escape character. Just checking before I approve.",
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"\r\nAfter evaluating both design approaches for the XmlRecorder in Graphitti, I have decided to adopt the first design approach. This decision was made after conducting a comprehensive comparison based on various metrics including performance, code duplication, extensibility, and maintainability. The first design,... | 2023-10-23T20:17:01 | 2024-03-09T06:45:00 | 2024-03-09T06:44:59 | CONTRIBUTOR | null | {
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1. The first design utilizes Recordable inheritance and variants to store different types of Recordable objects in a single table.
2. The second design uses template instantiations and I stored different types of Recordable in separate tables.
To determine which design is a b... | {
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"From discussion and initial implementations, the agreed answer to this question is that all parameters that are common between all configurations (except for number of neurons) should be put in the GraphML file. This means the sections in the XML files labeled:\r\n\r\n1. \"NLIST\" (Vertice Property, Already Implem... | 2023-10-21T22:51:09 | 2024-05-23T21:26:14 | 2024-05-23T21:26:14 | CONTRIBUTOR | null | {
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"Should have been closed by PR."
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"Hi, I'd like to pick this up. Do I need to check all cpp files for functions with unused parameters?",
"> Hi, I'd like to pick this up. Do I need to check all cpp files for functions with unused parameters?\r\n\r\nI believe the author of this issue may be interested in working on this. Also, we have switched our... | 2023-10-14T16:21:48 | 2024-02-27T00:51:24 | null | COLLABORATOR | null | {
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While reviewing the codebase, we have identified instances where function parameters are declared but not used within the function body. The goal is to identify and remove such unused function parameters while ensuring that if the function is overridden, other derived classes don't use those parameters.... | null | {
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This PR removes the `const` qualifiers from the relevant code, making the Graphitti codebase more consistent and easier to maintain. `const` qualifiers are removed from `int`, `BGFLOAT`, and `BGSIZE`. | {
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"This PR has been superseded by [PR-743](https://github.com/UWB-Biocomputing/Graphitti/pull/743) and is now being closed as stale. Please refer to the new PR for the updates."
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Created a visualization of King County 911 system from GraphML data. Color coded nodes for ease of use. | {
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Issues #10 and #7 can be addressed as... | null | {
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This PR mainly renames the `summationMap_` member variable of AllVertices to `summationPoints_`. The changes are also reflected in the PlantUML diagrams.
Successfully tested for GPU execution. | {
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Fixed bug in updateSynapsesWeightsDevice where a synapse between the same neuron could be created. | {
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Moved the `width_` and `height_` parameters from `Simulator` to `FixedLayout`. The method in `Model` that printed debugging layout output was also moved to `FixedLayout` to conserve it, although it is currently not being used. | {
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"One important principle we should adhere to is to record fundamental data during simulation and defer all analysis to external code in Matlab (or, occasionally, Python). Relevant to this, the two histories are fundamental data and the two measurements are computed from that, so the histories should be recorded.\r\... | 2023-09-26T04:11:02 | 2023-11-09T03:33:27 | 2023-11-09T03:33:26 | CONTRIBUTOR | null | {
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- **System utilization:** The proportion of the time during the simulation that the servers are busy.
- **Time Average Queue Length:** The time-weighted average number o... | {
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"> Just to double-check, these were code snippets in classes that are still being retained, right?\r\n\r\nThat's right. This was commented-out code because it was copied from the Neuro classes, and code that used a vertex grid with quadrants to crate the 911 nodes and edges.",
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Cleans up old 911 code no longer being used, either because the parameters are now part of the Graphml input file or because the model has changed completely. | {
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"Closing this as substantially complete. `HDF5Recorder` is functionally equivalent to `XMLRecorder`."
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See the [write HDF5 file incrementally to speed simulator clean up at the end](https://github.com/UWB-Biocomputing/BrainGrid/commit/6b23f46fa569a8e7452862d5e867ed558... | {
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Fixes #533
Implements the basic logic for finding the responder closest to the emergency event and assigns the call to it. It also fixes a bug where the waiting queue was not accounting for the fact that we queued up every call, therefore we were getting more dropped calls than we should.
At the mom... | {
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This PR implements call redials using a redial probability parameter provided through the config file.
The implementation assumes that once the caller decides to redial, he will do so immediately and will try until the call is answered by the PSAP.
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} | null | Currently, the random number generator used in Graphitti is implemented in the `MTRand` class because our code pre-dates the C++ standard library's implementation of a Mersene Twister random number generator. Both `MTRand` and `std::mt19937` implement the Mersene Twister algorithm for generating uniformly distributed i... | null | {
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When all operators and phone lines are busy at a PSAP, calls are dropped or disconnected, in which case the caller could decide to redial or not. The probability of redialing for 911 is relatively high since a person in an emergency situat... | {
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In the current implementation, the `addEdge` method within the `AllEdges` class passes a reference to the `iEdg` variable for population. This approach can be confusing and may affect code readability. To address this concern, this pull request returns the `iEdg` value directly instead of passing i... | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/526 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/526/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/526/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/526/events | https://github.com/UWB-Biocomputing/Graphitti/issues/526 | 1,887,986,276 | I_kwDOEEdqD85wiGJk | 526 | Look into adding a .cff file to the repo | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/525 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/525/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/525/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/525/events | https://github.com/UWB-Biocomputing/Graphitti/pull/525 | 1,887,032,130 | PR_kwDOEEdqD85Z183s | 525 | [Issue 489] Implement call abandonment modeled with patience time | {
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Implementation of call abandonment using a patience time parameter as in the Erlang A Queueing model.
Call abandonment and average patience estimations are described in the following papers:
Gans, N., Koole, G., & Mandelbaum, A. (2003). Telephone Call Centers: Tutorial, Review, and Research Prospec... | {
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