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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:
Removed the additional slot from the event buffer initialization, ensuring consistency between CPU and GPU implementations and enhanced the condition for detecting a full buffer using `numEventsInEpoch_`.
Adjusted the buffer size on the GPU side to match the modified event buffer, ensuring compatibility with the CPU implementation.
- [x] Tested for GPU with 12 configuration files. GPU testing was also conducted on `test-large-very-long.xml` file for both `XmlRecorder` and `Hdf5GrowthRecorder` till epoch 50. | {
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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 CPU and GPU accessible location.
- [x] Tested for GPU with test-long-connected.xml and test-medium-connected.xml files | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/620 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/620/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/620/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/620/events | https://github.com/UWB-Biocomputing/Graphitti/pull/620 | 2,211,991,704 | PR_kwDOEEdqD85q_Ry3 | 620 | [ISSUE-594] Update CUDA Standard to 17 for C++17 Features | {
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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 [f6320b2 ](https://github.com/UWB-Biocomputing/Graphitti/commit/f6320b2e1ccd74cf49440adc93c4c5201fec1061) on the master branch. The results show no difference in the output, indicating compatibility with the standard 17.
Additional testing may be planned for configurations `test-large-very-long.xml` and `911` for completeness.
- [x] Tested for GPU configuration files from tiny to long as noted above. | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/619 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/619/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/619/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/619/events | https://github.com/UWB-Biocomputing/Graphitti/issues/619 | 2,182,188,806 | I_kwDOEEdqD86CEY8G | 619 | Redesigned Recorder currently is not able to register numVertices Variable(Primitive Type) in neural network simulation | {
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"The same applies to other primitive type simulation metadata."
] | 2024-03-12T16:50:39 | 2025-03-23T10:15:21 | null | CONTRIBUTOR | null | {
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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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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/618 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/618/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/618/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/618/events | https://github.com/UWB-Biocomputing/Graphitti/issues/618 | 2,180,636,801 | I_kwDOEEdqD86B-eCB | 618 | Refactor NG911 All911Vertices variables from 2-D Vectors to Vector<EventBuffer> | {
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We can refactor code in the All911Vertices class from vector<vector<uint64_t>> to Vector<EventBuffer>
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/617 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/617/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/617/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/617/events | https://github.com/UWB-Biocomputing/Graphitti/issues/617 | 2,180,463,536 | I_kwDOEEdqD86B9zuw | 617 | Update Regression Testing Files and Define Variables for Neuron Network Simulations with Redesigned Recorder Subsystem | {
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} | null | Following the redesign of the Recorder subsystem, we need to update our neuron network simulation regression testing files. The updated Recorder subsystem now supports only 1-D variables, leading to compatibility issues with certain types of data previously recorded in the main branch, particularly primitive types. To adapt to this change and update related output files , we need to modify variable owner classes to allow they register their variables for each type of neural network simulation. This update involves:
1. Variables in the XmlRecorder: Identifying variables within XmlRecorder simulations to fit the 1-D variable requirement.
2. Variables for Neural Growth Simulations (GrowthRecorder): registering variables related to neural growth simulations to to ensure they are recorded correctly under the redesigned Recorder subsystem.
3. Variables for STDP Simulations (STDPRecorder): registering variables involved in STDP (Spike-Timing-Dependent Plasticity) simulations to ensure they are recorded correctly under the redesigned Recorder subsystem. | null | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/616 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/616/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/616/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/616/events | https://github.com/UWB-Biocomputing/Graphitti/issues/616 | 2,180,440,223 | I_kwDOEEdqD86B9uCf | 616 | Update Documentation for Recorder (Agile Data Recording) Subsystem in Development Branch | {
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"This issue is resolved by pull request #631 "
] | 2024-03-11T23:32:26 | 2024-11-13T20:01:59 | 2024-11-13T20:01:25 | CONTRIBUTOR | null | {
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} | null | With the recent reengineering of the Recorder subsystem within the development branch, it's essential to update our documentation to reflect the changes and enhancements made to this redesigned (agile data recording) subsystem.
1) Add sequential diagram for Recorder workflow
2) Add Recorder Class Diagram
3) Update GitHub Page with Recorder Notes((Section 4.6))
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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 constantBuffer concrete class (initial plan), the RecordableBase interface was utilized as the base class of Matrix for recording VectorMatrix variables. This design decision was made to avoid disruption to existing code in the neural network simulation component.
4. Did unit testing for XMLRecorder.
5. Updated variant to support uint64_t, bool, int, BGFLOAT types
Note: Although XmlRecorder now supports recording locations, this pull request does not include changes to output files.
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Should also include current import of actual caller data, if we have that. | null | {
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Reminder that these changes should also be merged to development | {
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} | null | There is a small "spelling" mistake in simulatorSetup.puml. The PNGs and SVGs are generated with the name "graphitti setup" when it should be "simulatorSetup".
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 shouldn't be yellow.
- Add hotfix section showing branch off of master, merge into master, merge of development into hotfix, then merge of hot fix into development.
- Redo merge into master to show creation of release branch, etc. | {
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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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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 Recorder will append k values to the 1-D vector .
2. the Recorder works with a two-D vector
-Select the variable to record. The variable owner class would inform the Recorder whether the recorded variable is one or two-dimensional through the `registerVariable` argument (future thing). Instead of appending to a one-dimensional vector, the Recorder will add a new row in the second dimension for each epoch.
Now, the Recorder supports method 1 only. In the future implementation, we would like to add Method 2 to the Recorder.
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"This will require careful verification of all GPU test results."
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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, RecordableBase
- [x] Tested for GPU with test-long-connected.xml and test-medium-connected.xml files | {
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- [x] #692
- [x] #697
- [x] #703
- [x] #706
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"It seems like the plantUML generation action is broken. But, why is that running anyway? Perhaps @jardiamj knows?",
"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 linked in and displaying in the GitHub pages.
- Double-check diagrams against the code. Do the diagrams show the startup that is actually implemented in master? Any changes here would be a hotfix. | {
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} | null | Closes #572
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 classes.
Classes Targeted:
1. Connections, ConnStatic, ConnGrowth
2. Core: EdgeIndexMap
3. AllEdges, AllDSSynapses, AllDynamicSTDPSynapses, AllNeuroEdges, AllSTDPSynapses, AllSpikingSynapses
4. Matrix, CompleteMatrix, VectorMatrix
5. MTRand, Norm
- [x] Tested for GPU with test-small-connected.xml and test-medium-connected.xml files | {
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} | null | Fixes #510 by removing the file named "StudentSetup" in docs/User. The file under docs/User was removed instead of docs/Developer under the assumption that the majority of students using the simulator are contributors and under the fact that the file under docs/Developer is more updated. | {
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"Looks good so far.",
"Closing due to age."
] | 2024-01-01T20:59:49 | 2024-12-20T21:35:50 | 2024-12-20T21:35:46 | CONTRIBUTOR | null | {
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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)
- Removed "magic numbers" refactoring the hard-coded parameters to be more general, parameters are now user-inputted values from the GUI (no longer specific to a simulation).
- Reorganized files (cluster_point_process_functions.py has the functionalities, cluster_point_process.py has the GUI)
- output files (XML) are generalized, descriptions in the XMLs also reflect this. | {
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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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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/576 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/576/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/576/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/576/events | https://github.com/UWB-Biocomputing/Graphitti/issues/576 | 2,042,968,422 | I_kwDOEEdqD855xTlm | 576 | Modify time distribution of secondary process in the cluster point process script | {
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} | null | Currently, the exponentially distributed time intervals of the secondary events are added to the time stamp of the
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 clusters closer to the real call arrival behavior. Conceptually, an emergency incident kicks into motion a homogeneous Poisson process that starts at that particular time. | {
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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 the preprint (doi: https://doi.org/10.1101/2023.12.07.570537), we provide a major update on the current scope of the NeuroML standard, the software ecosystem and describe the newly extended online resources for helping researchers incorporate NeuroML into their modelling work. We show how the modular nature and hierarchical structure of NeuroMLv2, combined with the flexibility of coding in Python, has created a powerful "building block" approach for constructing standardised models from scratch. Moreover, we illustrate how the ecosystem of NeuroML compliant tools supports users at all stages of the model development life cycle. This includes automated model validation, advanced analysis, visualisation, and sharing/reuse of models. The paper demonstrates how NeuroML unifies and standardises the diverse approaches to biologically-detailed computational modelling of neural systems, by enabling an ecosystem of interoperable tools that support the FAIR principles and promotes open, tra
> nsparent and reproducible science.
>
> In the newly updated NeuroML online resources (https://docs.neuroml.org) we provide tutorials on how to use NeuroML to build, validate and share standardised models together with extensive documentation on this INCF approved community standard.
>
> We hope you find these resources useful for your modelling work.
>
> On behalf of the NeuroML community,
> Ankur Sinha, Padraig Gleeson, and Angus Silver. | null | {
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} | null | So far, we have considered only recording events which is the variable of Neuron network simulation so the only thing that needs to be recorded is the time. However, there is a need to extend the functionality of the Recordable class to accommodate the recording of values for NG911 simulation, enabling the capture of time-series data comprising both time and corresponding values(may be pair?). | 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 for recorded variables. Additionally, the unit tests for XmlRecorder have been revised to accommodate these changes.
The RecordableBase class serves as the base class for all variables that need to be recorded during simulation. It defines the interface for accessing information about recorded variables.
The Recordable class template extends the `RecordableBase` interface and provides a concrete implementation for recording variables during simulation. It is templated to accommodate different data types for recording. | {
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} | null | ISSUE #76 and ISSUE #459 has successfully laid the groundwork for implementing serialization and deserialization functionality for all objects within Graphitti. We should proceed with the implementation of serialization and deserialization for all objects.
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 from the Seattle PD PSAP one, using the same caller region but leaving only 3 EMS, 4 LAW, and 2 FIRE nodes. The list of calls (twenty in total) and the resources of the vertices ensure that the simulation yields 1 abandoned call, and 1 dropped call (which is immediately redialed). Whereas the 30 minutes of simulation time guarantees that all 20 calls are recorded (calls are recorded right after being successfully served).
The positioning of all responder nodes ensures that each node receives at least one dispatch order throughout the simulation. | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/567 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/567/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/567/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/567/events | https://github.com/UWB-Biocomputing/Graphitti/issues/567 | 2,023,126,083 | I_kwDOEEdqD854lnRD | 567 | Replace the `test-small-911` simulation with a verified "known good" configuration | {
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This `small 911` simulation should be added to the regression tests in our github actions. | {
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} | null | The location of the Seattle PD PSAP, obtained using the `representative_point()` function of `geopandas`, appears to fall way outside the service boundary. This does not affect the simulation, since that location is never used, but it does affect the look of the graph when using the graph visualization tool. | {
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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. This enables consistent use of the `serialize` method, thereby streamlining the codebase and eliminating the need for separate `load` and `save` methods in the cereal library.
Opting for `unsigned char` brings about a more memory-efficient solution compared to `int`. Additionally, it distinguishes itself from other member variables that store char.
- [x] I have tested this change for GPU
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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)
- Updated index.md docs to support new file (gitflowdiagram.md)
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} | null | In the XmlRecorder class, we utilize vectors to store variables since the total number of variables to be recorded is unknown in advance. To add new elements, we use push_back() to insert them at the end of the vector. However, this approach may lead to reallocation of the vector, wherein a new vector is allocated and all elements are moved to it. This reallocation process can be computationally expensive, particularly when dealing with a large number of elements. We can try some strategies to optimize vector usage in the Recorder.
For example, we can implement a custom growth strategy to balance memory usage and relocation. In the neuron network simulation, when data is being accumulated into the vector container in the Recorder, even though the exact number of epochs may be unknown, we do have knowledge of the number of events in each epoch This information can be leveraged to design a growth strategy that dynamically adjusts the capacity of the vector based on the number of events per epoch.
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"I don't think I did the pull request correctly, sorry. "
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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. This change was based on some research papers, which are described as comments in the scripts. | {
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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. | {
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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) when the items wrapped around the buffer. | {
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https://github.com/UWB-Biocomputing/Graphitti/blob/6c392438d9e5367b0ddfee9c7fb257df27a05bf4/Simulator/Utils/CircularBuffer.h#L135C41-L135C41 | {
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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.",
"In Linux, the backsla... | 2023-10-27T23:14:33 | 2023-10-30T21:55:28 | 2023-10-30T21:55:19 | CONTRIBUTOR | null | {
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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 better fit for Graphitti, we will conduct a metric-based comparison. | {
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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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} | null | We are moving to use GraphML to feed Graphitti with predefined graphs. In addition, we have a config file that contains all the parameters associated with the simulation. The question is if we can or should include these parameters in the GraphML file as graph attributes. We need to think about the possible pros and cons of this approach.
GraphML allows the declaration of attributes under four domains: `graph`, `node`, `edge`, and `all`. See [GraphML primer](http://graphml.graphdrawing.org/primer/graphml-primer.html) for more information. | {
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"Should have been closed by PR."
] | 2023-10-19T21:16:40 | 2023-11-06T23:43:38 | 2023-11-06T23:43:37 | CONTRIBUTOR | null | {
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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.
## Example Function:
In the Connections class, there is a virtual function named `updateSynapsesWeights`. This function has overloads for CPU and GPU. Specifically, in the GPU implementation found in `ConnGrowth_d.cpp`, we observe the following API:
```
void ConnGrowth::updateSynapsesWeights(int numVertices, AllVertices &vertices, AllEdges &synapses,
AllSpikingNeuronsDeviceProperties *allVerticesDevice,
AllSpikingSynapsesDeviceProperties *allEdgesDevice,
Layout &layout)
```
The issue arises because `int numVertices` and `AllVertices &vertices` are not utilized in this function.
## Tasks
Identify and remove unused function parameters from all functions in Graphitti. | 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."
] | 2023-10-11T03:43:37 | 2024-12-21T00:12:53 | 2024-12-21T00:12:16 | CONTRIBUTOR | null | {
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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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} | null | Previously, Graphitti worked under the assumption of all Layouts being a grid with a width and height. That is no longer the case, so we moved the `width_` and `height_` parameters to the FixedLayout class. FixedLayout constructs a grid layout from the `poolsize` defined in the `SimInfoParams` section of the configuration file.
```XML
<SimInfoParams name="SimInfoParams">
<PoolSize name="PoolSize">
<x name="x">10</x>
<y name="y">10</y>
<z name="z">1</z>
</PoolSize>
```
Since these are now FixedLayout-specific parameters, we need to move them to the `<LayoutParams class="FixedLayout" name="LayoutParams">` section. This change has to be reflected in the `FixedLayout.cpp` file where the parameters are read:
```C++
ParameterManager::getInstance().getIntByXpath("//PoolSize/x/text()", width_);
ParameterManager::getInstance().getIntByXpath("//PoolSize/y/text()", height_);
```
Lastly, this needs to be done for all the configuration files that use a `FixedLayout`. | null | {
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Issues #10 and #7 can be addressed as part of this. | 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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} | null | We need to record system performance metrics for the 911 queueing model. There are two measurements that allow us to weigh the load of the system:
- **System utilization:** The proportion of the time during the simulation that the servers are busy.
- **Time Average Queue Length:** The time-weighted average number of customers in the queue during the simulation.
These measurements can be estimated from the history of the number of busy servers at each time step, and the history of the queue length at each time step; respectively. | {
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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.",
"I had to resolve a merging conflict... | 2023-09-25T14:16:40 | 2023-10-02T18:07:13 | 2023-10-02T18:07:04 | CONTRIBUTOR | null | {
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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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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/536 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/536/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/536/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/536/events | https://github.com/UWB-Biocomputing/Graphitti/issues/536 | 1,909,295,207 | I_kwDOEEdqD85xzYhn | 536 | Has this bug fix code from BrainGrid made it into Graphitti? | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/535 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/535/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/535/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/535/events | https://github.com/UWB-Biocomputing/Graphitti/issues/535 | 1,909,292,086 | I_kwDOEEdqD85xzXw2 | 535 | Implement re-engineered HDF5Recorder class | {
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"Closing this as substantially complete. `HDF5Recorder` is functionally equivalent to `XMLRecorder`."
] | 2023-09-22T17:40:22 | 2024-11-20T23:34:50 | 2024-11-20T23:34:50 | CONTRIBUTOR | null | {
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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/6b23f46fa569a8e7452862d5e867ed5582603095) commit from the BrainGrid repo for some potentially useful code that might have gotten lost in the transition to Graphitti. | {
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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 moment, the responder only logs that it received a call. The logic for the responder queue and response time will be implemented in a separate issue.
I also refactored the code in `advanceVertices` so that the logic is divided into `advancePSAP`, `advanceCALR`, and `advanceRESP`. Lastly, I renamed `agents` to `servers` to avoid confusion with agent-based parallel computing. | {
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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 integers, by Matsumoto and Nishimura. Therefore, we could replace the random number generator on the CPU with `std::mt19937` without altering the output.
Professor Stiber noted that we should also do some performance testing. | null | {
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} | null | We need to implement the logic for reading dropped calls in the NG911 models.
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 situation desperately needs their call to go through.
Nena uses the Extended Erlang B formula for estimating the Offered Call Volume, for staffing purposes, because it has an allowance for redialing. Their guidelines state that at least 85% of the time, the caller immediately redials ( https://www.nena.org/?PSAP_StaffingGuide). Therefore, we could use the following probability for redialing:
P = 0.85
The redial rate could be calculated from actual data if we had call records that contain unique identifiers for the caller.
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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 it as a reference parameter.
Changes Made:
1. Refactored the addEdge API and its respective caller.
2. Rectified the PlantUML diagram to align with these changes.
All GPU executions passed. | {
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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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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 Prospects. Manufacturing & Service Operations Management, 5(2), 79–141. https://doi.org/10.1287/msom.5.2.79.16071
Mandelbaum, A., & Zeltyn, S. (2007). Service Engineering in Action: The Palm/Erlang-A Queue, with Applications to Call Centers. In D. Spath & K.-P. Fähnrich (Eds.), Advances in Services Innovations (pp. 17–45). Springer. https://doi.org/10.1007/978-3-540-29860-1_2 | {
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