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This PR updates the graphml file for the Seattle PD simulation with the actual coordinates of the [33 Fire Stations](https://www.seattle.gov/fire/about-us/fire-stations) and [5 Police Precincts](https://www.seattle.gov/police/about-us/police-locations) that serve the Seattle PD PSAP boundaries. It also m... | {
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"I just want to check that the GPU version passes its tests when run manually. Am I right in my impression, looking that the code, that in the creation and update of synapses on the GPU, summation point addresses are computed, and passed from one function to another, but never used? So, is it the case that the GPU ... | 2023-08-30T14:51:47 | 2023-09-27T17:31:08 | 2023-09-27T17:31:03 | COLLABORATOR | null | {
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This PR addresses the following 3 things:
01. Delete `summationPoint_ ` member variable from AllEdges
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The term "summationMap" is currently misleading, as it doesn't accurately reflec... | {
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Additional Info: See comments in PR #496 | {
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closes #495
Added changes requested from last PR & duplicate code of conduct removed | {
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However, after a closer analys... | {
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This PR removes all the Layout Files previously used with the 911 models. These files are no longer needed because all vertices attributes should now be added as vertex parameters in the GraphML file used to set up the graph. | {
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1. Renaming "Core" in the Testing folder to "UnitTesting" and making the corresponding changes in the CMAKE file and unit testing files.
2. Adding a subfolder "TestOutput" under the UnitTesting folder and adding entries in .gitignore to exclude tracking .xml and .h5 files in that folder. | {
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"@KamathScience I am assigning this to you because there are two `.xml` files in `build/output` that are yours. Should they be tracked in the repo? There are some files under build that should be, but most not. Let's document this.",
"Ack, they need not be tracked in the repo, they are created as part of the unit... | 2023-08-16T22:41:29 | 2023-09-28T23:03:01 | 2023-09-28T23:03:00 | CONTRIBUTOR | null | {
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"By overloading the registerVariable() function, it becomes possible for the Xml recorder to record a vector of EventBuffer."
] | 2023-08-15T06:20:11 | 2024-11-09T01:04:52 | 2023-09-06T02:06:19 | CONTRIBUTOR | null | {
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This PR creates a variable table within the XmlRecorder, which contains a list of variables that need to be recorded. With this enhancement, the XmlRecorder becomes capable of capturing and storing all event information for all neurons. | {
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"> Would be good to add README.md file(s) that describe the files within the directory.\r\n\r\nReorganized the script directories, renamed them to be more descriptive of what they contain, and added a README.md file."
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This PR adds a python script under Tools for modeling the call arrival process as a cluster point process. | {
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"Our initial design involves each Recorder class containing a variable table. However, issue 240 highlights that each variable has a temporal resolution, with some requiring updates every time step, while others may update less frequently, such as once per epoch. Additionally, a set of constants, such as neuron typ... | 2023-08-11T18:47:39 | 2024-04-24T06:36:10 | 2024-04-24T06:31:31 | CONTRIBUTOR | null | {
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This issue it a sub-issue of 240
This issue involves adding an interface to the XmlRecorder so that it can record constant variables, such as X and Y location. These constant variables only need to be recorded once because t... | {
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Currently, the EventBuffer only stores uint64_t data, but there is a need for the simulator to store other types of data such as double, To solve this problem, we need to create a recordable template for the EventBuffer class ... | {
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"Done; we're using it."
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"Moot, given move to personal development branches."
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The GIS files used for generating the graph are ... | {
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"Closing PR because I accidentally opened it against the `master` branch instead of `development`."
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This PR adds a python script under `Tools` for modeling the call arrival process as a cluster point process. | {
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"This branch is pretty outdated, I made a new branch and am revisiting the changes. I think this PR should be closed and a new one should be made."
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This PR adds creates new conditional compilation switch for Testing in CMakeLists.txt file | {
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"Closing PR as per the findings mentioned in issue #513 "
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This PR transforms `summationPoint_` into a vector of indexes, which can then be serialized and deserialized using the standard serialization methods provided by the Cereal Library.
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"Should have been closed by PR."
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Likely, this will just be Python code in the Tools subdirector... | {
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"I took care of the requested changes to attempt merging this PR."
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- Updates the command line option in the documentation under Student Quickstart
- Adds command line option in the documentation under Quickstart | {
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"I am facing the issue of modeling the responders' travel time and response time. Specifically, I need to figure out what kind of probability distributions are good fits and then do parameter fitting; for which data is needed.\r\n\r\nThis is a good research paper on travel time distribution: [Analyzing travel time ... | 2023-07-28T07:25:00 | 2023-11-07T02:28:24 | 2023-11-07T02:28:24 | CONTRIBUTOR | null | {
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- Responder travel time
- Responder response time
- Dispatch queue
- Units availability | {
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In order to implement this we need to model the emergency call types, in addition to time and location. Obtaining 911 data to link the calls to the em... | {
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Gans et al. (2003) used the Erlang A queuing model to demonstrate that call abandonment in heavily loaded call centers significantly a... | {
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- Adds documentation in section 303 in which 'make clean' is mentioned to clear cache before compiling for specific testing. | {
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"Had trouble with comment indentation but it should be good now."
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This PR checks to make sure switches on edgeType and makes sure they have default cases, with the ability to expand with throwing exceptions in the future if the switches return 0. In principle, return 0 in switch case if error. | {
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"@KamathScience, as per our conversation this evening I looked into removing the `summation_map` from the NG911 model. The following is what I found:\r\n\r\nThe addEdge method in `AllEdges.cpp` assumes that all models would have a `summation_point` by requiring it in the method's signature. This is the reason it is... | 2023-07-26T23:42:57 | 2023-07-27T06:42:51 | null | CONTRIBUTOR | null | {
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Added top-level page for oxygen documentation
Added links to Graphitti landing page for testing section, fixed Code of Conduct link
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"After testing on Raiju Machine:\r\nCPU: Minimal difference\r\nGPU: Around 3 seconds faster with -j enabled"
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This PR adds:
Added "make -j" to line 18 on README.md
Added line 28 on tests.yml "run: make -j" for GitHub Actions Workflow file, noticed a 2ms time difference on raiju ./tests run with -j option enabled on GPU.
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In the initial/first step, we focuses on migrating the variable registration functionality from the Recorder class to the appropriate variable owner classes. Currently, we enabled the XmlRecorder to record all events for a single neuron using the Ev... | {
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"The trigger on a `push` into `development` is probably caused by the action that generates the PlantUML diagrams, since it commits the generated files via a `push... | 2023-06-27T18:44:12 | 2025-01-22T17:58:31 | null | CONTRIBUTOR | null | {
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"Andrzej Dawiec went from Graduate to Undergradate section"
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This PR Revises Contributors.md and adds Andrzej Dawiec to Undergraduate section | {
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As a part of the onboarding task add Andrzej Dawiec to the Contributors list of Graphitti. Revised from graduate to undergraduate.
#### Files Contributors.md | {
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"I will add onto the contributing guide. ",
"Some notes:\r\n\r\n- [GitFlow article](https://datasift.github.io/gitflow/IntroducingGitFlow.html)\r\n- Need to update CONTRIBUTING.md\r\n- Should redraw diagrams, rather than copy them, so look into #501 "
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"Currently checking unit + regression tests"
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Closes #121
Closes #431
This PR documents the following:
1. Details on how to write unit tests when dealing with a Singleton Class
2. Useful Visual Studio Code extensions
3. Github etiquette
4. Update the PlantUML diagram
5. Document the `help` command line option of Graphitti
6. C++ design d... | {
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"Done check #475 for revision"
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As a part of the onboarding task add Andrzej Dawiec to the Contributors list of Graphitti.
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"> Can merge now, or we can add years for some of the students (I can search for them).\r\n\r\nSure I can wait"
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This PR adds the Contributors.txt file with all students' names.
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"The library is not well documented, and maybe not efficient to use since you have to manually go through the source code"
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"Resolved on PR #505"
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A spatiotemporal cluster point process provides a reasonable framework ... | {
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Removes the extra level in the Connections parameter node from the XML config file because it is not needed. | {
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Refactored the documentation to hopefully improve readability.
had to make another pr because too many broken files in other one. | {
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Graphitti, being a collaborative project managed on GitHub, would benefit from having an onboarding task for new joiners. This task aims to enhance their familiarity with Graphitti's GitHub environment. Currently, the proposed task involves adding new contributors' names to the contributor.txt file l... | {
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"This will likely also involve modifying our `cmake` configuration files.",
"Also, would be good to do some before/after performance measurement on raiju and otachi.",
"Just finished, see pull request but results are as follows on Raiju machine:\r\n\r\nGoogle unit tests: around 2ms faster\r\nCPU Test: Minimal D... | 2023-06-14T00:23:07 | 2023-08-03T19:07:35 | 2023-08-03T19:07:35 | COLLABORATOR | null | {
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The `-j` option in the `make` command allows users to control the number of simultaneous jobs executed by `make`, thereby improving the build process efficiency of Graphitti by leveraging multiple processors or cores on the system.
#### Usage
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Currently, Graphitti utilizes a dynamically allocated bool array `inUse_` in AllEdges to store boolean values.
` unique_ptr<bool[]> inUse_;`
However, Cereal Library does not serialize or deserialize dynamically allocated arrays. So, an alternative option considered was using a vector of bool, whi... | {
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"Closing this issue as per the findings mentioned in issue #513 "
] | 2023-06-12T17:22:56 | 2023-08-29T22:28:15 | 2023-08-29T22:28:15 | COLLABORATOR | null | {
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The `summationPoint_` member variable is currently a vector of raw pointers in the `AllEdges` base class. `summationPoint_` stores several addresses of indexes from the `summationMap_`.
` vector<BGFLOAT *> summationPoint_;`
However, the Cereal Library does not serialize raw pointers directly.... | {
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Graphitti currently has two unit tests that ensure error-free serialization and deserialization processes. However, in order to further improve the reliability of these unit tests, it is essential to verify that the obtained serialized output precisely matches the expected deserialized output.
### T... | null | {
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- Added 3 tables to the performance.md : Initialization, Access and Sum, and Random Access and Sum.
- If you prefer a different format or have any specific requirements, please let me know. | {
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"added presentation to google drive"
] | 2023-06-05T17:47:31 | 2023-08-29T21:36:47 | 2023-08-29T21:36:46 | CONTRIBUTOR | null | {
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> Computational neuroscientists have developed a diversity of software platforms for simulating neural network models at different scales. However, each simulator has its own programming or conf... | {
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"Hi @stiber, I would like to work on this issue",
"> Hi @stiber, I would like to work on this issue\r\n\r\nThanks for contacting us! If you think you can follow what's written there, then feel free to do so. Please fork the repo and make the change off of the master branch. See our contributing guide for more inf... | 2023-06-02T18:21:20 | 2023-06-06T17:42:23 | 2023-06-06T17:42:23 | CONTRIBUTOR | null | {
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"> Not sure if you're ready to merge quite yet. Re-request my review as needed. When you've done enough manual testing (or updated the regression tests) and are ready to merge, let me know explicitly and I will override the block due to not all tests passing, if needed.\r\n\r\nIt is not ready to merge. I discussed ... | 2023-05-31T06:12:48 | 2023-08-03T06:22:25 | 2023-08-02T00:00:05 | CONTRIBUTOR | null | {
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1.Remove all concrete classes in the XML Recorder except for the XmlRecorder class.
2. Change the recorder name to XmlRecorder in the related config files
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In this issue, our main concern is with the XmlRecorder, specifically enabling it to re... | {
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Refactored the documentation to hopefully improve readability. | {
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Currently, Graphitti utilizes generic CUDA functions for GPU operations. This issue suggests exploring the possibility of using [Thrust](https://docs.nvidia.com/cuda/thrust/index.html) CUDA library for GPU optimization. As per their official website, Thrust provides a higher-level interface and optim... | null | {
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Moved subcategories around in the testing, user, and developer documentation categories.
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This PR replaces the usage of `resize` followed by `assign` with a single call to `assign` to initialize a vector with default values. This simplifies the code and makes it more efficient by eliminating the need to resize the vector and then fill in the default values separately.
The changes have bee... | {
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Currently, the vector resizing operation in Graphitti is being performed using the resize function followed by the assign function to set new values to its elements. This approach results in unnecessary reallocation of memory when the vector is resized. A better system would use the assign function ... | {
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"Technically, we're returning a reference to the object, not a reference to the unique_ptr, right?",
"> Technically, we're returning a reference to the object, not a reference to the unique_ptr, right?\r\n\r\nYes, wrong choice of words! Corrected to say returns a reference to the object."
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Change the getter methods of AllVertices, AllEdges, Model, Layout, Connections, and Recorder to return a reference of the object than a raw pointer. | {
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check the output file extension for Hdf5 Recorders and XML Recorders | {
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Replaced `typedef` with the `using` keyword in the Graphitti codebase as it provides a more consistent syntax with the rest of the code and works well with templates. | {
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There are multiple benefits of adding `override` specifier to our Graphitti codebase:
1. Improves code readability- The function t... | {
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Removed #ifndef.
Changes:
1. Removed line number 11,12 and 199
2. Removed extra tab for the indentation (line number 12 to 53) | {
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"Note that this requires a thorough audit of all of our `.h` files so that they are all fixed."
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"I've been giving this a little bit of thought. If the `Recorder` method that is used to register variables for recording takes them by reference, and those references are saved, then the `Recorder` class doesn't need to be a `friend` and can still access and modify private variables. Conceptually, this is because ... | 2023-04-06T00:24:58 | 2023-04-06T20:10:38 | null | COLLABORATOR | null | {
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Reference: [Google Style Guide-Acc... | null | {
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More about namespac... | null | {
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