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} | null | There are places in our Graphitti codebase where we have "get" methods that return pointers to objects. These objects are not implemented as formal singletons but we only create one and use a unique_ptr to point to it. In addition, methods like getLayout() and getVertices() also return a pointer to the object, which is dereferenced and then used to initialize a reference.
Example :
```
Connections *Model::getConnections() const
```
```
Layout &layout = *Simulator::getInstance().getModel()->getLayout();
AllVertices &vertices = *layout.getVertices();
```
It would be better for those methods to return a reference to the object to avoid null pointer errors-- When a function returns a reference, we can be certain that it is pointing to a valid object. However, a pointer returned from a function can be null, which can lead to runtime errors. Also, passing a reference can improve readability and reduce memory leaks or other memory management issues.
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} | null | This PR documents the following cpp features:
1. Copy and Move operations
2. Smart Pointers
3. Aliases
4. Inputs and Outputs
This is a fix for issue #399 and extension of PR [#400](https://github.com/UWB-Biocomputing/Graphitti/pull/400) | {
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"Will it be OK to let the eventual merge of the development branch into master fix it there, or is this something that needs to be resolved in master before July?",
"> Will it be OK to let the eventual merge of the development branch into master fix it there, or is this something that needs to be resolved in mast... | 2023-03-03T21:16:48 | 2023-05-15T05:45:52 | 2023-05-15T05:45:47 | CONTRIBUTOR | null | {
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Upgrades GitHub checkout action v2 to v3, because actions that use Node.js 12 are being deprecated. | {
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"Thanks for finding this bug. I saw that empty space in the empty line. Do I need to update the file and push it to GitHub?",
"These two regression testing files were updated."
] | 2023-03-03T03:30:48 | 2023-06-12T15:47:17 | 2023-06-12T15:47:17 | CONTRIBUTOR | null | {
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} | null | The Regression tests for test-small and test-small-connected-long fail because there are empty spaces in the following lines:
Testing/RegressionTesting/GoodOutput/test-small-out.xml: Line 14
Testing/RegressionTesting/GoodOutput/test-small-connected-long-out.xml: Line 30
https://github.com/UWB-Biocomputing/Graphitti/blob/21a4b30fa671b5b5418cb9bafd7cdc0c60e9b87d/Testing/RegressionTesting/GoodOutput/test-small-out.xml#L14
https://github.com/UWB-Biocomputing/Graphitti/blob/21a4b30fa671b5b5418cb9bafd7cdc0c60e9b87d/Testing/RegressionTesting/GoodOutput/test-small-connected-long-out.xml#L30
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} | null | Node.js 12 GitHub actions are being deprecated and should be updated to use Node.js 16. See: [GitHub Actions: All Actions will begin running on Node16 instead of Node12](https://github.blog/changelog/2022-09-22-github-actions-all-actions-will-begin-running-on-node16-instead-of-node12/)
In our case, we need to upgrade actions/checkout@v2 to actions/checkout@v3
https://github.com/UWB-Biocomputing/Graphitti/blob/21a4b30fa671b5b5418cb9bafd7cdc0c60e9b87d/.github/workflows/tests.yml#L19 | {
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"Or just using the objects as \"ordinary\" class members and local variables, rather than dynamically allocating them."
] | 2023-02-27T20:44:43 | 2023-04-27T15:48:24 | 2023-04-27T15:48:24 | COLLABORATOR | null | {
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"I have looked over the code and everything I checked in test files and code have default cases which return ETYPE_UNDEF which is similiar to issue #409 "
] | 2023-02-26T22:10:29 | 2023-07-20T20:39:34 | 2023-07-20T20:39:34 | COLLABORATOR | null | {
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See also issue #409 and #404 | {
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"Closing this issue as it's no more relevant. "
] | 2023-02-26T22:05:49 | 2024-12-03T20:10:16 | 2024-12-03T20:10:16 | COLLABORATOR | null | {
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} | null | Let's run the latest version of Graphitti from the master branch for each configuration file in `Testing/RegressionTesting/configfiles` to create a corresponding `.h5` output for `GoodOutput`. Automating comparison with new output for regression testing will require a bit of playing around with `h5diff`. Making this something that can be done via GitHub may be very difficult, since it would require a VM that has HDF5 installed. But it should be doable to have shell scripts for manual regression testing. | null | {
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Closes #24
Closes #76
Closes #129
Closes #237
Closes #372
This PR addresses multiple issues as they are mostly interrelated. Some of the changes addressed in the PR are as follows :
1. C++ version has been updated to C++17 in the CMake file
2. Dynamically allocated arrays are changed to vectors
3. Raw pointers and shared_ptr are changed to unique_ptr
4. Use =default notation to mark the constructor and destructor to avoid using an empty body
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Fixes #401
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Added documentation for const and constexpr.
Fixed the existing coding style. | {
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} | null | Graphitti is primarily written in C++98 and as a part of upgrading the codebase to modern C++ (C++11, C++14, and C++17), new features will be adopted. These features must be recorded and documented in the `codingConvention.md` and `cppStyleGuide.md` files.
Features that must be added :
1. const and constexpr | {
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"> Since you raise the issue of C++17, consult with @KamathScience on her future plans for presenting language features and when the feels that she would be ready to facilitate a discussion of which C++ version we should target. My guess is that it will be C++17, but let's make sure we have heard about the key feat... | 2023-01-31T05:22:31 | 2023-02-20T06:27:50 | 2023-02-19T08:00:38 | CONTRIBUTOR | null | {
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} | null | This is a basic CircularBuffer class intended to be used in the implementation of the NG-911 Discrete Event Queueing model.
In the current implementation, the `get()` method returns a default constructed object when called on an empty buffer. If we decide that it's worth it, we could move our target standard to C++17 and take advantage of the `std::optional` data type. The main advantage is that we will get an obviously invalid value in such a case. | {
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"This is an important point for GPU compatibility: as currently designed, such CPU-side data structures should _never_ be resized, so this is actually a desirable behavior. If there is a reason for needing such a thing, then we need to talk about mid-level architectural decisions. In particular, being able to chang... | 2023-01-31T02:53:32 | 2023-06-23T19:08:12 | null | CONTRIBUTOR | null | {
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https://github.com/UWB-Biocomputing/Graphitti/blob/84d9f6ee28264e2a50ba211ec5efd2a30be6b7d2/Simulator/Vertices/EventBuffer.cpp#L25
I created a Unit Test under the branch `event-buffer-tests` for demonstration.
We cannot rely on the vector `empty` or `size` methods for this check, we would need to find another way to check for an empty buffer. | null | {
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"PR#492 is deleted because it contains unwanted commits."
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https://github.com/UWB-Biocomputing/Graphitti/blob/84d9f6ee28264e2a50ba211ec5efd2a30be6b7d2/Simulator/Vertices/EventBuffer.h#L66 | {
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} | null | This PR contains:
- The InputManager class implementation
- Unit tests for the InputManager class
- InputManager and GraphManager documentation
- A Python script for generating an XML file from a CSV formatted 911 call log
- Improvements to the Python script that generated the GraphML file | {
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"Serialization currently only includes version numbers for base classes, as a reminder/example. Could be extended to all classes, if desired, when this issue is addressed."
] | 2023-01-06T20:48:26 | 2025-03-06T22:52:02 | null | COLLABORATOR | null | {
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CEREAL_CLASS_VERSION is a macro defined in the Cereal library which is used to specify the version of a class when serializing and deserializing data.
When serializing an instance of a class, the version number specified with CEREAL_CLASS_VERSION will be stored in the serialized data. This version number is used to ensure that the correct version of the class is used when deserializing the data. Hence, if we make any changes to the class that affect how it is serialized or deserialized, we should increment the version number. This will ensure that the correct version of the class is used when deserializing data that was serialized with an older version.
#### Files
Classes that have defined the CEREAL_CLASS_VERSION macro. Example: AllEdges and ConnGrowth classes.
### Tasks
Several approaches can be taken to automate this task, two such approaches are the following:
**Approach 01: Using GitHub Actions**
To detect a breaking change in a class, we serialize a reference version of the class by creating a serialization file for the head, commit, and master using the same default config file. We can also use a shell script that produces a report of new and old serialized files. This can have three possible outcome
1. No difference in serialized files:
If the serialized files are identical then there are no breaking changes hence we don't increment any class version.
2. Difference in the serialized file, and the version is higher in the serialized file of the commit branch:
If the version number is higher skip the check.
3. Difference in serialized files:
If there is a difference, then we have to increment the respective class.
**Approach 02: Using Unit Tests**
Similar to the previous approach, run unit tests for each CEREAL_CLASS_VERSION class of the head, commit, and master with the same default config file. For example, make an instance of all edges, initialize it and serialize all edges class. If there is a breaking change increment the class version number.
NOTE:
1. Irrespective of any approach, the implementation must easily incorporate any new (CEREAL_CLASS_VERSION) class that might be added in the future.
2. Please note that these approaches are meant to be a starting point and not a detailed solution.
Related Issue:
1. https://github.com/UWB-Biocomputing/Graphitti/issues/387 | null | {
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This PR adds CEREAL_CLASS_VERSION macro on AllEdges and ConnGrowth class.
In addition, we also extend the serialization unit test to confirm that the output XML file contains the expected class version. | {
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1.2.2: "Download a release" hyperlink does nothing as we are already where the link is supposed to direct you to
I added a release page link
1.2.2: "Fork and Clone Graphitti" doesn't take you to a different page
I added a link pointing to the section header
1.2.2.1: Says there are no releases, but on BrainGrid GitHub page there are 5 releases
I deleted 1.2.2.1
1.2.3: Where is CMakeLists.txt located?
I added a link (https://github.com/UWB-Biocomputing/Graphitti/blob/master/CMakeLists.txt) | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/390 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/390/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/390/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/390/events | https://github.com/UWB-Biocomputing/Graphitti/pull/390 | 1,507,124,709 | PR_kwDOEEdqD85GAEUZ | 390 | [Issue-389] Update references of Driver.cpp to Core.cpp | {
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This PR modifies the below 3 Plant UML diagram script to change the reference of Driver to Core where required.
1. graphitti.puml
2. simulatorSimulate.puml
3. topLevelFlow.puml
In addition to the PlantUML script, the PR updates the helper comments in the code that refer to Driver.cpp. | {
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In the [PR-382](https://github.com/UWB-Biocomputing/Graphitti/pull/382), we refactored the main class (Driver.cpp) into Graphitti_Main.cpp, Core.h, Core.cpp, Serializer.h, Serializer.cpp to improve the testability of Serialization and Deserialization.
However, 20 places refer/mention the old class Driver.cpp in the Graphitti project. This has to be updated to match the refactored code accordingly.
#### Task
Update the reference of Driver.cpp.
#### Screenshot
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section 2
Create a PlantUML class diagram that is like the hand-draw block diagram | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/387 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/387/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/387/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/387/events | https://github.com/UWB-Biocomputing/Graphitti/issues/387 | 1,505,525,734 | I_kwDOEEdqD85ZvH_m | 387 | Add cereal class version to the classes that serialize values | {
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} | null | ### Description
CEREAL_CLASS_VERSION is a macro defined in the Cereal library which is used to specify the version of a class when serializing and deserializing data. When serializing an instance of a class, the version number specified with CEREAL_CLASS_VERSION will be stored in the serialized data. This version number is used to ensure that the correct version of the class is used when deserializing the data.
### Task
Add CEREAL_CLASS_VERSION macro on AllEdges and ConnGrowth class.
### Words of caution from Cereal documentation-
1. If the versioned serialization function and do not specify the version number using the macro, cereal will default to giving a version number of zero.
2. When performing loads, cereal will load versioning information if your serialization function is versioned.
3. If you did not use a versioned serialization function to create the archive you are loading from, your data will be corrupted and your program will likely crash. This loaded version number will be supplied via the version parameter you add to your serialization functions.
4. Data serialized without versioning cannot be loaded by a versioned serialization function (and vice versa).
5. If you choose to use versioning, you must ensure that all serialization functions for a type support the versioning parameter (both your load and save must have it in the case of split serialization). | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/386 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/386/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/386/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/386/events | https://github.com/UWB-Biocomputing/Graphitti/issues/386 | 1,500,942,752 | I_kwDOEEdqD85ZdpGg | 386 | Allow users to have a local log4cplus_configure.ini file for changing logging levels | {
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} | null | The current log4cplus_configure.ini file under `build/RuntimeFiles` is under version control by `git`. This means that when changing its settings for debugging purposes, you run the risk of committing and pushing those changes upstream if you don't take care to exclude the file from your commits.
An option would be to allow users to have a local `log4cplus_configure.ini` file in a specific directory. The Simulator would check for the existence of the local file, and only use the default one under `build/RuntimeFiles` if it doesn't exist. This will allow users to change their logging level without modifying a file that is under version control. | null | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/385 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/385/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/385/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/385/events | https://github.com/UWB-Biocomputing/Graphitti/issues/385 | 1,492,471,094 | I_kwDOEEdqD85Y9U02 | 385 | Look into adding more continuous integration checks as actions | {
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} | null | Idea is as follows:
- Within the action, and assuming all other tests pass, do a git merge into master just locally within that VM.
- Run all tests
Since this is just local to the VM, the merge has no effect on the repo | null | {
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} | null | This code change focuses on adding variable names to the serialized XML files to improve readability. Variable names are added using Cereal name-value-pair functionality as mentioned in issue #335.
The code change also improves the size validation checks of deserialized data by adding size variables for each vector in the serialized files. Finally, I have refactored the main method to enhance the testability of Serialization and Deserialization.
### Testing
Since each serialized and deserialized unit test requires a Simulator object (which is a singleton in nature), I had to create a separate main function for each test to avoid sharing the simulator object within the tests- which would otherwise lead to segmentation fault error.
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"all comments on PR #380 are addressed in this Pull Request along with Fixes to Code Style Errors"
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"Addressed all code style errors in #381.\r\n"
] | 2022-11-18T18:08:33 | 2022-11-23T20:16:23 | 2022-11-22T20:03:22 | CONTRIBUTOR | null | {
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} | null | This PR addresses most of what is needed for reading the initial graph from graphML files. I created a GraphManager class that wraps around some Boost Graph Library functionality.
It addresses most of what is needed for issue #369. Not all the parameters needed for a fully functional 911 implementation are there yet, but that will be addressed in a different PR so as to not make this one too big. | {
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"And to follow up, if we give each of the numbered items in the startup sequence a separate operation in the manager, then we can \"script\" the startup (and shutdown, which we haven't addressed) entirely using OperationManager, with top-level abstract classes registering appropriate methods. This will mean that, i... | 2022-11-08T05:51:21 | 2024-01-30T19:10:11 | 2024-01-30T19:10:11 | CONTRIBUTOR | null | {
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} | null | Moving into providing the initial Graph structure to Graphitti using GraphML files is forcing us to review its starting sequence.
- We must figure out where and when input and graph parameters must be loaded.
- We need to figure out if we can leverage the OperationsManager for some initialization steps that don't need to happen in a specific order.
- Finally, the naming of classes and methods must be reviewed.
This picture is a starting point.
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} | null | **Description**
Currently command line options for stimulusfile (-s), deserializefile(-r) and serializefile(-w) does not closely match their description. This can be hard for a user to remember or lead to confusion.
```
dkamath@otachi:~/Graphitti/build$ ./cgraphitti -help
[TRACE][2022-11-02 17:25:37] Instantiating Simulator
[TRACE][2022-11-02 17:25:37] Parsing command line
The UW Bothell graph-based simulation environment, for high-performance
neural network and other graph-based problems.
Usage: ./cgraphitti -c <configfile> -s <stimulusfile> -r <deserializefile>
-w <serializefile> -v
-c, --configfile=<configfile> parameter configuration filepath
-s, --stimulusfile=<stimulusfile> stimulus input filepath
-r, --deserializefile=<deserializefile> simulation deserialization
filepath (enables
deserialization)
-w, --serializefile=<serializefile> simulation serialization filepath
(enables serialization)
-v, --version output current git commit ID and
exit
* = required parameter
```
To improve the readability of the parameters we need to rename the options as follows:
1. Stimulus file - The stimulus file is the input file
Rename the description from `stimulus input filepath` to `input file path`
Rename the command from `--stimulusfile=<stimulusfile>` to `--inputfile=<inputfile>`
Rename the option from `-s` to `-i`
2. Deserialization file -
Rename the option from `-r` to `-d`
3. Serialization file -
Rename the option from `-w` to `-s`
**Files**
[Core.cpp](https://github.com/UWB-Biocomputing/Graphitti/blob/master/Simulator/Core/Core.cpp)
[Graphitti documentation](https://uwb-biocomputing.github.io/Graphitti/)
**Tasks**
1. Make the required changes to stimulusfile (-s), deserializefile(-r) and serializefile(-w) as mentioned above, in Core.cpp - `parseCommandLine` function
2. Add the command line option in the documentation under Quickstart
3. Test the changes. | {
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} | null | On this page section: https://uwb-biocomputing.github.io/Graphitti/Developer/StudentSetup.html#using-graphitti-servers
This link is broken: http://depts.washington.edu/cssuwb/wiki/computing_resources#raijuuwbedu
Can someone update the link with info on these hardware? | null | {
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} | null | Currently, the neurons' spike history is reset at the end of the Recorder `compileHistories()` in CPU code. Then, the equivalent GPU structure is updated by copying the values over using `cudaMemcpy`. This is confusing.
Perhaps, the resetting of spike history in GPU code should be done in a CUDA kernel call. The logic here is that we should only need to copy from the device to record the results, the state of the spike history should be kept current by GPU code so we don't have to copy from host to device after recording.
This code would have changed once the GPU implementation of the EventBuffer gets merged, but it still follows the same strategy.
https://github.com/UWB-Biocomputing/Graphitti/blob/f74594f82d7915778630632869569031f2eaeea1/Simulator/Vertices/Neuro/AllSpikingNeurons_d.cpp#L53 | null | {
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"This connects to one of the remaining \"most confusing\" parts of the simulator."
] | 2022-10-27T06:14:25 | 2023-04-10T17:18:06 | 2023-04-10T17:18:05 | CONTRIBUTOR | null | {
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} | null | The Simulator class contains the following pointers that are never used nor initialized:
- `vertexType *rgNeuronTypeMap_`, and
- `bool *rgEndogenouslyActiveNeuronMap_`
There are getters for these but they are not called anywhere. They should be removed if not needed.
Besides, the class has a pointer (`pSummationMap_`) to the vertices `summationMap_`. The getter for this pointer is called in two places:
- HostSInputRegular.cpp, and
- SInputPoisson.cpp
If we really need to get the vertices `summationMap_` from the Simulator class, we could get it from `model_->getLayout()->getVertices()->summationMap_` rather than having the same pointer in two places. It also presents the assumption that all models have a summation map.
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} | null | GraphML files will be used in the NG911 model to generate the initial graph structure (see #369). The same can be done for the Neural Network model, and we will have a unified interface for both models.
With this, we will also merge several config files (for vertex types) into one.
Tied to Workbench issue: https://github.com/UWB-Biocomputing/WorkBench/issues/131 | {
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"I am using XML as the format for the input files. At the moment it holds a `data` element that contains a list of `event` items each representing an event that occurs at a given vertex. In the case of 911 calls, they have the following attributes:\r\n- vertex_id\r\n- time (time of occurrence)\r\n- duration\r\n- x\... | 2022-10-18T17:54:59 | 2023-02-25T16:00:54 | 2023-02-25T16:00:54 | CONTRIBUTOR | null | {
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} | null | An Input class that load calls from an external file and then feeds them to Caller Regions will allow us to test different models of call arrivals (real data, inhomogeneous Poisson process, cluster point process, etc). The idea is that the list of calls can be pre-generated in a more flexible way using a scripting language, without modifications to the Graphitti codebase.
Because Graphitti's architecture is designed to take advantage of parallelization for performance improvement, the Input class should not make calls to directly modify any vertex. Input classes previously implemented in Braingrid got around this constraint by creating a set of `Edges` that are then used to feed the inputs into the corresponding vertices.
We will work on an Input class for the NG911 model and then evaluate if this concept can be extended to the Biological Neural Network one. | {
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} | null | The previous proof of concept used a grid layout for setting up the initial 911 graph structure. Since the communication links between 911 entities (Caller Regions, PSAPs, and Responders) depend on their geographical location and boundaries, we are now extracting these relationships from a set of Geographic Information Systems (GIS) files into a graph. This graph is saved to a GraphML file that can later be loaded into the Simulator.
We need to modify the corresponding `Layout`, `Connections`, `AllVertices`, and `AllEdges` classes to use the GraphML file to create vertices, edges, index maps, and their properties. | {
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"Also add at least a `TestOutput` subdirectory, and entries in `.gitignore` to not track `.xml` and `.h5` files there."
] | 2022-10-14T06:15:50 | 2024-04-24T06:47:40 | 2024-04-24T06:47:40 | COLLABORATOR | null | {
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} | null | #### Description
The subfolder `Core` under Testing has unit tests from all the components of the simulator, not just the Core. Hence the name should be replaced with `UnitTesting`. This name will also be consistent with the names of other sub-folders in Testing like `RegressionTesting`. Finally, it is important to reflect this change in CMakeLists.txt and any other file that uses the unit tests.
#### Files
- [Graphitti](https://github.com/UWB-Biocomputing/Graphitti)/Testing/
- [Graphitti](https://github.com/UWB-Biocomputing/Graphitti)/CMakeLists.txt
#### Tasks
- Change the name of the sub-folder 'Core' to 'UnitTesting'.
- In theCMAKEList.txt, update the path of the unit tests.
- Check if any other files need to be updated.
- Test the changes.
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Tested and verified and Output compared with v0.9 branch | {
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"2. Garbage collection in Vector allocation ",
"Appears to be obsolete."
] | 2022-10-06T20:50:08 | 2025-01-10T19:20:47 | 2025-01-10T19:20:46 | CONTRIBUTOR | null | {
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1. Replace shared_ptrs with make_shared while instantiating the Objects
[reference: 15.2.1: https://learning.oreilly.com/library/view/a-tour-of/9780136823575/ch15.xhtml#sec15_2_1 ]
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"I have completed the following this.\r\n1. Renaming `copyNeuronHostToDevice()` to `copyToDevice()`\r\n2. Renaming `copyNeuronDeviceToHost()` to `copyFromDevice()`\r\n3. This change has been cascaded from top level neuron class to all its sub classes "
] | 2022-09-17T19:45:25 | 2022-12-02T18:10:36 | 2022-12-02T18:10:36 | CONTRIBUTOR | null | {
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Note that, for subclasses, at each level in the hierarchy, should copy the corresponding *new* elements of the device properties `struct`. So, it should call the superclass copy method first.
Also, all of these methods should take a single argument that is a device address. Right now, we're using `void *`; let's use a `typedef` to define `DeviceAddress` as the same thing as `void *` temporarily.
https://github.com/UWB-Biocomputing/Graphitti/blob/c21552bd8ae06ac828cce9ba711bba413935803d/Simulator/Vertices/AllVertices.h#L94-L102 | {
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The python script to turn GIS data into a graph representation was not working on Linux because of capitalization inconsistencies with the file names, this fixes that. I also removed the spaces from the names of files and directories.
In addition, I added a `.graphml` format output. The reasoning is that the only C++ library for GEXF that I found (`libgexf`) is no longer being maintained and we might have better luck with GraphML. For instance, boost provides a read_graphml function that builds a BGL (Boost Graph Library) graph from a `.graphml` file. | {
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I've also edited the docs/index.md file to include the new documentation. | {
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} | null | All factory classes have a map with key names associated with a pointer to the create method of a given class. Currently, the create method loops through the map data structure to find the correct class; this is unnecessary and unexpected since you can access the class name from a map using `find`.
These classes should be changed to use `find`, if nothing else it would make the code easier to read. | {
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2. Serialized config file test-large-very-long.xml using GPU (8 hours)
3. Edited config file full-100x100-cpu-stdp.xml to use with the above serialized file
4. Collected CPU output using command (./cgraphitti -c ../configfiles/full-100x100-cpu-stdp.xml -r Output/Results/GPUSERIAL_test_large_very_long.xml)
5. Collected GPU Output using command (./ggraphitti -c ../configfiles/full-100x100-cpu-stdp.xml -r Output/Results/GPUSERIAL_test_large_very_long.xml)
6. Compared both Outputs
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"Hi Professor @stiber , we can merge this branch now. Tested all clang-format changes on CPU and GPU Outputs ,no change in any output or time of running input config files. I will now check the time change during compilation. "
] | 2022-07-11T18:03:18 | 2022-07-15T22:14:14 | 2022-07-15T22:13:37 | CONTRIBUTOR | null | {
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} | null | Professor @stiber , creating this pull request for review. The performance for GPU and CPU input config files(tiny to large) deviate not more than 2 sec. Here is the google spreadsheet for the performance.
" https://docs.google.com/spreadsheets/d/1WW1iFUQ-m6wms38ipnbmw4X_CgMmMdAKxw0CbkBFYcs/edit?usp=sharing " | {
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"Thoughts on work to close this out:\r\n1. Add 'GoodOutput/CPU' and 'GoodOutput/GPU' directories to 'Testing/RegressionTesting/'.\r\n2. Move current xml files into 'GoodOutput/CPU'.\r\n3. Change all instances of 'GoodOutput' to 'GoodOutput/Cpu' in .github/workflows/tests.yml.\r\n4. Add a variable to 'Testing/RunTes... | 2022-07-08T23:59:22 | 2024-08-28T19:50:23 | 2024-08-28T19:50:23 | CONTRIBUTOR | null | {
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} | null | Right now, we really just have things set up to do the automated CPU testing using GitHub actions. We will shortly have a shell script to do manual regression testing, which includes GPU-based build and test. However, none of the support file locations distinguish CPU vs. GPU. I suggest adding `CPU` and `GPU` subdirectories under `Testing/RegressionTesting/GoodOutput` at least (and maybe `Testing/RegressionTesting/TestOutput`; think about it) and modifying the actions and the manual shell script to work with this. This will allow direct CPU-CPU and GPU-GPU regression testing, in advance of dealing with issue #319. | {
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"CONTRIBUTING.md looks good. \r\n\r\nIn near future we can add link to Google unit tests documentation Link and GPU tests script location in this. "
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"completed the following things.\r\n1. multiple methods were present to accomplish the copy to or from Device. Clubbed them into one.\r\n2. completed the the renaming of copy methods to to avoid confusion "
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"The event buffer data structure to capture neuron spike has been extended to GPU side. We are only writing CPU side code to copy to-from the GPU side that translates between the CPU and GPU data structure reorganization"
] | 2022-06-29T17:53:35 | 2022-12-02T18:10:35 | 2022-12-02T18:10:35 | CONTRIBUTOR | null | {
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"I think these can be a set of small things that you could work on to familiarize yourself with our software development processes. Read our contributing guide and then touch bases with me on this."
] | 2022-06-11T00:56:31 | 2023-01-11T23:22:58 | 2023-01-11T23:22:58 | CONTRIBUTOR | null | {
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} | null | 1.2.2: "Download a release" hyperlink does nothing as we are already where the link is supposed to direct you to
1.2.2: "Fork and Clone Graphitti" doesn't take you to a different page
1.2.2.1: Says there are no releases, but on BrainGrid GitHub page there are 5 releases
1.2.3: Where is CMakeLists.txt located?
1.3.2: Where do I open my Linux terminal to call the screen command?
3.2: Isn't int main supposed to return a 0 at the end? (https://uwb-biocomputing.github.io/Graphitti/Testing/CastingTest/CastingTest.cpp) | {
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"Can we merge this?",
"Sorry for the slow response time..."
] | 2022-06-10T00:02:52 | 2022-09-28T17:03:51 | 2022-09-28T17:03:43 | CONTRIBUTOR | null | {
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I did some cleaned up of the various factory classes. If nothing else, this should improve readability.
Summary:
- Switched to using `find`, instead of looping over the `createFunctions` map.
- Changed `noiseRNG` from a naked pointer to a `shared_ptr`.
- Removed not needed class member pointer to the instance created by the factory.
- Wrote Unit Tests for all factory classes.
- Fixed Segmentation fault on destruction of `Connections911` class (revealed by the unit tests). | {
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"I think we need to schedule an \"architecture day\" (or, maybe \"architecture cleanup day\") for mid-summer 2022. The Graphitti architecture, at the top level, is greatly improved from BrainGrid. There are some parts of the envisioned architecture that aren't yet fully implemented or universally used (new Recorder... | 2022-06-06T14:52:36 | 2022-06-29T18:36:00 | null | CONTRIBUTOR | null | {
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https://github.com/UWB-Biocomputing/Graphitti/blob/f4e82884eb9f7273aca729fbb8024f03c350ec5a/Simulator/Core/GPUModel.h#L122-L128
The code for allocating and copying memory between CPU and GPU is in subclasses of AllEdges and AllVertices, so I wonder if it would be better to place them in their respective subclass. | null | {
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> After extensive testing done by the IT CSS/STEM Liaisons with the CSS remote lab computers, the Infrastructure Committee has decided that in order to provide better computing services to CSS students and faculty, the CSS Linux labs (both in-person and remote environments) should be running Rocky8 OS (RHEL based OS).
> We want to begin the roll-out of this environment after the Summer quarter (the week of August 22 – 26 or August 29 – September 2, 2022).
>
> Below are some key highlights and context about this change.
>
> Why Rocky8?
> More Reliable Update Delivery. All CSS lab computing systems will be compatible with our Ansible automation platform, increasing the efficiency and overall quality of system update delivery. Additionally, Rocky8 will be actively maintained until 2029.
> Improved Security Posture. Installations adhere to the industry's best practices and conform to the high standards set by the upstream Red Hat Enterprise Linux distribution that it is rebuilt from.
> Improved User Experience. It will allow students to gain experience in a community enterprise OS designed to be 100% bug-for-bug compatible with Red Hat Enterprise Linux distribution used on multiple cloud platforms like Google Cloud, AWS, Azure, VMware Cloud, and UW IT VDC services.
> Reduces IT STEM/CSS Liaisons Overhead. Debian, the currently installed OS on CSS Linux machines, has taken much manual effort from our IT Liaisons for the last school year, given the VSCode compatibility issues and Microsoft's Hyper V partial support for Debian.
> Cost Saving. We can make all 22 Linux VMs the same with 32 GB of RAM and 12 vCPUs without purchasing additional memory. Compared to the cost of the UW VDC configuration (12 VMs, 8 GB RAM and 2 vCPUs for each VM), the Rocky8 move would be a considerable cost saving and gain ten extra VMs.
> Potential Impacts. For some native code (e.g., C and C++), given Rocky8's newer GCC toolchain, it is suggested that the native code should be recompiled. This may directly impact CSS 342 and CSS 343. Additionally, some software's default versions in Rocky8 may differ from Debian. [The comparison can be found here](https://docs.google.com/spreadsheets/d/1Dk0pgFu461B05vWHVITGRvRMylhws0UbuIUF44wD_Rs/edit?usp=sharing). In order to avoid any software compatibility issues, we welcome faculty's input with testing and verification using our dedicated VMs: [csslab13.uwb.edu](http://csslab13.uwb.edu/) and [csslab14.uwb.edu](http://csslab14.uwb.edu/). These two VMs have been configured with the latest stable software version release for Rocky8. | null | {
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I only included the Neuro classes since NG911 is still a work in progress and the Domain diagram could be improved by grouping the entities into related packages. | {
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"I'm a little worried about this. First of all, the method being modified stores a bunch of GPU addresses in a struct for that purpose that is passed by reference. This in itself is fine, though one might ask why it doesn't access that struct as a member variable instead of a parameter. Then, it directly sets the `... | 2022-05-28T00:28:18 | 2022-06-06T14:18:59 | 2022-06-06T14:18:44 | CONTRIBUTOR | null | {
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Fixes the segmentation fault at the end of GPU simulations. See conversation in issue #333 for more details. | {
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"I wonder if we take away the `force_orphan: true` would the monthly script come in and wipe out the commit history for us? The point of this manual script was to not have to regenerate Doxygen files all the time. @stiber do you have a preference for what fix should be implemented? I would think removing `force_orp... | 2022-05-27T20:57:02 | 2022-06-01T21:30:44 | 2022-06-01T21:30:44 | CONTRIBUTOR | null | {
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We have two options to fix this:
- Modify the action so that it also generates the Doxygen documentation.
- Remove the `force_orphan: true` statement so that it will show as a commit with history: I believe this should leave files in gh-pages even if they don't exist in our master branch, but I am not sure. | {
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"I have a couple of observations about this:\r\n\r\n## Can we move the method to Connections?\r\n\r\nThe CPU version of it is very similar but without the downcasting. It seems to me that the CPU version can be very easily moved to the `Connections` class since it already has or can obtain the needed information fr... | 2022-05-27T19:02:03 | 2023-09-26T05:05:07 | null | CONTRIBUTOR | null | {
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} | null | A you can see in `GPUModel::updateConnections()` below (and this also presumably occurs in the CPUModel class), we take a pointer to the top-level vertex and edge classes and immediately down cast it to a neuron class. Now that we support multiple application domains, this can't be done. Probably, we need to move `updateConnections()` to the Connections class, but let's audit the design more carefully to think this through well.
https://github.com/UWB-Biocomputing/Graphitti/blob/f4fe4abaa4458fa7cdae25010299e84badd2435a/Simulator/Core/GPUModel.cu#L195-L212 | null | {
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"I was able to create the clang-tidy file using the command: $ clang-tidy -dump-config >> .clang-tidy\r\nTo use the file, I ran this command: $ clang-tidy `find . -type f \\( -iname \"*.cpp\" -or -iname \"*.h\" \\) ! -path \"./Testing/li... | 2022-05-23T00:49:11 | 2023-12-07T23:40:30 | null | CONTRIBUTOR | null | {
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"The reason Graphitti is failing to build is because `log4cplus/loggingmacros.h` is being included after `IRecoder.h` in `Simulator/Core/Model.h`:\r\n\r\n```\r\n#include \"AllVertices.h\"\r\n#include \"IRecorder.h\"\r\n#include \"Layout.h\"\r\n#include <log4cplus/loggingmacros.h>\r\n#include <memory>\r\n ```\r\n\r\... | 2022-05-16T21:39:23 | 2022-05-18T01:57:57 | 2022-05-18T01:57:54 | CONTRIBUTOR | null | {
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"Actually, I'm not sure the body of the loop can be put inside the `EventBuffer` method. That loop is actually reading the equivalent of one `EventBuffer` object for each iteration. Also, it seems that there is also a need to implement a `copyToGPU()` method. Also, from conversation with @PoojaPal2021, there is a l... | 2022-05-11T16:54:09 | 2022-12-02T18:10:35 | 2022-12-02T18:10:35 | CONTRIBUTOR | null | {
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} | null | Note: `AllIFNeurons:: allocDeviceStruct()` does allocation of all of the neuron data structures on the GPU.
Class needs at least one additional methods:
First, we definitely need something like `EventBuffer::copyFromGPU()`. This should implement the current functionality of much of `AllSpikingNeurons::copyDeviceSpikeCountsToHost()` and the body of the loop in `AllSpikingNeurons::copyDeviceSpikeHistoryToHost()`. I suggest that these two methods be merged into one (that calls `EventBuffer::copyFromGPU()`) within the `AllSpikingNeurons` class and the place that calls these two methods be changed to just call that one method. This will minimize changes to the existing code base (and require no changes to the GPU code), and it's really not possible at this point in time to further encapsulate things because all GPU side data is stored within arrays pointed to by the `allVerticesDevice` struct.
Then we need to think about `AllSpikingNeurons::clearDeviceSpikeCounts()`. At first glance it seems we need to have conditional compilation (for GPU) statements in `EventBuffer::clear()` that will call this method. The problem here is that the `EventBuffer` object doesn't know the address of the corresponding data structure on the GPU. Instead, we need to look at where the `EventBuffer` objects are cleared and where `AllSpikingNeurons::clearDeviceSpikeCounts()` is called.
I believe that we haven't yet pushed `EventBuffer` into the IZH neuron model; perhaps we need to pull that code temporarily out of the code base and roll it into an undergrad project to mirror the changes to the spiking/IF/LIF classes. | {
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"I don't think we need the 911 simulation code from the JCPenny-advanceEdges branch anymore. The model has changed significantly and made this code irrelevant."
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"We determined no longer needed."
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"first version of documentation for EventBuffer changes"
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"Merging changes for Event Buffer and impacted classes. \r\nNote: This merge might break the code at the GPU side as the implementation is incomplete."
] | 2022-05-10T17:32:09 | 2022-05-10T21:48:45 | 2022-05-10T21:44:35 | CONTRIBUTOR | null | {
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} | null | This pull request has `Event Buffer` changes( new vector based data structure to eliminate dynamic array implementation).
It also has changes in impacted Vertex classes and Recorder classes by introducing Event Buffer.
Changes are tested with Manually by taking different simulation instances and comparing the output.
```
test-medium-2.xml
test-small-911.xml
test-small.xml
test-tiny-stdp.xml
test-medium-stdp.xml
test-small-connected.xml
test-tiny.xml
```
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"@stiber and @rashwini21, hunting this bug down wasn't easy but I finally found the source of the segmentation fault. The bug is in `AllIFNeurons_d.cu` line 63:\r\n\r\n```\r\nsummationMap_ = allVerticesDevice.summationMap_;\r\n```\r\n\r\n`summationMap_` is a host pointer in AllVertices.h but it is being assigned th... | 2022-05-06T21:51:39 | 2022-06-06T14:18:44 | 2022-06-06T14:18:44 | CONTRIBUTOR | null | {
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} | null | Simulations run with the GPU version of Graphitti throw a `segmentation fault` at the very end. The simulation runs, and the results are saved normally. It segfaults after the elapsed time is printed to the console, which might indicate that the segfault is coming from a destructor somewhere. | {
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"This is addressed in PR #336 "
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"Looking at commit #348 we now have PlantUML class diagrams, but they are very flat and not human-friendly. It would be good to have PlantUML diagrams that are more like the hand-drawn block diagram at https://uwb-biocomputing.github.io/Graphitti/Developer/ClassDiagrams/hand-drawn.pdf"
] | 2022-05-06T20:03:45 | 2023-01-11T23:24:00 | 2023-01-11T23:24:00 | CONTRIBUTOR | null | {
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} | null | Right now, we have hand-drawn class diagrams, which are included as images. They were drawn in OmniGraffle on a Mac, so are not easily modifiable by anyone else and, of course, GitHub can't track changes in the source document. Let's switch to PlanUML, as with other UML diagrams, to eliminate these problems and to generate up-to-date diagrams. | {
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"node_id": "MDU6TGFiZWwyM... | open | false | null | [] | null | [] | 2022-05-03T17:38:05 | 2024-05-09T19:45:57 | null | CONTRIBUTOR | null | {
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"How can I reproduce this bug? What input file should I use for the serialized simulation run and when deserializing it?",
"I believe that there is a serialized network file available on the research machines; we can verify this at an upcoming lab meeting. Sorry that this reply is so opaque; it's rather complicat... | 2022-05-03T17:23:36 | 2025-01-22T18:55:43 | null | CONTRIBUTOR | null | {
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} | null | Deserialization should completely overwrite the connection (weight) matrix. However, if `ConnStatic`'s parameters are set to create edges randomly, then the deserialized edges will be created in addition to those edges, resulting in inconsistent edge data structures. This is caught (luckily) by [`AllEdges::createEdgeIndexMap()`](https://github.com/UWB-Biocomputing/Graphitti/blob/bf4a3e45e46c8160c0939db4039b8472c3878204/Simulator/Edges/AllEdges.cpp#L220).
Ideally, the edge data structures should be cleared out (all edges deleted) before deserialization. | null | {
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"Actually, I don't think \"build\" can be a separate workflow; not sure what I was thinking.",
"Correction: I was thinking of a workflow that just verified that the simulator could be built. If there is a way to have an action do a test build, and prevent other actions from running if the build fails, then that c... | 2022-04-28T18:59:56 | 2023-06-20T04:59:08 | null | CONTRIBUTOR | null | {
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} | null | Here is what I'm thinking:
- Build
- Unit tests
- Regression tests
The disadvantage of this is that there are two extra builds: one for the unit tests and one for the regression tests. This will add about 4 minutes total to the entire suite of tests. However, if we can condition running the unit and/or regression tests to only a subset of files (or only run the unit tests if the build passed, and only run the regression tests if the unit tests passed), then that might in aggregate still be a saving in test time (and therefore waiting time to see if tests have passed after pushing to a pull request).
And, of course, this would increase the number of badges displayed in the top-level readme, which is a plus because more badges is always better than fewer! | null | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/325 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/325/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/325/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/325/events | https://github.com/UWB-Biocomputing/Graphitti/issues/325 | 1,219,033,851 | I_kwDOEEdqD85IqPr7 | 325 | Include simulator version number and other info in Recorder output files | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/324 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/324/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/324/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/324/events | https://github.com/UWB-Biocomputing/Graphitti/issues/324 | 1,218,980,519 | I_kwDOEEdqD85IqCqn | 324 | Create a set of STDP regression tests that mirror the growth regression tests | {
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"Closed as superseded by #625 "
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