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} | null | - Simulation tested and runs on tiny, small, and medium config files. Not certain about the accuracy since I'm not familiar with running simulations.
- There still things that need to be done, for example, it only works for CPU Model and XML recorder.
- Deserialization/Serialization has not been touched or tested and is still in BGDriver for now.
- PrintParameters added as an OperationManager operation.
Closes #93, Closes #125 | {
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"I _think_ this has been taken care of and can be closed after being double-checked."
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} | null | Re-think which classes we need. It's quite possible that we pro-actively created classes that don't really make sense. On the other hand, we are not shooting for a minimal set for right now; we may choose to have a class in the hierarchy because we expect that it is likely to add multiple subclasses that can make use of it as a common parent. | {
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} | null | This is a fix that was incorporated into the BrainGrid repo in the master branch at commit [ee530847b997d3cbaaee689b9500c679699787e8](https://github.com/UWB-Biocomputing/BrainGrid/commit/ee530847b997d3cbaaee689b9500c679699787e8), but apparently not in the single-threaded-master branch. | {
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} | null | There's a demonstration implementation in the chain of responsibility manager, I think. We should discuss and document what to put in each log level. Also, I _think_ that the configuration file is a runtime file; if so, it should be moved to the runtime directory. | {
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"I _think_ this is done; just want to verify.",
"Yes, this is done.\n\nOn Thu, Apr 1, 2021 at 5:25 PM Michael Stiber ***@***.***>\nwrote:\n\n> I *think* this is done; just want to verify.\n>\n> —\n> You are receiving this because you were assigned.\n> Reply to this email directly, view it on GitHub\n> <https://gi... | 2020-08-14T19:39:41 | 2021-04-04T20:59:43 | 2021-04-04T20:59:43 | CONTRIBUTOR | null | {
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resolves #72
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"Types of tests:\r\n\r\n- Very small, no synapses (test-tiny.xml)\r\n- Very small, using ConnStatic to test basic synapse function\r\n- Small, with large initial radii, to test synapse creation from ConnGrowth\r\n- Larger, both CPU and GPU, testing ConnGrowth reasonably\r\n- Use Emily's contributions to develop CPU... | 2020-08-14T18:46:53 | 2021-08-02T03:02:18 | 2021-08-02T03:02:18 | CONTRIBUTOR | null | {
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} | null | Right now, I'm thinking that we would use test-tiny.xml (or something similar), outputting XML so that we can produce a reference simulation result and then use tools like diff to see if new results match old ones. I think this is feasible for simple simulations on the CPU. Exact reproducibility on the GPU may be more difficult, as it's possible that threads associated with the same neuron in two different simulations may get different RNG-generated noise in two different simulations. But we should be able to take a first step towards this relatively straightforwardly. | {
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"@christopherdokeefe, let's make sure to talk about this to outline what strategy to pursue. You don't need to implement that strategy, so this is just transfer of knowledge.",
"From what I understand, integration testing is the testing of links between modules, so for this project, I assume that would mean to as... | 2020-08-14T18:39:04 | 2023-09-27T06:15:56 | null | CONTRIBUTOR | null | {
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- Should we use Google test, or instead use log4cplus and automate checking its output using tools like grep and diff?
- What do we want from integration testing versus regression testing? Clearly, we can have integration tests that don't require the entire simulation to be running, while that is not the case for regression testing. | null | {
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"It appears that there's a CMake problem with the log4cplus addition."
] | 2020-08-12T19:38:51 | 2020-08-17T01:51:13 | 2020-08-16T23:42:17 | COLLABORATOR | null | {
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} | null | log4cplus version 2.0.2 added to the project under third party. This version requires CMake version 3.12 and C++ 11. This version no longer uses deprecated auto_ptr.
The only class that has it implemented is the OperationManager and there are some small changes to RunTests.cpp that must be included to initiate the log4cplus.
If this solution is acceptable we can merge then add a logger member to all other classes.
Closes #92, Closes #25 | {
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"Looks good. Ready to merge."
] | 2020-08-11T20:12:49 | 2020-08-11T23:56:27 | 2020-08-11T23:55:23 | CONTRIBUTOR | null | {
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to harmonize Simulator methods and member variable names.
resolves #87 | {
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} | null | - Parameter Manager is working and fully implemented into the project,
- 5 out of the 6 required factories are implemented and working (Input factory is missing).
- Hierarchy change: Connections owns Synapses and Layout owns Neurons.
- Smart pointers for object hierarchy ownership and factories implemented.
- Cleanup of all Connections, Layout, Synapses and Neurons classes.
- Added new operation to ParameterManager which reads the NList config files and returns a vector<int>.
**BGDriver Progress**
- Parsing command line (mostly unchanged).
- Simulator loads parameters from the configuration file.
- Simulator instantiates all simulation objects.
- OperationManager executes loadParameter operation which invokes all loadParameter methods in simulation objects.
**Closed Issues**
Closes #48, Closes #56, Closes #63, Closes #77, Closes #66
**Related Issues**
#24, #23, #93
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> Switching to C++11 built-ins for regular expressions should be straightforward. I'm sure I had some reason at the time for choosing boost over stl, but whatever the reason, it probably wasn't well-founded.
>
> The original diff for the std-to-boost conversion is here: https://github.com/etcadinfinitum/BrainGrid/commit/b09f93821b6cdefd2ff113c8963c627b5fe2a6b6#. It should be trivial to reverse engineer proper usage using the standard library; the function signatures are virtually identical. I know that some of the deleted regexes didn't work -- see line 129 and compare the new regular expression with the diff in the previous line, which originally used the same backslash convention for general character groups. (\\d is interpreted as \d, which is any of the numeric digits, for example.) At any rate, running the tests I wrote, or some derivation of them, should reveal whether changes to the regular expression library or pattern has broken expected validation behavior.
>
> Optionally, you may choose to do away with some or all of the (kind of kludgy) type validation which is done using regex. Personally, I think it is reassuring to have the simulator warn users about grabbing a particular text node which will lose information in an explicit cast (float-type text node into integer reference, for example), and it is necessary for affirming that a text node can be interpreted as numeric when a numeric value is required. | {
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- [x] Check with Janet McDaniel on formats and deadlines for any files you need to deliver
- [x] Schedule practice talk for 8/19
- [x] Develop draft of talk and poster
- [x] Get feedback from Prof. Stiber around 8/17
- [x] Do practice talk | {
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"Went over this with group."
] | 2020-07-31T20:59:50 | 2020-08-12T17:06:21 | 2020-08-12T17:06:21 | CONTRIBUTOR | null | {
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"It seems like we're leaning towards there being a directory with such files at a fixed path relative to the executable. Let's document this and make sure it is incorporated into issue #88.",
"Overlaps with issue #88 "
] | 2020-07-31T18:48:49 | 2021-04-02T00:21:28 | null | CONTRIBUTOR | null | {
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"Add a define for `TIXML_USE_STL` in the CMake build, so that `tinyxml.h` can be reverted back to its original state."
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- Added lower level classes (Connections, Layouts, Synapses, and Neurons).
- Added Recorders and Input classes (Hdf5 Recorders don't compile yet).
- All classes refactored to account for recent architecture changes (Singleton Simulator, no IModel etc.)
- Directory reorganization.
- CMake structure added to reduce redundancy.
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edited new docs
made subdir with just temporary summer of brain files
very in progress.... not complete in the slightest | {
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} | null | Things to do:
- [x] Get parameter manager working
- [x] Get simulator loading global parameters
- [x] One class hierarchy, get factory working
- [x] One class hierarchy at a time, get initialization from parameters working
- [x] Get setup working
- [x] Get shutdown working
- [ ] Get serialization/deserialization working (Needs to be moved, and need to think about how this interoperates with chain of responsibility.)
- [ ] Review simulation code organization, fix broken relationships
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- ParameterManager changed to singleton implementation
- Minor changes to ParameterManager for compilation and coding standards.
- Introduced support for boost libraries in CMake.
- Created TinyXml Library in CMake and moved it to the ThirdParty directory
- Altered the ParameterManagerTests into GoogleTest format.
- Wasn't able to change member variables to smart pointers. The objects get created every time a new file is loaded which caused the program to fail when running tests with smart pointers.
- Added the config files to the repo for testing.
Only look at the following files: ParameterManager.cpp, ParameterManager.h, ParameterManagerTests.cpp, RunAllTests.cpp and CMakeList.txt | {
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"See also #64.",
"Done \r\nhttps://github.com/UWB-Biocomputing/Graphitti/blob/416b0c42beefdcc951e2b4ec441efafa0d6e529d/docs/BGDocs/02a_installRequirements.md",
"refer to issue #47 for current updates. closing this. "
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Also, determine what needs to be updated/installed on CSS research machines. | {
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"Note that there is an example Neuron factory in [@etcadinfinitum's fork](https://github.com/etcadinfinitum/BrainGrid).",
"Also note the thoughts in #63.",
"See also #66."
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"Note that there is an example Neuron factory in [@etcadinfinitum's fork](https://github.com/etcadinfinitum/BrainGrid).",
"Also note the thoughts in #63.",
"See also #66."
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} | null | Look in Lizzy's fork in her [test directory](https://github.com/etcadinfinitum/BrainGrid/tree/parameter-refactor/Tests), especially [`tests_ParameterManager.cpp`](https://github.com/etcadinfinitum/BrainGrid/blob/parameter-refactor/Tests/tests_ParameterManager.cpp). | {
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load a XML file and query it for entries based on a known node
hierarchy. Since the parameter files in this project use
well-understood patterns, this strategy is useful for navigating
a set of parameters in an explicit, user-friendly manner.
A ParameterManager object is created by a controlling entity
(probably within an executable's main() function or some other
high-level entity). The parameter manager object contains a ptr/ref
to the XML tree, and can traverse the tree according to an XPath
provided by the object's client.
For classes which require an additional parameter file to be read
(as is the case for the existing FixedLayout class), a new
stack-scoped or heap-allocated instance of the class can be created
to parse that file as needed.
Language spec: https://www.w3.org/TR/1999/REC-xpath-19991116/
XPath tutorial: https://www.w3schools.com/xml/xpath_syntax.asp
For a syntax and usage example, see
https://github.com/etcadinfinitum/BrainGrid/blob/parameter-refactor/Tests/,
particularly the tests_ParameterManager.cpp file. | {
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"We may want to move `Utils/RNG/MersenneTwister/data/MersenneTwister.dat` into a different directory. It's not a source/build file; it's a runtime data file that is loaded to seed the main RNG. Right now, we don't really have a \"deploy\" or \"install\" element of the build, but when we do, that file needs to end u... | 2020-07-21T23:33:59 | 2020-08-11T19:14:45 | 2020-07-22T16:57:18 | COLLABORATOR | null | {
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CPU/GPU models updated and refactored, siminfo eliminated
Added Utils & Global & ThirdParty directory files from BG, included Matrix under Utils. | {
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"Do we need to add a check that we're not updating the (nonexistent) synapse from a neuron to itself in a ConnGrowth simulation? See commit [\r\nee53084](https://github.com/UWB-Biocomputing/BrainGrid/commit/ee530847b997d3cbaaee689b9500c679699787e8)",
"Do we need to [Use double precision CUDA exp() to get the iden... | 2020-07-21T00:24:33 | 2021-04-02T00:15:59 | null | CONTRIBUTOR | null | {
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"A better comparison might be [between v1.5 and v1.0](https://github.com/UWB-Biocomputing/BrainGrid/compare/v1.0...v1.5)",
"I believe that the commit we're looking for is [this](https://github.com/UWB-Biocomputing/BrainGrid/commit/6b23f46fa569a8e7452862d5e867ed5582603095).",
"I believe this is working. Ran test... | 2020-07-20T23:54:20 | 2020-08-06T19:36:29 | 2020-08-06T19:36:29 | CONTRIBUTOR | null | {
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} | null | I (@stiber) need to go through the commits since 9/6/18 (v1.0). The comparison between single-threaded-master and master is [here](https://github.com/UWB-Biocomputing/BrainGrid/compare/single-threaded-master...synapse_weight_serialization_modification). At the very least,
As I identify commits, I will note them in comments below. | {
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- Wrote unit tests for SynapseIndexMap.
- Applied coding standard and comment adjustments. | {
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- Implemented the change to the instance to be stored as a local variable in OperationManger::getInstance(). This seemed like the better option as the it simplifies code and is thread safe.
- Moved files to correct directories to remove the ChainOfOperation directory.
- Added some style changes specified in the google c++ guidelines, the changes are not final as some decisions still need to be made.
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"Also incorporate [coding conventions](https://github.com/UWB-Biocomputing/BrainGrid/blob/master/CONTRIBUTING.md#coding-conventions) from the BG repo.",
"@torisalvatore this is written, right? Just needs to be linked in?",
"At least part of this is done under https://github.com/UWB-Biocomputing/Graphitti/tree/m... | 2020-07-11T18:40:23 | 2023-09-30T00:43:25 | 2023-09-30T00:43:24 | CONTRIBUTOR | null | {
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} | null | See issue #31 for some examples. Will include picayune details. Big things would include:
- Avoid raw pointers whenever possible, instead either avoiding pointers altogether (using reference, etc.) or using smart pointers.
- Guard against problems by using things like marking operations `= delete`.
- Rather than dynamically allocated arrays, we will use `vector`s, which we will set to a particular size. We can always access the array within the `vector` to do numerical operations, loops, etc.
- Many more things. I believe that Google has a public style guide, which we can liberally steal from. | {
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} | null | Here are some items that likely would be good to take care of:
- We need to decide if we should stick with a member variable for the pointer to the instance, or should go with a static local variable in `getInstance()`.
- If the former, we should change it from a raw pointer to a `shared_pointer`, and have `getInstance()` return a `weak_pointer`. This would first be in [`OperationManager.h`](https://github.com/UWB-Biocomputing/SummerOfBrain/blob/43d51fd7a59fbe9a210b0d25031091026d483f65/Core/OperationManager.h#L43). There would no longer need to be an initialization at the top level in `OperationManager.cpp`, since the default constructor for a smart pointer initializes it. The `instance` pointer can just be checked as described at [cplusplus.com](http://www.cplusplus.com/reference/memory/unique_ptr/operator%20bool/) to see if the object has been created.
- If the latter (see [this stack overflow article](https://stackoverflow.com/questions/1008019/c-singleton-design-pattern/1008289#1008289) for a good example), then `getInstance()` can return a reference. This may have advantages, in terms of being thread safe, which would be useful as part of the singleton `Simulator` class.
- Make the copy constructor and assignment operator deleted (see the stack overflow article).
Sorry to be anal about these, but we should spend some time early on establishing code style standards — something I neglected to do at the beginning.
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"The repository had commits which tracked changes to explicitly ignored CMake files. These have also been removed, since they are machine-specific and get regenerated at compile time.\r\n\r\nWith these changes, on my machine, only one file has tracked changes after building and running tests; it is a cmake file und... | 2020-07-10T19:03:18 | 2020-07-11T18:56:49 | 2020-07-11T18:56:44 | COLLABORATOR | null | {
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use cases (and current problematic directories). | {
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"Let's incorporate this into a code review 7/8 @ 5PM.",
"Let's go over this at our next meeting. I'd like to close off all of the items from sprint 2.",
"Sounds good!\n\nOn Sat, Jul 11, 2020 at 11:52 AM Michael Stiber <notifications@github.com>\nwrote:\n\n> Let's go over this at our next meeting. I'd like to cl... | 2020-07-07T18:32:41 | 2020-07-20T23:16:39 | 2020-07-20T23:14:46 | COLLABORATOR | null | {
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} | null | @torisalvatore I'd like to involve you, too. Seems like only one person can be assigned to review and one person is the primary assignee. Not clear when that changed.
First, however, have a good weekend; we can deal with this next week. | {
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"We're using Google's test framework? Anything we need to write up relevant to issue #32? Let's talk about this at the next meeting."
] | 2020-06-24T21:53:50 | 2020-07-20T23:55:48 | 2020-07-20T23:55:48 | CONTRIBUTOR | null | {
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"See #92 for a possible pointer."
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/24 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/24/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/24/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/24/events | https://github.com/UWB-Biocomputing/Graphitti/issues/24 | 644,943,368 | MDU6SXNzdWU2NDQ5NDMzNjg= | 24 | Switch from dynamic arrays to <valarray> or <vector> | {
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"For the record, [here](https://hackernoon.com/c-investigation-arrays-vs-vectors-e9ba864468b6) is an interesting page that compares primitive array and vector access performance with different levels of optimization in the compilation.\r\n\r\nThis probably requires us to address issue #159, so that we can compile w... | 2020-06-24T20:41:14 | 2023-04-18T20:14:46 | 2023-04-18T20:14:46 | CONTRIBUTOR | null | {
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"Some references:\r\n\r\n- [Microsoft VS C++ docs](https://docs.microsoft.com/en-us/cpp/cpp/smart-pointers-modern-cpp?view=vs-2019)\r\n- [GeeksforGeeks](https://www.geeksforgeeks.org/smart-pointers-cpp/)\r\n- [Modernes C++](https://www.modernescpp.com/index.php/c-core-guidelines-rules-to-smart-pointers)\r\n- [Effec... | 2020-06-24T20:39:17 | 2023-04-10T17:18:05 | 2023-04-10T17:18:05 | CONTRIBUTOR | null | {
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} | null | This will hopefully force us to decide what objects own what data and are responsible for managing it, and which are merely accessing stuff. It will also enable easier serialization using cereal, for the future.
Connects to #24 and #129 and may not be necessary once that is done (all that will be left is use of pointers to support late binding). | {
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"On 6/24, we decided on a simple dependency injection approach. We will merge the contents of SimulationInfo into Simulator, and will pass Simulator by reference to the constructors of all created objects so that they can retain a reference to the Simulator. We will implement accessors for these data members (which... | 2020-06-24T20:32:05 | 2020-07-20T23:55:36 | 2020-07-20T23:55:36 | CONTRIBUTOR | null | {
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} | null | Right now, we have an issue of "opaque, fat" interfaces, where we have objects like SimulationInfo/ClusterInfo that we pass everywhere, to avoid accessing information from global variables. Most often, a method receives this as a parameter either so it can pass it on to another method (without using anything in it directly) or just to access one or two items. This gives the illusion of good interfaces, but in reality there's no way to look at the parameter list for a method to know what it uses anyway. So, here are some ideas and links to start thinking about ideas to address this:
- These "global" objects should be implemented using [singleton patterns](https://sourcemaking.com/design_patterns/singleton).
- A [dependency injection](http://en.wikipedia.org/wiki/Dependency_injection) framework might be a better way to implement this. See also https://www.fluentcpp.com/2019/06/07/write-your-own-dependency-injection-container/
- Another approach might be a [registry approach](https://codereview.stackexchange.com/questions/186730/registry-a-global-store-for-things).
A set of books that looks like it might be promising are the [_Large-scale C++ Software Design_](https://www.google.com/books/edition/_/cw3BDwAAQBAJ?hl=en&gbpv=0) books by John Lakos. | {
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"I believe this is done; just want to verify before closing.",
"We can set a upper limit in the parameters now, but we still don't have it implemented for inhibitory neurons. Given that most models implement it just for excitatory neurons, this isn't a very major thing. I did find papers about inhibitory implemen... | 2020-05-22T15:48:22 | 2021-06-21T16:55:02 | 2021-06-21T16:55:02 | CONTRIBUTOR | null | {
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1. The change from each pair of spikes seems too large.
2. There is no upper limit on the amount of strength increase; an arbitrary hard limit is used instead.
3. There is no model for inhibitory synapses.
We need to do more research into STDP models to see how to address these shortcomings.
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"We should replace this issue with a new one, or close it, depending on exactly what the strategy was for the 2021 implementation.",
"We made a different weightModification function to enable us to add different implementations. We should definitely modify it depending on the direction of the lab and what our vis... | 2020-05-22T15:45:09 | 2021-06-21T20:51:55 | 2021-06-21T20:51:54 | CONTRIBUTOR | null | {
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} | null | Right now, the STDP synapse classes combine "vanilla" STDP and a model in froemke-dan02 that takes into account sequential dependency among spike pairs. We should split these into two classes. Ideally, we should be able to use a "vanilla" method that computes individual spike pair effects for both classes (by inheritance in the case of the froemke-dan model), but then override the actual weight change operation in the latter.
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} | null | Given that, from the point of view of time-step by time-step updates, spikes occur rarely (generally, once every several thousand time steps), it may be the case that a large fraction of synapses have the PSR (postsynaptic response) decayed effectively to zero much of the time. There may be a significant performance improvement available if we can, in the update synapses code, load only the minimum data to determine that a synapse doesn't need updating (because no spike is arriving this time step and its PSR is effectively zero) and then just return, instead of loading all of the data to do the full PSR update.
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"Deferred into summer to audit code in detail, particularly about clarity and branch prediction/thread divergence.",
"Probably fixed with new STDP code; something to check during merge."
] | 2020-04-28T18:34:17 | 2021-06-21T20:52:14 | 2021-06-21T20:52:14 | CONTRIBUTOR | null | {
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} | null | In the literature, STDP models are described so that they match experiments where pre and post synaptic spike trains are accumulated over some time period and then, after the fact, those spike trains are used to compute a change in synaptic strength. In that computation, each (pre, post) or (post, pre) spike pair is used once.
In our simulations, we have an ongoing simulation and are trying to compute changes in synaptic strength "on the fly" as each pair occurs. This means that we should only modify a synaptic strength right after a pre or post spike, looking retrospectively back something like 100ms to find preceding post or pre spikes. **Each pair of spikes should only be used once to modify the synaptic weight.**
I'm not convinced that that is what's happening in the current code. It certainly seems quite complex and isn't clearly documented. At the least, it should be gone through carefully to determine if it's doing what is indicated above. @eeemily17 is preparing a document that clearly describes the applicable mathematical models. Even better would be to rewrite the code to improve clarity and, ideally, see if branch prediction/thread divergence can be improved.
This is written against the CPU implementation on the single-threaded simulator branch, but any changes need to appear for the GPU and also on the multi-cluster (main) branch.
https://github.com/UWB-Biocomputing/BrainGrid/blob/4f4e674e3a673fcc52eeaaabc92e8f5d5b9bc890/Synapses/AllSTDPSynapses.cpp#L285
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"Which version of source code is this? At the latest master branch, all *.cu files are obsolete under Synapses and Neurons directory, and ***Device() functions are now unified with CUDA_CALLABLE class member function in Neuron and Synapses.",
"This is the serialization_plus_version1_0 branch."
] | 2020-04-23T19:13:47 | 2025-03-06T22:52:01 | null | CONTRIBUTOR | null | {
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} | null | Subclasses of ```AllSpikingSynapses``` may at times want to re-use the synapse advance logic of ```AllSpikingSynapses```. By making this logic part of a kernel function, ```advanceSpikingSynapsesDevice()```, it's not reusable by any other kernel on the GPU. So, for example, if an STDP synapse advance kernel wants to do the generic update, it has to duplicate the logic from ```advanceSpikingSynapsesDevice()```. Pretty much any synapse subclass will want to do the updating encapsulated by ```advanceSpikingSynapsesDevice()```. I suggest we pull that logic out as a separate device function so that it can be called where needed.
https://github.com/UWB-Biocomputing/BrainGrid/blob/4f4e674e3a673fcc52eeaaabc92e8f5d5b9bc890/Synapses/AllSynapsesDeviceFuncs_d.cu#L203-L225 | null | {
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} | null | You'll see in the code below that it appears that each synapse gets a copy of the set of STDP parameters. However, the value assigned is the same for every neuron. Unless we have a plan to incorporate variability in these parameters, there is no need for this and there can just be a set of ordinary member variables to hold these values for all synapses (and, for the GPU, these perhaps don't need to be in regular global memory).
https://github.com/UWB-Biocomputing/BrainGrid/blob/4f4e674e3a673fcc52eeaaabc92e8f5d5b9bc890/Synapses/AllSTDPSynapses.cpp#L255-L274 | null | {
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"I believe this has been addressed and/or will be addressed when the STDP code is merged into the master branch.",
"Yes. All the parameters for STDP are now read from the parameter file"
] | 2020-04-16T19:29:31 | 2021-04-09T15:34:47 | 2021-04-09T15:34:47 | CONTRIBUTOR | null | {
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https://github.com/UWB-Biocomputing/BrainGrid/blob/4f4e674e3a673fcc52eeaaabc92e8f5d5b9bc890/Synapses/AllSTDPSynapses.cpp#L258-L274 | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/60 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/60/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/60/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/60/events | https://github.com/UWB-Biocomputing/Graphitti/issues/60 | 665,636,822 | MDU6SXNzdWU2NjU2MzY4MjI= | 60 | Change to weight in STDP models needs to take into account sign of weight | {
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"How about fix it like this? \r\n``\r\n if(W >= 0) { \r\n W += epost * epre * dw;\r\n } else {\r\n W -= epost * epre * dw;\r\n }\r\n``\r\nIt can apply to both CPU and GPU.",
"Each synapse has a synapse type (II, IE, EI, and EE). This is dependent on the relation between pre and post neurons... | 2020-04-16T19:28:04 | 2021-06-21T20:51:45 | 2021-06-21T20:51:45 | CONTRIBUTOR | null | {
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} | null | The STDP model in froemke-dan02 assumes that weights are unsigned and therefore that changes to the weights can just be added. However, we incorporate the excitatory/inhibitory nature of a synapse into the sign of the weight. Bottom line: depending on the sign of the weight, we need to either add or subtract the change. The STL function `std::copysign()` will work work on the CPU, but maybe not on the GPU, where we might need `(W > 0) - (W < 0)`.
https://github.com/UWB-Biocomputing/BrainGrid/blob/4f4e674e3a673fcc52eeaaabc92e8f5d5b9bc890/Synapses/AllSTDPSynapses.cpp#L490
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/59 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/59/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/59/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/59/events | https://github.com/UWB-Biocomputing/Graphitti/issues/59 | 665,636,797 | MDU6SXNzdWU2NjU2MzY3OTc= | 59 | STDP model needs more detailed research | {
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"AllSynapses::SYNAPSE_STRENGTH_ADJUSTMENT is a dimensionless parameter that is used to convert the overlapping area of two neurons to synapses strength. So it only makes sense in using growth model, and this value should be defined in growth model. (not in synapse)\r\nIn the STDP model, the scaling factor Aneg and ... | 2020-04-16T19:20:50 | 2021-06-21T20:52:05 | 2021-06-21T20:52:05 | CONTRIBUTOR | null | {
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} | null | As can be seen, the computed delta w (see froemke-dan02) is added to the weight. However, this delta w is not scaled in the same range as W, which is generally scaled down to a small value. I suggest that it be scaled like W is in ConnGrowth, using `AllSynapses::SYNAPSE_STRENGTH_ADJUSTMENT`.
https://github.com/UWB-Biocomputing/BrainGrid/blob/4f4e674e3a673fcc52eeaaabc92e8f5d5b9bc890/Synapses/AllSTDPSynapses.cpp#L490
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} | null | This method returns the global simulation time step for the spike in question. Documentation for this method needs more precision and clarity.
https://github.com/UWB-Biocomputing/BrainGrid/blob/4f4e674e3a673fcc52eeaaabc92e8f5d5b9bc890/Neurons/AllSpikingNeurons.cpp#L179 | {
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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/52 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/52/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/52/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/52/events | https://github.com/UWB-Biocomputing/Graphitti/issues/52 | 665,636,599 | MDU6SXNzdWU2NjU2MzY1OTk= | 52 | Neuron max firing rate limit can break non-ConnGrowth simulations | {
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"Maximum firing rate used for computing outgrowth is stored in m_growth.maxRate which is set at ConnGrowth::readParameters().\n\nThe maximum firing rate in sim_info->maxFiringRate is used to allocate spiking buffer for recording .\n\n> 2020/04/09 12:03、Michael Stiber <notifications@github.com>のメール:\n> \n> \n> Neuro... | 2020-04-09T19:02:16 | 2020-08-06T00:49:00 | null | CONTRIBUTOR | null | {
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So, we can just up the max rate for those simulations and leave the line of code below alone. However, perhaps it would be better to set things up so that, if we set the max rate parameter to zero, then the check below just isn't done.
https://github.com/UWB-Biocomputing/BrainGrid/blob/c6c95eb63655ae73b32cd784f3853fd73bc3c9e9/Neurons/AllSpikingNeurons.cpp#L114 | null | {
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"It seems that issue 281 is handled. Since #67 is already a separate issue in this repo, this issue can be closed."
] | 2020-03-31T17:41:16 | 2020-08-17T16:51:00 | 2020-08-17T16:50:59 | CONTRIBUTOR | null | {
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} | null | ## *What kind* of issue is this?
* [X] Bug report
* [ ] Feature request
* [ ] Question not answered in documentation
* [ ] Cleanup needed
See issues UWB-Biocomputing/BrainGrid#281 and UWB-Biocomputing/SummerOfBrain#67; this applies here, too.
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"Lines 369 and 371 also need to be moved up above the new test.\r\n\r\n```C++\r\n BGFLOAT lenAB2 = (*layout->dist2)(i, j); \r\n BGFLOAT r12 = r1 * r1; \r\n BGFLOAT r22 = r2 * r2; \r\n```",
"Can add the attached information to the documentation.\r\n\r\n![Screen Shot 2020-03-31 at 10 35 14 AM](https://user-images.g... | 2020-03-31T17:33:55 | 2021-08-05T17:40:37 | 2021-08-05T17:40:36 | CONTRIBUTOR | null | {
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} | null | A problem arises due to lack of precision in the computation of area of overlap, when the cosine of a chord angle is computed, erroneously, to be greater than 1. We should reorganize the computation to catch this edge case (inside the else on line 367):
```C++
BGFLOAT cosCBA = (r22 + lenAB2 - r12) / (2.0 * r2 * lenAB);
BGFLOAT cosCAB = (r12 + lenAB2 - r22) / (2.0 * r1 * lenAB);
if (fabs(cosCBA) >= 1.0 || fabs(cosCAB) >= 1.0) {
(*area)(i, j) = 0.0;
} else {
// The rest of the existing computation goes here
```
https://github.com/UWB-Biocomputing/BrainGrid/blob/90cac03e8c1ab4472aacc40ab05962c9334fa2ae/Connections/ConnGrowth.cpp#L368-L381
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"Actually, if we make sure that we set synaptic weights to zero if a synapse doesn't exist, then we can do away with the in_use flag for each synapse and use the weight instead.",
"From conversation with Fumitaka, this line can be changed to \"<=0\". It may be the case that the overlap computation can't produce a... | 2020-02-20T20:34:47 | 2020-08-17T16:39:47 | 2020-08-17T16:39:47 | CONTRIBUTOR | null | {
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* [X] Bug report
* [ ] Feature request
* [ ] Question not answered in documentation
* [X] Cleanup needed
<!-- Make sure you use appropriate labels for this; don't manually set labels that start with a numeral! -->
This *might* be a source of potential bugs. On about line 436 of ConnGrowth.cpp, there is a test to determine if a synapse should be deleted. This is based on whether the newly computed area of overlap is less than zero. A couple questions:
1. Is this even possible? Can the area of overlap computation ever produce a value less than zero?
2. Why not delete synapses with area of overlap equal to zero? One supposes that there's no harm, during the simulation, to allow synapses with weights of zero to continue to exist; they will have no effect (except in terms of compute time).
Zero weight synapses seems like it isn't a problem for serialization/deserialization. We only recreate synapses with non-zero weights. What isn't clear is whether deleting synapses with a weight of zero will cause problems in the simulation. Perhaps that hasn't been debugged, and that's why this line 436 is the way it is?
## *What* is affected by this?
<!-- Ex. simulator, workbench, performance, correctness, file(s) -->
## *How* do we replicate the issue/how would it work?
<!-- Please be specific as possible. Use dashes (-) or numbers (1.) to create a list of steps -->
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"See also issue UWB-Biocomputing/SummerOfBrain#50 ",
"This should be replaced with an issue for each kind of file that is opened, which right now means a test for the recorder (data) output file and the serialization output file.",
"PR #261 adds result file access check before simulation.\r\nPR #482 adds serial... | 2020-02-14T20:26:46 | 2023-08-10T17:52:32 | 2023-08-10T17:52:32 | CONTRIBUTOR | null | {
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## *What* is affected by this?
<!-- Ex. simulator, workbench, performance, correctness, file(s) -->
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"Here are the common operations provided by simulation entities:\r\n\r\n- retrieveParameters()\r\n- allocateCPUMemory()\r\n- allocateGPUMemory()\r\n- initializeState()\r\n- copyToGPU()\r\n- copyFromGPU()\r\n- deallocateGPUMemory()\r\n- deallocateCPUMemory()\r\n- shutdown()\r\n\r\nAnd maybe serialization/deserializa... | 2019-12-17T18:30:02 | 2020-07-16T03:18:17 | 2020-07-16T03:18:17 | CONTRIBUTOR | null | {
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* [ ] Feature request
* [ ] Question not answered in documentation
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<!-- Make sure you use appropriate labels for this; don't manually set labels that start with a numeral! -->
Right now, we have a high degree of nesting of objects in other objects, which means that operations done at a high level, for example from main(), must be passed down a long chain of method calls to reach the object that can actually perform the operation. We need to fix this.
## *What* is affected by this?
<!-- Ex. simulator, workbench, performance, correctness, file(s) -->
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"As of now, we have a stopgap measure to \"manually\" copy stuff back from the GPU. We need to re-do the top-level \"finish\" operation to split it in two:\n\n1. Copy everything into locations to be saved, if desired.\n2. Clean up memory, etc.",
"This should be handled by chain of responsibility. Given that it in... | 2019-12-05T20:38:59 | 2024-05-06T16:47:56 | null | CONTRIBUTOR | null | {
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} | null | ## *What kind* of issue is this?
* [ ] Bug report
* [ ] Feature request
* [ ] Question not answered in documentation
* [X] Cleanup needed
<!-- Make sure you use appropriate labels for this; don't manually set labels that start with a numeral! -->
Right now, simulator::finish() copies information back from the GPU to the CPU, frees memory on the GPU, and also triggers deletion of some CPU-side objects. We should separate the last of those three into a separate method, so we have one method that copies everything back from the GPU and frees the GPU storage (or maybe that should even be two methods) and a method that deletes CPU-side objects. In fact, maybe we can move all of the deletion of CPU-side stuff to destructors, which would accomplish that.
## *What* is affected by this?
<!-- Ex. simulator, workbench, performance, correctness, file(s) -->
## *How* do we replicate the issue/how would it work?
<!-- Please be specific as possible. Use dashes (-) or numbers (1.) to create a list of steps -->
## Expected behavior (i.e. solution or outline of what it would look like)
<!-- What should have happened/should happen? -->
## Other Comments
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* [ ] Bug report
* [ ] Feature request
* [ ] Question not answered in documentation
* [X] Cleanup needed
<!-- Make sure you use appropriate labels for this; don't manually set labels that start with a numeral! -->
In both code and parameter files.
###Code
* SimulationInfo: maxSteps -> numEpochs
* SimulationInfo: currentStep -> currentEpoch
* Simulator.cpp::simulate(): currentStep -> currentEpoch
* SimulationInfo: resultOutputFileName -> resultFileName
* SimulationInfo: resultInputFileName -> parameterFileName
* SimulationInfo: stimulusInputFileName -> stimulusFileName
###Parameter file
* numSims -> numEpochs
* Tsim -> epochDuration
## *What* is affected by this?
<!-- Ex. simulator, workbench, performance, correctness, file(s) -->
## *How* do we replicate the issue/how would it work?
<!-- Please be specific as possible. Use dashes (-) or numbers (1.) to create a list of steps -->
## Expected behavior (i.e. solution or outline of what it would look like)
<!-- What should have happened/should happen? -->
## Other Comments
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} | [] | 2019-07-08T19:49:11 | 2020-08-19T16:42:04 | 2020-08-19T16:42:04 | CONTRIBUTOR | null | {
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} | null | ## *What kind* of issue is this?
* [ ] Bug report
* [ ] Feature request
* [ ] Question not answered in documentation
* [X] Cleanup needed
<!-- Make sure you use appropriate labels for this; don't manually set labels that start with a numeral! -->
Everything is now inherently multi-threaded (even if the number of threads is 1). We really mean, in this case, simulation thread(s) that run on the CPU.
## *What* is affected by this?
<!-- Ex. simulator, workbench, performance, correctness, file(s) -->
## *How* do we replicate the issue/how would it work?
<!-- Please be specific as possible. Use dashes (-) or numbers (1.) to create a list of steps -->
## Expected behavior (i.e. solution or outline of what it would look like)
<!-- What should have happened/should happen? -->
## Other Comments
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"I think this is done/moot; just want someone to look at it before closing.",
"Yeah, I don't think this is needed. ClusterInfo only exists in the old BG repo."
] | 2019-06-07T21:29:14 | 2021-04-04T20:59:59 | 2021-04-04T20:59:59 | CONTRIBUTOR | null | {
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} | null | ClusterInfo contains per-cluster data, rather than data global to all clusters. So, there's no need for this extra class; its contents can become part of Cluster.
## *What* is affected by this?
<!-- Ex. simulator, workbench, performance, correctness, file(s) -->
simulator
## *How* do we replicate the issue/how would it work?
<!-- Please be specific as possible. Use dashes (-) or numbers (1.) to create a list of steps -->
## Expected behavior (i.e. solution or outline of what it would look like)
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"It seems now that it takes much longer to start up a CUDA program, apparently due to the need to translate NVIDIA's intermediate CUDA code into the code for a particular device. This can be sped up by producing the right compilation command line. We can run code ahead of time to figure out the right command line f... | 2019-05-20T18:19:00 | 2021-04-04T21:05:29 | 2021-04-04T21:05:28 | CONTRIBUTOR | null | {
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* [ ] Bug report
* [ ] Feature request
* [ ] Question not answered in documentation
* [X] Cleanup needed
<!-- Make sure you use appropriate labels for this; don't manually set labels that start with a numeral! -->
## *What* is affected by this?
<!-- Ex. simulator, workbench, performance, correctness, file(s) -->
Affects simulator. Currently, there is a CXX variable for g++. We should add a CXX_cuda variable so we can set the CUDA compiler. Then, the rules at the bottom of the Makefile should use CXX_cuda, instead of having "nvcc" hard-coded.
## *How* do we replicate the issue/how would it work?
<!-- Please be specific as possible. Use dashes (-) or numbers (1.) to create a list of steps -->
## Expected behavior (i.e. solution or outline of what it would look like)
<!-- What should have happened/should happen? -->
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"See also issue UWB-Biocomputing/SummerOfBrain#63"
] | 2019-02-06T20:11:53 | 2020-08-11T01:12:57 | 2020-08-11T01:12:57 | CONTRIBUTOR | null | {
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* [ ] Bug report
* [ ] Feature request
* [ ] Question not answered in documentation
* [X] Cleanup needed
<!-- Make sure you use appropriate labels for this; don't manually set labels that start with a numeral! -->
So, a few things about this class to look into:
1. Is the class name the best name to use for a factory class?
2. This is actually a set of four factory classes; will that be a problem as we refactor parameter reading?
3. This also implements a singleton pattern, using the static get() method. Is this the "classic" pattern implementation approach?
4. The code that registers the available neuron, synapse, connection, and layout classes is in the FClassOfCategory constructor. It would probably be better if this were in the classes that might be instantiated, to establish a good pattern for additional ones, to avoid the need for others to modify the factory, and to be consistent with our plans for registering parameters to a parameter reading class.
5. The createX() methods all read the name of the class to create and then call a createXWithName() method to do the instantiation. The class name reading needs to be moved into the "phase 1" parameter reading method.
6. The readParameters() method appears to be reading all of the instantiated classes' parameters, via the VisitEnter() method. This is the top-level core of the "phase 2" (model component instance) parameter reading code.
## *What* is affected by this?
<!-- Ex. simulator, workbench, performance, correctness, file(s) -->
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"Overlaps with issue #51 "
] | 2018-12-03T20:50:21 | 2023-04-12T18:07:20 | 2021-10-29T19:10:06 | CONTRIBUTOR | null | {
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} | null | When the simulator is run, if it can't create the output file ("stateOutputFileName", from config file) at the end of thew simulation, it just terminates without any error message, leaving the reason why there's no output file a mystery. It at least should produce an error message. Even better would be for it to check at startup that it can create the file, terminating with a useful error message right away (rather than after several day's of chugging along).
## *What* is affected by this?
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Simulator
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"This may be done. Since we'll be working to merge the new STDP synapse code into the master branch, web can check this as that is done.",
"May already by done; need to check.",
"I renamed some of them but not all. I think they might have been renamed during the refactoring. We can check.\r\n"
] | 2018-07-24T21:32:25 | 2021-04-13T15:06:06 | 2021-04-13T15:06:06 | CONTRIBUTOR | null | {
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} | null | Method names are *ad hoc*. Let's make their names clearer, indicate if they apply to single synapses (class name implies all synapses, so no need to explicitly write that).
## *What* is affected by this?
<!-- Ex. simulator, workbench, performance, correctness, file(s) -->
## *How* do we replicate the issue/how would it work?
<!-- Please be specific as possible. Use dashes (-) or numbers (1.) to create a list of steps -->
## Expected behavior (i.e. solution or outline of what it would look like)
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"Let's verify that all code at the end of sprint 5 is consistent with this, then reschedule this to again be examined at the end of sprint 6. Thereafter, we'll be done moving code from the BG repo and this will all be incorporated into our coding standards.",
"Can we close this issue? ",
"Good question. There i... | 2018-07-11T00:11:15 | 2023-04-18T20:15:02 | 2023-04-18T20:15:02 | CONTRIBUTOR | null | {
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} | null | See issue UWB-Biocomputing/BrainGrid#232 to see the bug aspect of this. Currently, the Makefile is set to compile code using the C++98 standard. There is a problem with initialization of static const member variables, however. Also, generally, there can be some code cleanup and modernization (that might also have a small positive impact on performance). This is a worthwhile project.
## *What* is affected by this?
<!-- Ex. simulator, workbench, performance, correctness, file(s) -->
Simulator
## *How* do we replicate the issue/how would it work?
<!-- Please be specific as possible. Use dashes (-) or numbers (1.) to create a list of steps -->
## Expected behavior (i.e. solution or outline of what it would look like)
<!-- What should have happened/should happen? -->
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"Dependencies in \"pom.xml\" in the Maven project for the Workbench. Next step is to go through elements one by one to find out what the libraries are.\n<dependency>\n <groupId>commons-codec</groupId>\n <artifactId>commons-codec</artifactId>\n <version>1.6</version>\n </depen... | 2017-11-15T19:21:46 | 2022-11-10T16:53:50 | null | CONTRIBUTOR | null | {
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"Depends on issue UWB-Biocomputing/BrainGrid#208",
"This is related to issues #135, #96, and #88 "
] | 2017-10-13T15:39:40 | 2021-04-02T00:47:16 | null | CONTRIBUTOR | null | {
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This is the format used by the Allen Insitute, among others. It's being put forward as a standard for neuroscience data exchange and archiving.
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"See issue UWB-Biocomputing/BrainGrid#139 for in-depth information about synapse type lookups and threads.",
"Merging in issue UWB-Biocomputing/BrainGrid#195 and closing it. Here was the info from it:\n\nSynapses can have a variety of parameters, such as time constant (PSP decay), delay, etc. Right now, this is p... | 2017-06-27T21:37:09 | 2025-03-12T00:44:37 | null | CONTRIBUTOR | null | {
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} | null | Right now, we attach attributes such as "excitatory" or "inhibitory", etc. to the synapse, which is the "correct" way to do things. However, this doesn't work for the Izhikevich model, because there are some neuron parameters that vary by type. Right now, we encode this information in the Layout. We should think through how to deal with this in the long run.
See segundo86, figure 22 for starting point for many different synapse (actually, PSP) types. Need to do a little research about whether neurons can actually have different synapse types.
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This will require some thought, because we want it to be efficient on both the CPU and the GPU.
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"We should at least be able to add a check in the various load parameter functions that validates neuron IDs against the total number of neurons. This should leverage log4cplus."
] | 2017-05-24T18:01:01 | 2021-04-02T00:18:44 | null | CONTRIBUTOR | null | {
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} | null | Right now, the factory class's constructor has a bunch of calls to register the various types of neurons, etc. I think that it would be simpler conceptually if the registerX() calls were made from the neuron, etc. classes. That way, there would be a very clear implementation pattern for a new class, and no need to modify other code (like the factory class). Perhaps this would require a static method for each of those classes, plus a mechanism to trigger all of those static methods at program load time? I believe I have some musty old code that demonstrates this, in SourceVersions.
[SourceVersions.zip](https://github.com/UWB-Biocomputing/BrainGrid/files/974216/SourceVersions.zip)
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"It's likely that this is already done; need to check with team.",
"This is already done; right?",
"[x@x Simulator] grep -R saveData\r\nCore/Simulator.h: void saveData() const; /// Writes simulation results to an output destination.\r\nCore/Simulator.cpp:void Simulator::saveData() const {\r\nCore/Simulator.cp... | 2017-02-15T18:36:57 | 2021-07-26T18:47:53 | 2021-07-26T18:47:53 | CONTRIBUTOR | null | {
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"Would be better to add 'm_' prefix, like 'm_varname', for member variables.",
"Agreed. This is a good cleanup for me to do this quarter.",
"Is this moot?",
"I think Chris changed the variable names and I removed some of the extra this's. "
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"There are 3 types of data: global to all neurons/synapses, depend on neurons/synapses type, and individual. ",
"Ideally workbench (macro language to identify data structure for workbench) can identify the type of data (constant, type dependent, and individual), and we will provide some common framework to alloca... | 2016-12-16T19:51:29 | 2021-04-04T21:10:23 | null | CONTRIBUTOR | null | {
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"We probably need to call cudaDeviceSynchronize every time to measure performance of kernel functions. Good place to call the cudaDeviceSynchronize is at the first line of cudaLapTime. ",
"Will do, at the same time that I investigate why raiju startup takes so long.",
"And I should add timers to compute times f... | 2016-12-13T18:50:01 | 2021-04-02T00:38:24 | null | CONTRIBUTOR | null | {
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