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"Same as #199"
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- [ ] Create test config files
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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
resolves #74 | {
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"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 ... | null | {
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"It appears that there's a CMake problem with the log4cplus addition."
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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 ... | {
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to harmonize Simulator methods and member variable names.
resolves #87 | {
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- 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.
- Cle... | {
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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 ... | {
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} | null | - [x] Go to [CSS 497 website](http://courses.washington.edu/css497/) to see about the poster and presentation
- [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 ... | {
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"Went over this with group."
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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 "
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- 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.)
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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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- [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/deserializati... | {
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- Introduced support for boost libraries in CMake.
- Created TinyXml Library in CMake and moved it to the ThirdParty directory
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"See also #64.",
"Done \r\nhttps://github.com/UWB-Biocomputing/Graphitti/blob/416b0c42beefdcc951e2b4ec441efafa0d6e529d/docs/BGDocs/02a_installRequirements.md",
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Also, determine what needs to be updated/installed on CSS research machines. | {
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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 ... | {
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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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As I identify commits, I will note them in ... | {
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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... | {
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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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- 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 d... | {
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- 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 `getInst... | {
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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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First, however, have a good weekend; we can deal with this next week. | {
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"@christopherdokeefe @torisalvatore Let's get in the habit of doing formal reviews of pull requests before merging them. This will allow us to discuss commenting styles and small-scale coding matters. I would expect that, as the summer progresses, such reviews will become very quick.\r\n\r\nAs a side effect, this w... | 2020-07-02T21:29:50 | 2020-07-10T20:38:56 | 2020-07-02T21:30:37 | COLLABORATOR | null | {
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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."
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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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Connects to #24 and #129 and may not be necessary once that is done (all that will be left is use of poin... | {
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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 mod... | {
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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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"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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"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... | 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 ... | 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... | {
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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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"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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https://github.com/UWB-B... | {
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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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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/73 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/73/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/73/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/73/events | https://github.com/UWB-Biocomputing/Graphitti/issues/73 | 665,638,587 | MDU6SXNzdWU2NjU2Mzg1ODc= | 73 | Need to fix edge cases in most recent master branch commit | {
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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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```C++
BGFLOAT cosCBA = (r22 + lenAB2 - r12) / (2.0 * r2 * len... | {
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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 ConnGr... | {
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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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"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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* [ ] Bug report
* [ ] Feature request
* [ ] Question not answered in documentation
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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.",
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In both code and parameter files.
###Code
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* [ ] Bug report
* [ ] Feature request
* [ ] Question not answered in documentation
* [X] Cleanup needed
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Everything is now inherently multi-threaded (even if the number of thre... | {
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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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## *What* is affected by this?
<!-- Ex. simulator, workbench, performance, correctness, file(s) -->
simulator
## *How* do we replicate the issue/ho... | {
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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
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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 th... | {
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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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"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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"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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"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 "
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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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"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."
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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. "
] | 2017-01-06T19:47:47 | 2022-01-21T20:31:30 | null | CONTRIBUTOR | null | {
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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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https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/83 | https://api.github.com/repos/UWB-Biocomputing/Graphitti | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/83/labels{/name} | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/83/comments | https://api.github.com/repos/UWB-Biocomputing/Graphitti/issues/83/events | https://github.com/UWB-Biocomputing/Graphitti/issues/83 | 665,640,083 | MDU6SXNzdWU2NjU2NDAwODM= | 83 | Fix performance calculations | {
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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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