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"Well, the whole reason to have a if/then is for the test to be true sometimes, right? :^)\r\n\r\nRegarding the seed in the config files, I'm not sure it's used in the simulator. Note that there are two RNGs -- one to initialize parameters and one to generate simulator noise. It would be good to seed them from the ... | 2021-07-14T22:52:01 | 2021-07-26T18:47:54 | 2021-07-26T18:47:54 | COLLABORATOR | null | {
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`if((delayQueue & (0x1 << idx)) != 0)`
We changed this last week.
`test-tiny.xml` provides a constant rng seed, so I'm not sure why it doesn't break (or not break) with every single run. | {
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"This sounds like an excellent mini-project for a new lab member.",
"One note: the calling method (`advanceEdges()`) is in the abstract base class and just inherited. However, `advanceEdge()` is implemented in the (concrete) subclasses. So, the question is, how to do the dynamic cast in the inherited code?"
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By doing this in `advanceEdges` and passing in an instance of `AllSpikingNeurons`, we can save many thousand casts per timestep.
I'm not sure if this is enough to create a noticeable speedup though. | null | {
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"OK, let's go over this code at our next meeting."
] | 2021-07-12T18:37:31 | 2021-07-26T18:47:54 | 2021-07-26T18:47:54 | COLLABORATOR | null | {
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I'm fairly certain that there's no way to be confident about the value of `dw`. | {
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"Should these all just be fatal? We never check for successful reads, so we always end up using uninitialized variables, which is bad.",
"Yeah true, if the parameter isn't in the config file then the simulation will probably be wrong and the simulator should exit rather than continue.",
"Related to #196. There ... | 2021-07-09T18:39:58 | 2023-09-26T05:13:47 | null | CONTRIBUTOR | null | {
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"This could be analogous to the newly-added command line option that has Graphitti just output its GitHub commit ID."
] | 2021-07-07T23:31:40 | 2021-08-13T00:43:59 | null | CONTRIBUTOR | null | {
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"Did a substantial update which included adding all the information suggested."
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"I think there's an error in the bitwise queue initialization.\r\n`AllSpikingSynapses::isSpikeQueue` near line 236:\r\n`delayQueue &= ~(0x1 << delayIdx);`\r\n\r\nIf `delayQueue` is initialized to 0, then this will do nothing.\r\n\r\nThen, in `AllSpikingSynapses::preSpikeHit` near line 260:\r\n`(delayQueue & (0x1 <<... | 2021-07-05T02:42:26 | 2021-07-05T18:21:34 | 2021-07-05T18:21:34 | CONTRIBUTOR | null | {
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"This should be accomplished in conjunction with having the recorder class load its parameters and moving the specification of the output file in the config file from the global simulation parameter section to the recorder class section."
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} | null | BrainGrid's documentation has a section 5 titled Implementation which never made its way to Graphitti's docs:
https://github.com/UWB-Biocomputing/BrainGrid/blob/master/docs/braingrid_implementation.md
If it is relevant to Graphitti, it should be added to Graphitti's documentation with whatever changes necessary. | {
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"I think this is a case where the config files need to be updated, or where they were typoed during an untested update.",
"Snigdha's code implemented `AllSpikingSynapses::loadParameters`, which asks for these floats. None of them are defined in any of the old config files:\r\n\r\n```\r\n//tau/ii/text()\r\n//tau/i... | 2021-06-24T18:43:48 | 2021-07-09T18:18:15 | 2021-07-09T18:18:15 | CONTRIBUTOR | null | {
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```
Parsed parameter could not be parsed as a float. Value:
Parsed parameter could not be parsed as a float. Value:
Parsed parameter could not be parsed as a float. Value:
Parsed parame... | {
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* Seems that it's missing a top-level page.
* Links to source code don't work.
* Seems that not all of the information in the comment at top of class .h file is getting into doxygen class description. | null | {
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Created readme for updating documentation
Updated documentation | {
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"I don't have a problem with this, but right now the simulator isn't working. I would prefer that we hold off on any additional tweaks/modifications to the simulator until we have it completely operational."
] | 2021-05-19T15:51:50 | 2021-07-14T15:43:19 | 2021-07-14T03:40:40 | COLLABORATOR | null | {
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Does not switch to `valarrays` or `vectors`, that can be done independently later.
Allocates some more memory than it used to, but shouldn't affect how it works.
It used to allocate the minimum required space, now allocates space for `numVertices ... | {
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"Yes, the GPU build is currently a mess. Let's get the CPU version completely working and validated first, and then we will tackle the GPU version step by step."
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I'm unsure about whether its declaration should be in such a block too, or if the definition should be outside this block. | {
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"For that matter, I don't think `modDelta` is used; should consult with @sky1204 on this. Same goes for `AllSTDPSynapses::synapticWeightModification()`",
"I included it because some STDP implementations use modDelta. I did not get to use those but if someone wants to implement them in the future, it will be easie... | 2021-05-16T22:55:19 | 2021-07-26T18:47:54 | 2021-07-26T18:47:53 | CONTRIBUTOR | null | {
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```C++
if (delta < -STDPgap) {
// depression
dw = synapticWeightModification(iEdg, W, delta);// normalize
} else if (delta > STDPgap) {
// potentiation
dw = synapticWeightModification(iEdg, W, delta); // normalize
}
else {
return;
}
... | {
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"And, for that matter, which is `EdgeIndexMap` dynamically allocated?",
"Same as #188 "
] | 2021-05-16T21:08:31 | 2021-07-14T03:40:40 | 2021-07-14T03:40:40 | CONTRIBUTOR | null | {
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"Moreover, there are methods that are overridden that aren't labeled that way (such as `AllSpikingSynapses::resetEdge()`).",
"Maybe `AllSTDPSynapses::initSpikeQueue()`",
"Maybe `AllSTDPSynapses::isSpikeQueuePost()` and `AllSTDPSynapses::postSpikeHit()`.",
"I think that `AllSTDPSynapses::initSpikeQueue()` does... | 2021-05-16T19:05:49 | 2021-07-26T18:47:53 | 2021-07-26T18:47:53 | CONTRIBUTOR | null | {
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"I'd be happy to take this on for a first issue. Looks like a good way to dip my toes in."
] | 2021-05-13T20:25:22 | 2025-01-22T19:02:35 | null | CONTRIBUTOR | null | {
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```C++
fstream("../Output/Debug/logging.txt", ios::out | ios::trunc);
fstream("../Output/Debug/vertices.txt", ios::out | ios::trunc);
fstream("../Output/Debug/edges.txt", ios::out | ios::trunc);
```
Presumably, these should appear in the classes that actually declare the corres... | null | {
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"Seems like these are in the Matrix classes.",
"These are probably there because `weightsHistory_`, `sourceNeuronIndexHistory_`, and `destNeuronIndexHistory_` are not Matrix but vector type. The methods are exact copies for different types, so there should be just one template method and in that sense, it does s... | 2021-05-11T23:21:22 | 2025-01-22T19:06:00 | 2025-01-22T19:05:58 | CONTRIBUTOR | null | {
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"This has been obsoleted by the Recorder class re-engineering."
] | 2021-05-11T17:50:43 | 2024-12-18T21:59:42 | 2024-12-18T21:59:42 | CONTRIBUTOR | null | {
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"I think there can be a generic version of this: an \"input combiner\". This will allow for uniformity in the vertex interface and is likely necessary for any domain for GPU implementation.",
"Closing this issue as it is addressed in the PR #789"
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- When a raw pointer is needed to copy a block of memory to/from the GPU.
- For now, for serialization/deserialization, though probably that code could be cleaned up because it might support sma... | {
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"Add zone dimensions in Layout parameters. Perhaps assign a zone to each vertex and maintain a zoneMap? This would allow us to have non-rectangular uniform zones too.",
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"Seems like this was resolved with #286 "
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Might be some clues here: https://gist.github.com/francesco-romano/351a6ae457860c14ee7e907f2b0fc1a5 | {
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"Same as #220 "
] | 2021-04-30T17:08:36 | 2021-07-27T04:24:25 | 2021-07-27T04:24:24 | COLLABORATOR | null | {
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"This may be superceded/solved by #240 ",
"Plan is to eliminate probled neuron feature from the simulator. "
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- Certainly, the neuron layout classes should load the probed neuron list file name from the parameter manager and then load that neuron list, so this part definitely needs to... | {
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"Basically the same as #133 ",
"It is fixed by PR #315 "
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- Shift the queue instead of incrementing a front index value.
- Always insert new spikes at the same bi... | {
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"The `Model` (base class) uses these accessors in the `logSimStep()` method, which I believe is only used for debugging purposes. With the current plan to incorporate the 911 system, neither `Simulator` nor `Model` should assume that there will be a `width` and `height` in the Layout.\r\n\r\n```\r\nvoid Model::logS... | 2021-04-26T19:32:54 | 2023-10-04T15:42:20 | 2023-10-04T15:42:20 | COLLABORATOR | null | {
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and changing all configfiles. | {
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"Closing this one because it is no longer relevant."
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"Looks good. This branch is ready to merge."
] | 2021-04-20T18:43:28 | 2021-05-05T21:02:51 | 2021-05-05T21:02:51 | CONTRIBUTOR | null | {
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"Let's make sure there is a list someplace of those classes that need improved documentation. Or is that just \"all classes\"? :^)"
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Fixes #156 | {
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Moves edgSign from AllEdges to AllNeuroEdges
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"So basically if we compile with CUDA_ENABLED in CMakeList.txt it should only compile ggraphitti otherwise we should only compile cgraphitti, right?",
"If I understood you correctly then the solution is provided in the above PR",
"@stiber you could close the issue now"
] | 2021-04-15T17:38:31 | 2021-05-14T17:12:34 | 2021-05-14T17:12:34 | CONTRIBUTOR | null | {
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**GPU:** ggraphitti | {
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CPUSpikingModel.h --> CPUModel.h
GPUSpikingModel.cpp -->GPUModel.cpp
GPUSpikingModel.h -->GPUModel.h
BGDriver --> Driver
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"We have just gone through major merges of large changes in the code base, so this will have to be reviewed very carefully. Files have moved, files have been renamed, classes have been merged/split/created, and class and variable names have been changed.",
"Should be done now"
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} | null | Probably should call methods like this something like: `allocateGPUMemory()`, to parallel `allocateCPUMemory()` methods.
https://github.com/UWB-Biocomputing/Graphitti/blob/40197651fce05e21ac39b7fd4f92ffe33ed851d6/Simulator/Core/GPUSpikingModel.cu#L112 | null | {
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Needs to be done because there are a lot of other changes to a number of files from other branches that need to be merged; this merge will just complicate merging those branches.
opens #147 | {
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- Simulator executable is named 'graphitti'.
- Applied new path changes to all config files from previous out-of-source build changes.
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"There are setup methods for a variety of classes, should they all be called \"allocateMemory\", or keep the class descriptions?\r\n\r\nsetupEdges() --> allocateMemory() and setupVertices -->allocateMemory()\r\nOR\r\nsetupEdges() --> allocateEdgeMemory() and setupVertices -->allocateVertexMemory()?",
"I would pre... | 2021-04-13T16:16:27 | 2021-04-20T16:46:00 | 2021-04-20T16:46:00 | COLLABORATOR | null | {
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"Seems that an internal project member had fixed this just a little while ago; he just hadn't closed the issue. We are still a work in progress, and are learning to be more disciplined in doing things like linking pull requests to issues and/or indicating in commits that they close particular issues."
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"* Current top-level Graphitti page should be (with light edits) the lab repo landing page, linking to the sub-repo landing pages.\r\n* Can still point to old BG repo, since that still works and is the only multi-GPU simulator.",
"Working on this issue, but not sure how to assign myself to it. Maybe I lack a perm... | 2021-04-06T17:32:39 | 2021-07-03T18:44:34 | 2021-07-03T18:44:34 | CONTRIBUTOR | null | {
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https://github.com/UWB-Biocomputing/Graphitti/blob/2d15fe3ae34c3f4900946179d3c6f3f2b7780908/Simulator/Core/BGDriver.cpp#L2 | {
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"done in chris's commit. "
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https://github.com/UWB-Biocomputing/Graphitti/blob/2d15fe3ae34c3f4900946179d3c6f3f2b7780908/Testing/Utils/ParamaterManagerTests.cpp#L2 | {
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"requires manually going through every init of an array in the simulator. good first project. ",
"And that connects to #24, switching from arrays to vectors.",
"I don't think you can use initializer lists at all for any heap arrays.\r\n`std::fill_n(array, count, value)` sets the first 'count' elements of the ar... | 2021-03-30T03:20:10 | 2023-10-02T02:46:19 | null | CONTRIBUTOR | null | {
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"- The lib files are deleted in this branch so the files will be gone completely when the branch is merged. \r\n- I also fixed the small syntax problem with the include path. \r\n- I haven't changed the conflicting config files yet because the changes I made are pretty small and I'm not familiar with changes that h... | 2021-03-18T19:29:15 | 2021-03-30T20:07:28 | 2021-03-30T20:07:21 | COLLABORATOR | null | {
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NOTE: When running ... | {
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"Just notices of error. no implementation. \r\n```/// Copy GPU Synapse data to CPU. (Inheritance, no implem)\r\nvoid CPUSpikingModel::copyGPUtoCPU() {\r\n LOG4CPLUS_WARN(fileLogger_, \"ERROR: CPUSpikingModel::copyGPUtoCPU() was called.\" << endl);\r\n exit(EXIT_FAILURE);\r\n}\r\n\r\n/// Copy CPU Synapse data to... | 2021-02-20T00:30:20 | 2021-04-13T14:31:56 | 2021-04-13T14:31:56 | CONTRIBUTOR | null | {
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https://github.com/UWB-Biocomputing/SummerOfBrain/blob/416b0c42beefdcc951e2b4ec441efafa0d6e529d/Simulator/Core/CPUSpikingModel.h#L65-L68 | {
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"Also, I have a fairly decent list of what year each student contributed."
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"Ready to merge!"
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-test-small.xml works
-also passes unit tests. | {
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"I would say that it only applies to our files (not th... | 2021-02-12T17:44:44 | 2021-04-16T20:46:40 | 2021-04-16T20:46:40 | CONTRIBUTOR | null | {
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"collapse away \"I\" classes (example: iallvertices, ialledges, etc\" )\r\n\r\n",
"Part of what you're working on now; may already be done."
] | 2021-02-04T17:32:44 | 2021-04-13T14:32:38 | 2021-04-13T14:32:38 | CONTRIBUTOR | null | {
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- Need to propagate name changes through the rest of the code.
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"Is this the same as #521? Perhaps an old version of that new issue? @stiber ",
"Yes.",
"Yes. Closing this one."
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"Done, via Recorder class re-engineering."
] | 2020-11-19T18:15:08 | 2024-12-18T22:00:21 | 2024-12-18T22:00:20 | CONTRIBUTOR | null | {
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"Vivek going to update from Snigdha's branch. She has a good implementation of it. ",
"- [ ] Figure out and document ConnStatic parameters\r\n- [ ] Create test config files\r\n- [ ] Implement loadParameters for ConnStatic",
"@VivekGandhi54 is this... | 2020-11-19T17:44:04 | 2021-06-21T21:02:25 | 2021-06-21T21:02:25 | CONTRIBUTOR | null | {
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"@rashwini21 this pull request may have useful CUDA code or it may not. Just want to make sure before we toss this and its associated branch as having already been (manually) merged into the codebase. Snigdha starts the pull request off by mentioning CUDA and fixes to event queueing and the synapse index map, so I ... | 2020-11-10T20:20:11 | 2024-07-30T22:17:12 | 2024-07-30T22:17:01 | COLLABORATOR | null | {
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"First need to validate GPU results against reference simulator release from BrainGrid repo.",
"we need to fix the GPU first before addressing this issue. Chris is working on this (maybe?)"
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"Can this pull request be simplified now?"
] | 2020-10-29T18:00:17 | 2020-11-17T21:44:58 | 2020-11-17T21:44:54 | COLLABORATOR | null | {
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"This is an old issue and is superseded by #181 and others."
] | 2020-10-27T19:19:48 | 2022-04-05T22:33:26 | 2022-04-05T22:33:26 | CONTRIBUTOR | null | {
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2. Rather than a circular array implementation, really should just shift bits upon dequeue. This would allow enqueue at a fixed bit location.
3. We really need to clean up unnecessary use of references merely to index into arrays. Why is this there? Is there ... | {
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- GPU build can be toggled setting ```BRAINGRID_CUDA``` variable to either ```YES``` or ```NO```
- CPU deallocation logic moved to destructors and deallocation methods we're removed. GPUSpikingModel is responsible for deallocation on ... | {
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"Includes #130 and #122.",
"Here's a note from [PR 693](https://github.com/UWB-Biocomputing/Graphitti/pull/693#discussion_r1747538637):\r\n\r\nBefore this change, `registerSpikeHistoryVariable` (now `registerHistoryVariables`) was a member function of `AllSpikingNeurons` and was called within `AllSpikingNeurons::... | 2020-10-23T18:45:04 | 2025-03-31T22:35:40 | null | CONTRIBUTOR | null | {
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- [ ] copyFromGPU
- [ ] deallocateGPUMemory
- [ ] copyToGPU
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"I think this is done, but should be part of pushing the operation manager approach into the post-simulation part of the program."
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"Or maybe valarrays?"
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"This is also an opportunity to get rid of some of the stuff that we compute during simulation that we can compute afterwards."
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"Yeah, as of #212 if an xpath doesn't exist it will say `Failed loading simulation parameter for xpath <path>`."
] | 2020-09-03T20:13:31 | 2021-07-14T05:00:00 | 2021-07-14T05:00:00 | CONTRIBUTOR | null | {
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