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It does not include support for gap junctions to allow the use of\r\ndomain decomposition for some distributed network generation.\r\nThe general idea is a DSL based on set algebra, which operates on the\r\nset of all possible connections, by selecting based on different\r\ncriteria, such as the distance between cells or lists of labels. By\r\noperating on all possible connections, a separate definition of cell\r\npopulations becomes unnecessary. An example for selecting all inter-cell\r\nconnections with a certain source and destination label is:\r\n`(intersect (inter-cell) (source-label \\\"detector\\\") (destination-label\r\n\\\"syn\\\"))`\r\n\r\nFor parameters such as weight and delay, a value can be defined in the\r\nDSL in a similar way with the usual mathematical operations available.\r\nAn example would be:\r\n`(max 0.1 (exp (mul -0.5 (distance))))`\r\n\r\nThe position of each connection site is calculated by resolving the\r\nlocal position on the cell and applying an isometry, which is provided\r\nby a new optional function of the recipe. In contrast to the usage of\r\npolicies to select a member within a locset, each site is treated\r\nindividually and can be distinguished by its position.\r\n\r\nInternally, some steps have been implemented in an attempt to reduce the\r\noverhead of generating connections:\r\n- Pre-select source and destination sites based on the selection to\r\nreduce the sampling space when possible\r\n- If selection is limited to a maximum distance, use an octree for\r\nefficient spatial sampling\r\n- When using MPI, only instantiate local cells and exchange source sites\r\nin a ring communication pattern to overlap communication and sampling.\r\nIn addition, this reduces memory usage, since only the current and next\r\nsource sites have to be stored in memory during the exchange process.\r\n\r\nCustom selection and value functions can still be provided by storing\r\nthe wrapped function in a dictionary with an associated label, which can\r\nthen be used in the DSL.\r\n\r\nSome challenges remain. In particular, how to handle combined explicit\r\nconnections returned by `connections_on` and the new way to describe a\r\nnetwork. Also, the use of non-blocking MPI is not easily integrated into\r\nthe current context types, and the dry-run context is not supported so\r\nfar.\r\n\r\n\r\n# Example\r\nA (trimmed) example in Python, where a ring connection combined with\r\nrandom connections based on the distance:\r\n```py\r\nclass recipe(arbor.recipe):\r\n def cell_isometry(self, gid):\r\n # place cells with equal distance on a circle\r\n radius = 500.0 # μm\r\n angle = 2.0 * math.pi * gid / self.ncells\r\n return arbor.isometry.translate(radius * math.cos(angle), radius * math.sin(angle), 0)\r\n\r\n def network_description(self):\r\n seed = 42\r\n\r\n # create a chain\r\n ring = f\"(chain (gid-range 0 {self.ncells}))\"\r\n # connect front and back of chain to form ring\r\n ring = f\"(join {ring} (intersect (source-cell {self.ncells - 1}) (destination-cell 0)))\"\r\n\r\n # Create random connections with probability inversely proportional to the distance within a\r\n # radius\r\n max_dist = 400.0 # μm\r\n probability = f\"(div (sub {max_dist} (distance)) {max_dist})\"\r\n rand = f\"(intersect (random {seed} {probability}) (distance-lt {max_dist}))\"\r\n\r\n # combine ring with random selection\r\n s = f\"(join {ring} {rand})\"\r\n # restrict to inter-cell connections and certain source / destination labels\r\n s = f\"(intersect {s} (inter-cell) (source-label \\\"detector\\\") (destination-label \\\"syn\\\"))\"\r\n\r\n # normal distributed weight with mean 0.02 μS, standard deviation 0.01 μS\r\n # and truncated to [0.005, 0.035]\r\n w = f\"(truncated-normal-distribution {seed} 0.02 0.01 0.005 0.035)\"\r\n # fixed delay\r\n d = \"(scalar 5.0)\" # ms delay\r\n\r\n return arbor.network_description(s, w, d, {})\r\n```\r\nCo-authored-by: Thorsten Hater <24411438+thorstenhater@users.noreply.github.com>","shortMessageHtmlLink":"Feature: High-level network specification (#2050)"}},{"before":"08a157fb52455c3a45b7ffae1bf6aabd33a43023","after":"9f20e8380e58ee2a61c243254d2d0c093ecf666d","ref":"refs/heads/master","pushedAt":"2024-04-03T15:34:19.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"thorstenhater","name":"Thorsten Hater","path":"/thorstenhater","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24411438?s=80&v=4"},"commit":{"message":"Remove `simulation::inject_events` (#2265)\n\nThis removes `simulation::inject_events` which is made obsolete by\r\n`recipe::event_generators`.\r\nThe method exposed internals by giving access to the `lid` of synapses\r\n(over labels) and broke\r\nabstractions (`gid` must be present on this MPI rank and all events must\r\nbe deliverable during\r\nthe current time (as per documentation)). 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This is most\r\nlikely connected to the external `spack` buildcache, maintained by spack\r\ndevelopers (https://github.com/spack/github-actions-buildcache).\r\nTherefore, we disable the `latest_release` case until a workaround is\r\nimplemented or a compatible `spack` buildcache is available.","shortMessageHtmlLink":"disable spack latest_release (#2246)"}},{"before":"d4579b12992900fa920e029cabda7d9b0ef442c3","after":"21f5029015f65e9e2fe4ea9b229b9924a469d305","ref":"refs/heads/master","pushedAt":"2024-01-11T13:40:57.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"boeschf","name":null,"path":"/boeschf","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/48126478?s=80&v=4"},"commit":{"message":"fix gpu warp intrinsics (#2247)\n\n`reduce_by_key` depends on warp level intrinsics to transfer values\r\nbetween different threads (lanes) participating in the reduction. The\r\npertinent intrinsic is `__shfl_down_sync` which is accessed through\r\nArbor's wrapper function `shfl_down`. However, the contribution from\r\neach thread to the reduction was erroneously truncated to an integer\r\nvalue. This PR fixes the signature of the respective wrapper functions\r\nand modifies the unit test in order to check that floating point\r\nreductions are not truncated.\r\nWhile cleaning up the cuda code path, the workaround using two 32-bit\r\nshuffle instructions for 64 bit data types (doubles) was removed - this\r\nwas probably a leftover from cuda versions prior to 9.0.","shortMessageHtmlLink":"fix gpu warp intrinsics (#2247)"}},{"before":"5a965a3075dcf16f6cf5a1071085a7992b589919","after":"d4579b12992900fa920e029cabda7d9b0ef442c3","ref":"refs/heads/master","pushedAt":"2023-12-22T13:10:57.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"AdhocMan","name":"Simon Frasch","path":"/AdhocMan","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/26937327?s=80&v=4"},"commit":{"message":"Doc upgrades (#2229)\n\n- Polish & modernise two cells + gap junction example.\r\n- Investigate problems with mathjax\r\n- Update spike data format docs.\r\n- Switches theme to FURO, which is better maintained and document (like\r\n... at all)\r\n- with the new theme, we gain dark mode, yet we need to fix our graphics\r\nto make it a really nice experience.\r\n\r\nFixes #2227 \r\nFixes #2228\r\n\r\n---------\r\n\r\nCo-authored-by: Simon Frasch ","shortMessageHtmlLink":"Doc upgrades (#2229)"}},{"before":"ce6dd9d59dde8e8efaa35bac4f7d58c8469dbd8c","after":null,"ref":"refs/heads/Helveg-patch-2","pushedAt":"2023-12-08T11:12:42.000Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"Helveg","name":"Robin De Schepper","path":"/Helveg","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/28923979?s=80&v=4"}},{"before":"af0e286d92a308bde3e4608eedcf01de6944445f","after":"5a965a3075dcf16f6cf5a1071085a7992b589919","ref":"refs/heads/master","pushedAt":"2023-12-08T07:47:43.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"thorstenhater","name":"Thorsten Hater","path":"/thorstenhater","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24411438?s=80&v=4"},"commit":{"message":"Update `segment` to `msegment` as name present in arbor module (#2237)\n\nIt seems the `segment` class has been renamed to `msegment`, I updated\r\nthe morphology docs to reflect this (probably breaking a couple labels\r\nelsewhere?)","shortMessageHtmlLink":"Update segment to msegment as name present in arbor module (#2237)"}},{"before":"562ba9ebd14eba04bcdd6a48c37243b3461d681f","after":"af0e286d92a308bde3e4608eedcf01de6944445f","ref":"refs/heads/master","pushedAt":"2023-12-08T07:46:11.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"thorstenhater","name":"Thorsten Hater","path":"/thorstenhater","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/24411438?s=80&v=4"},"commit":{"message":"Backport tinyopt pr#16 EOF comparison fix (#2242)\n\n* Use `int` for `istream::get()` result for correct EOF checks when char\r\nis unsigned.\r\n\r\nFixes #2059.","shortMessageHtmlLink":"Backport tinyopt pr#16 EOF comparison fix (#2242)"}}],"hasNextPage":true,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEY3CIawA","startCursor":null,"endCursor":null}},"title":"Activity · arbor-sim/arbor"}