Add tutorial about homeostatic plasticity #2418
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Fix DOI link.
Utter a dire warning for those who try to build with outdated and/or weird compilers. XLC is no longer a thing, so we remove checking for it.
Some justifications: - power & Co: only useful on Cray, likely outdated. Use external power measurements if this is relevant. - trace.hpp was never used and was locked_ostream's only user.
This PR rectifies a long-standing issue since the introduction of `decor`: CV discretization was treated as a defaultable value instead of a cell property, along with bio-physical properties. This lead to some awkward facts: - Intermingling of bio-physics and numerical settings - Discretization is treated like a default without override. - Discretization cannot be changed once set, e.g. if read from `.acc`, requiring the copy+update of a decor instead Thus: - Discretization can now be set during `cable_cell` construction - It can be read and updated later - Refactor `cv_policy` to use type erasure like other, similar constructions, e.g. schedules. - Hide internal `cv_policy` constructors.⚠️ Breaks `.acc` by upgrading from 0.9 to 0.10⚠️ Closes arbor-sim#1408 --------- Co-authored-by: boeschf <[email protected]>
This concludes the introduction of 'labels' for synapse identification / placements started back in PR arbor-sim#1504 by @noraabiakar. Labels are now used when probing a synapse's state.
Bubbling up ion access information from modcc allows us to skip allocation of `Xi` and `Xo` iff no mechanism reads those values. A minor problem: Sampling may try to touch data that doesn't exist; however who'd ask for `Xi` if they never use it? Stacking this PR on top of arbor-sim#2393 the memory consumption drops by a further 5% down to 77% if the original value. ### Todo - [x] Guard against sampling non-existing `Xi`/`Xo` --------- Co-authored-by: Jannik Luboeinski <[email protected]>
- fix event stream when more than one cell in a cell group have same synapse - events would previously no longer necessarily be sorted by time - in order to simplify: also sort with respect to mechanism index (as was previously only required for the gpu backend) - add pertinent test - while cleaning up: overhauled the event related files and data structures - removed dead code - made event handling less generic (this feature was not used anywhere)
We require at least gcc12
# Introduction - Do not allocate and fill storage for resetting ion concentrations if these are never changed. Reasoning: If concentrations are never changed, we do not reset them and thus do not need to store the values. - Remove a duplicate of the CV area in solver and shared state and pass a reference during solving - Remove redundant `solution` from GPU solver - Do not store / allocate diffusion values if not needed. This saves **per CV** - `1 x 8B` for `cv_area` unconditionally - `1 x 8B` for `Xd` for each ion with no diffusion is in use (majority of cases) - `2 x 8B` for `Xi` for each ion (`reset` and `init`) if not written (reasonably often) - `2 x 8B` for `Xo` for each ion (`reset` and `init`) if not written (majority of cases) - `1 x 8B` for `eX` reset for each ion if not read (majority) - `1 x 8B` for `eX` for each ion if not read (rarely) In my standard benchmark, `busyring` with complex cells, this saves about 18% of the total GPU allocation for the cell data (`shared_state`). This has become a mixed bag, fixing a few additional things that came up during testing this: - a bug in event handling on GPU - pybind11 stub generation --------- Co-authored-by: Jannik Luboeinski <[email protected]> Co-authored-by: boeschf <[email protected]>
# Tree
Fixes --- likely a spurious --- warning in `tree.cpp`:
```
[2/6] Building CXX object arbor/CMakeFiles/arbor.dir/tree.cpp.o
In file included from /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/algorithm:60,
from /Users/hater/src/arbor/arbor/tree.cpp:1:
In function 'typename __gnu_cxx::__enable_if<std::__is_scalar<_Tp>::__value, void>::__type std::__fill_a1(_ForwardIterator, _ForwardIterator, const _Tp&) [with _ForwardIterator = unsigned int*; _Tp = unsigned int]',
inlined from 'void std::__fill_a(_FIte, _FIte, const _Tp&) [with _FIte = unsigned int*; _Tp = unsigned int]' at /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_algobase.h:998:21,
inlined from '_OutputIterator std::__fill_n_a(_OutputIterator, _Size, const _Tp&, random_access_iterator_tag) [with _OutputIterator = unsigned int*; _Size = long unsigned int; _Tp = unsigned int]' at /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_algobase.h:1151:20,
inlined from '_OI std::fill_n(_OI, _Size, const _Tp&) [with _OI = unsigned int*; _Size = long unsigned int; _Tp = unsigned int]' at /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_algobase.h:1180:29,
inlined from 'static _ForwardIterator std::__uninitialized_default_n_1<true>::__uninit_default_n(_ForwardIterator, _Size) [with _ForwardIterator = unsigned int*; _Size = long unsigned int]' at /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_uninitialized.h:668:29,
inlined from 'static _ForwardIterator std::__uninitialized_default_n_1<true>::__uninit_default_n(_ForwardIterator, _Size) [with _ForwardIterator = unsigned int*; _Size = long unsigned int]' at /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_uninitialized.h:660:9,
inlined from '_ForwardIterator std::__uninitialized_default_n(_ForwardIterator, _Size) [with _ForwardIterator = unsigned int*; _Size = long unsigned int]' at /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_uninitialized.h:712:20,
inlined from '_ForwardIterator std::__uninitialized_default_n_a(_ForwardIterator, _Size, allocator<_Tp>&) [with _ForwardIterator = unsigned int*; _Size = long unsigned int; _Tp = unsigned int]' at /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_uninitialized.h:779:44,
inlined from 'void std::vector<_Tp, _Alloc>::_M_default_initialize(size_type) [with _Tp = unsigned int; _Alloc = std::allocator<unsigned int>]' at /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_vector.h:1720:36,
inlined from 'std::vector<_Tp, _Alloc>::vector(size_type, const allocator_type&) [with _Tp = unsigned int; _Alloc = std::allocator<unsigned int>]' at /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_vector.h:558:30,
inlined from 'arb::tree::iarray arb::tree::select_new_root(int_type)' at /Users/hater/src/arbor/arbor/tree.cpp:219:34:
/opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_algobase.h:952:18: warning: 'void* __builtin_memset(void*, int, long unsigned int)' offset 4 is out of the bounds [0, 0] [-Warray-bounds=]
952 | *__first = __tmp;
```
Also use `iota` to generate contiguous indices.
# Tests
## `test_simd.cpp`
GCC doesn't acknowledge that `simd v[i] = x` for all `i = 0 ... len(v)`
initializes `v`. Force initialization to zero.
## `test_network_generation.cpp`
Compare across signs
## `test_distributed_for_each.cpp`
Compare across signs; resolve by casting to correct type.
## `test_range.cpp`
GCC really turns the dial up to 11 here, complaining about oob access in
```
char str[] = "howdy";
auto rg = range_n(str, strlen(str)); // NOTE: Putting 5 here is OK, so is sizeof(str) - 1
util::sort(rg);
```
Same happens with `std::sort(str, str + strlen(str))`, so I am pretty
sure this is not a real thing.
For reference:
```
/Users/hater/src/arbor/test/unit/test_range.cpp: In member function 'virtual void range_sort_Test::TestBody()':
/Users/hater/src/arbor/test/unit/test_range.cpp:446:14: note: at offset [8, 4611686018427387903] into object 'cstr' of size 6
446 | char cstr[] = "howdy";
| ^~~~
In function 'std::_Require<std::__not_<std::__is_tuple_like<_Tp> >, std::is_move_constructible<_Tp>, std::is_move_assignable<_Tp> > std::swap(_Tp&, _Tp&) [with _Tp = char]',
inlined from 'void std::iter_swap(_ForwardIterator1, _ForwardIterator2) [with _ForwardIterator1 = char*; _ForwardIterator2 = char*]' at /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_algobase.h:185:11,
inlined from 'void std::__move_median_to_first(_Iterator, _Iterator, _Iterator, _Iterator, _Compare) [with _Iterator = char*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_algo.h:91:20,
inlined from '_RandomAccessIterator std::__unguarded_partition_pivot(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = char*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_algo.h:1855:34,
inlined from 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = char*; _Size = long int; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_algo.h:1889:38,
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = char*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_algo.h:1905:25,
inlined from 'void std::__sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = char*; _Compare = __gnu_cxx::__ops::_Iter_less_iter]' at /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_algo.h:1900:5,
inlined from 'void std::sort(_RAIter, _RAIter) [with _RAIter = char*]' at /opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/stl_algo.h:4771:18,
inlined from 'std::enable_if_t<((bool)(! std::is_const<typename arb::util::impl_seqtrait::sequence_traits<Seq&&>::reference>::value))> arb::util::sort(Seq&&) [with Seq = range<char*, char*>]' at /Users/hater/src/arbor/arbor/util/rangeutil.hpp:154:14,
inlined from 'virtual void range_sort_Test::TestBody()' at /Users/hater/src/arbor/test/unit/test_range.cpp:448:19:
/opt/homebrew/Cellar/gcc/14.2.0/include/c++/14/bits/move.h:223:11: warning: array subscript [8, 4611686018427387903] is outside array bounds of 'char [6]' [-Warray-bounds=]
223 | __b = _GLIBCXX_MOVE(__tmp);
| ^
/Users/hater/src/arbor/test/unit/test_range.cpp: In member function 'virtual void range_sort_Test::TestBody()':
/Users/hater/src/arbor/test/unit/test_range.cpp:446:14: note: at offset [8, 4611686018427387903] into object 'cstr' of size 6
446 | char cstr[] = "howdy";
```
I am still going to 'fix' this, since I am for warning free code and
don't want to annotate with a pragma.
# General
Remove spurious includes.
---------
Co-authored-by: boeschf <[email protected]>
Tiny oversight.
ErbB4
previously approved these changes
Nov 11, 2024
ErbB4
previously approved these changes
Nov 19, 2024
thorstenhater
dismissed
ErbB4’s stale review
The merge-base changed after approval.
|
Ok, something weird happened during merging. I'll fix that. |
ErbB4
previously approved these changes
Nov 20, 2024
thorstenhater
dismissed
ErbB4’s stale review
The merge-base changed after approval.
Merged
ErbB4
previously approved these changes
Nov 25, 2024
thorstenhater
dismissed
ErbB4’s stale review
The merge-base changed after approval.
|
Superseded by #2426 (same content, none of the merging mess) |
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Add a tutorial on how to engineer structural plasticity in Arbor using a homeostatic rule.
Read the preview here
https://arbor--2418.org.readthedocs.build/en/2418/tutorial/plasticity.html
Here's a teaser of the final result:
Update: finished the tutorial.