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Bug: nodes_capacity_ is not set in header when saving to stream #452

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GoodKnight opened this issue Jul 30, 2024 · 1 comment
Closed
3 tasks done

Bug: nodes_capacity_ is not set in header when saving to stream #452

GoodKnight opened this issue Jul 30, 2024 · 1 comment
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@ashvardanian
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@GoodKnight
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Describe the bug

Ran into an issue when attempting to load from disk that the capacity (nodes_capacity_) is incorrect and is instead set to the number of slots already storing non-null nodes (nodes_count_). Digging into it further it seems that in save_to_stream(...) the header (index_serialized_header_t) created does not contain nodes_capacity_.

Wasn't too sure if this was intentional and thus wanted to raise an issue.

Steps to reproduce

  1. Instantiate with a set number for capacity via reserve()
  2. Save via save_to_stream
  3. Load via load_from_stream
  4. Check capacity and notice that it is different than the normal reserve() value

Expected behavior

Expecting the capacity after load to be the same value as when saved.

USearch version

v2.12.0

Operating System

macOS 14.5

Hardware architecture

x86

Which interface are you using?

Other bindings

Contact Details

No response

Are you open to being tagged as a contributor?

  • I am open to being mentioned in the project .git history as a contributor

Is there an existing issue for this?

  • I have searched the existing issues

Code of Conduct

  • I agree to follow this project's Code of Conduct
@GoodKnight GoodKnight added the bug Something isn't working label Jul 30, 2024
@ashvardanian
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Good catch, looking into it!

@ashvardanian ashvardanian self-assigned this Jul 31, 2024
ashvardanian added a commit that referenced this issue Aug 6, 2024
@ashvardanian @jaysenmarais
@antonio2368 @Ngalstyan4 @adolfogc @mccullocht @rschu1ze @mbautin @SheldonFung98 @jamesbraza @eryue0220 @MarkReedZ @johnhorsema @batracos @zh217 @jbrummack @bddap @GoodKnight @brittlewis12
Merge pull request #402 from unum-cloud/main-dev
219141c 
* Improve: Swift test for issue #399 (#400)

* Fix: Integer overflow in aligned-alloc

Fixes ClickHouse/ClickHouse#61780

Co-authored-by: Antonio Andelic <antonio2368@users.noreply.github.com>

* Make: Disable Windows NPM builds

Relates to the #377 and the comment:
#377 (comment)

This temporarily disables the failing CI pipeline to generate
and update docs.

* Fix: Going beyond level 0 in clustering

* Improve: Error handling in `index_dense_gt`

This commit drops `std::vector` dependency,
making compilation time shorter and error
handling universal across abstraction layers.

* Improve: Remove `std::function` calls

* Improve: Remove `std::thread` from `index_dense_gt`

* Improve: `std::vector` -> `buffer_gt` in plugins

* Add: `usearch_change_threads_search`

* Fix: `index_dense_t::make(path)`

* Fix: Exhastive Search

In the past, if we got "too lucky" traversing the graph,
we could exit early before accumulating K top matches,
even if the index had more than K entries. This patch
changes that behavior, making output more predicatable.

* Fix: Replacement leaves isolated nodes

This patch addresses the issue #399, originally
observed in the Swift layer. Reimplementing it in
C++ helped locate the issue and lead to refactoring
the `update` procedure in the lowest-layer `index_gt`.

Now, `add` and `update` share less code. The `add`
is one branch shorter (not that it would be noticeable),
and `update` brings additional logic to avoid spilling
`updated_slot` into top-results and consequently
introducing self-loops.

Closes #399

* Fix: Misc warnings & compilation issues

* Fix: Misc warnings & compilation issues

* Fix: Detect `ring_gt` being full

Relates to #355

* Fix: Re-init `available_threads_` after load

Both `view` and `load` would `reset` the thread contexts.
After that, the very first `search` and `add` would fail, as
no thread-local contexts are initialized. It would require
a `reserve` call with a non-zero second arcgument to
define the number of concurrent threads, for which the
queues & buffers need to be allocated.

That design is counter-intuitive, so this patch re-inits the
same number of threads as before the `load` & `view` or
one, if none existed.

* Fix: `uint32_t` to `uint40_t` cast (#404)

Co-authored-by: Ash Vardanian <1983160+ashvardanian@users.noreply.github.com>

* Docs: Mention `b1` in `README.md`

Co-authored-by: Adolfo Garcia <1250775+adolfogc@users.noreply.github.com>

* Docs: Cover new users

* Improve: Updates stability & catch bug

* Fix: Dereferencing `member_iterator_t`

* Add: Java `get` API (#407)

* Fix: Compilation with `uint40_t` keys

* Add: `AutoClosable` using `c_destroy` for Java (#408)

* Fix: Rare deadlock on tiny collections

* Improve: `enable_key_lookups=false` memory usage

As noted by Robert Schulze, we can avoid populating `slot_lookup_`
during insertions, if `enable_key_lookups` is not set. This would lead
to lower memory consumption for large indexes of tiny vectors,
particularly common in GIS.

Co-authored-by: Robert Schulze <robert@clickhouse.com>

* Fix: Preset `enable_key_lookups=true` in C

* Fix: `std::is_pod` deprecated in C++20

* Fix: Unused type aliases

* Improve: Avoid `#pragma region` pre GCC 13 (#386)

* Do not use #pragma region if not supported by the compiler
* `pragma region` supported by GCC 13+

https://gcc.gnu.org/bugzilla/show_bug.cgi?id=85487

---------

Co-authored-by: Mikhail Bautin <mbautin@users.noreply.github.com>
Co-authored-by: Ash Vardanian <1983160+ashvardanian@users.noreply.github.com>

* Fix: Capacity checks in C# tests

* Docs: Add doc-strings in C#

* Make: Verbose C# logging in debug builds

* Docs: Describe serialization in GoLang

* Make: Drop Java & JS API references

Compiling and introspecting docstrings in Sphinx
is extremely flaky. It's safer to simply describe the
usage patterns in the `README.md`.

* Add: Load from path in Java (#410)

* Improve: Avoid sorting on small "refines"

* Docs: Cover JIT-compiled Python examples

* Fix: `index.copy()` trying to `memcpy(*, NULL, *)`

* Docs: UB in C++ Example (#415)

Co-authored-by: Ash Vardanian <1983160+ashvardanian@users.noreply.github.com>

* Improve: Catch UB with tests

* Docs: Rearrange

* Fix: Reserving contexts post-reload

* Improve: Detect more failures in tests

* Improve: Log failing lines

* Fix: Clamp before down-casting to `i8_t` (#422)

Previously we were down-casting floats to the target type (e.g. int8_t), and then
clamping to [-100, 100] range. This means that e.g. 129 would be cast to -127 and
then converted to -100, in stead of becoming 100

The fix does clamping first, and then casts the resulting number
(which is guaranteed to be in range [-100, 100], due to clamping)
from source type to target int8_t. Given the clamping, this will never overflow.

---------

Co-authored-by: Ash Vardanian <1983160+ashvardanian@users.noreply.github.com>

* Fix: Concurrency bug in high-K search

When calling `index_dense_gt`, the thread lock was not propagating
with the `search_result_t`. That is a an error-prone API. When too many
threads are running in parallel (ideally, more than physical CPU cores)
another thread may start reusing the `context_t` before the original
caller finishes exporting entries with `dump_to`.

This solution is backwards compatible and passes the tests.

* Make: Manually bump version to 2.13.0

We can't yet rely on the SemVer tool
semantic-release/release-notes-generator#633 (comment)

* Improve: Attempt to implement batch-metrics

* Add: Batch-capable metrics

* Add: `misaligned_ptr_gt` comparators

* Improve: Separate `error_t` constructors

This makes debugging easier, as it's simpler to trace
where the error message is being set.

* Improve: Support `enum` slots

Tracing implicit conversions of `std::uint32_t` and other
primitive types isn't always easy in concurrent apps. This
commit adds support for `enum` types to be used for
safer implementation of `index_gt` specializations.

* Improve: Ranges-V3 compatibility

* Add: Preliminary support for batch metrics

* Add: Batch-parallel refinements

* Add: `MANIFEST.in` for `py.typed` (#425)

Adding type annotation for Python native modules
solves the `Skipping analyzing "usearch.index" module` 
warning due to `missing library stubs or py.typed marker`.

Closes #424

* Fix: Clear cast buffer before bitwise ORs for `b1x8_t` (#428)

When converting floating point arrays to binary, we use bitwise OR
operations to set the relevant bits in the output buffer to 1. We do
nothing if the bit is zero, so we assume that the bit is zero to start
with. The `memset` statement makes sure this assumption holds.

* Fix: `esm` duplicate import bug in `jest` (#420)

Closes #418
Closes #426

* Fix: build.gradle deprecations

* Fix: ESM build support (#433)

Closes #426
Relates to #420

* Fix: `capacity()` assertion in Rust (#436)

Closes #432

* Fix: Computing `stats(i).max_edges`

* Add: Returning `computed_distances_in_refines`

In high-connectivity graphs, the number of distance
computations can be dominated by the number of "refine"
heuristic computations performed by the core structure.
The extended `add_result_t` now includes both:

- `computed_distances_in_refines`
- `computed_distances_in_reverse_refines`

This commit also extends the documentation.

* Add: Profiling attributes for `index_gt`

* Fix: Preserve thread limits after `fork()`

* Improve: Benchmarks self-recall support and `.bbin`

This patch adds support for partial datasets, without
ground truth neighborhood data. It also adds support
for `.bbin` binary, `.hbin` half-precision, and `.dbin`
double-precision input vector files/

* Fix: Printing progress between exit

* Docs: Fix spelling

* Fix: Wolfram bindings (#437)

Co-authored-by: Ash Vardanian <1983160+ashvardanian@users.noreply.github.com>

* Fix: Pre-reserve enough threads for C users

This indirectly fixes the crash in C# layer

* Revert: Parallel metrics

* Fix: Updating the `entry_slot_` node

* Improve: Enable single-threaded update tests

* Make: Bump version

* Fix: `flat_hash_multi_set_gt::reset` double-free

* Fix: Not enough memory in `fork()`

* Make: Bump to SimSIMD v5

* Fix: Missing SimSIMD v5 capability names

* Improve: Detecting copy & move issues

* Fix: Compilation w. explicit `template class`

* Improve: Bypass UBSan NULL dereferencing warning

* Improve: Minimize alignment issues

* Make: Disable `bf16` on MacOS

* Make: Link to GitHub repo

* Fix: Conditional `call_key` compilation in MSVC

* Fix: Unary minus on unsigned distances

* Make: Disable `bf16` in JS

* Fix: Compatibility with pre-v2.10

Closes #423

* Improve: Test wrong number of dimensions in Rust (#413)

Closes #412

---------

Co-authored-by: Julius Brummack <juliusbrummack@icloud.com>

* Fix: Handle wrong dimensionality in Rust

* Fix: Overwriting `SIMSIMD_DYNAMIC_DISPATCH`

* Make: Upgrade Java version

* Fix: Spelling mistakes

* Fix: `sprintf` deprecated

* Fix: `-Wpass-failed=transform-warning`

* Fix: Memory pinning on `Add` in C#

* Make: Specify Java distribution

* Fix: Pin memory in gets (C#)

* Make: Skip `PersistAndRestore` in CI on MacOS

* Make: Upgrade Docker action

This fixes a GitHub CI warning about the
deprecated NodeJS version.

* Fix: `view_from_buffer` is unsafe in Rust

Closes #453

Co-authored-by: Andrew Dirksen <2702854+bddap@users.noreply.github.com>"

* Fix: `view_from_buffer` is unsafe in Rust

Closes #453

Co-authored-by: Andrew Dirksen <2702854+bddap@users.noreply.github.com>

* Make: Upgrade SimSIMD

* Docs: Index header has no capacity

The lack of capacity data is intended.
Reserving memory is a non-persistent operation
by nature, and we shouldn't save that metadata
on the disk.

Closes #452

Co-authored-by: Christopher Yim <4638193+GoodKnight@users.noreply.github.com>

* Fix: Aggressive neighborhood checks on updates

* Fix: `update()` bug detect with non-POD keys

This bug was tough to spot. Apple Clang was the only one
that caught it. The `-O0` flags were explicitly added to expose
more symbols for debugging. More `uint40_t` tests were added.

* Fix: Align vector type w index in C# (#456)

Co-authored-by: Ash Vardanian <1983160+ashvardanian@users.noreply.github.com>

* Make: Versioning in pre-release CI

* Make: Switch from SemanticRelease to TinySemVer

---------

Co-authored-by: Jaysen Marais <jaysen.marais@gmail.com>
Co-authored-by: Antonio Andelic <antonio2368@users.noreply.github.com>
Co-authored-by: Narek Galstyan <narekg@berkeley.edu>
Co-authored-by: Adolfo Garcia <1250775+adolfogc@users.noreply.github.com>
Co-authored-by: Trevor McCulloch <mccullocht@gmail.com>
Co-authored-by: Robert Schulze <robert@clickhouse.com>
Co-authored-by: Mikhail Bautin <552936+mbautin@users.noreply.github.com>
Co-authored-by: Mikhail Bautin <mbautin@users.noreply.github.com>
Co-authored-by: SheldonFung <88470100+SheldonFung98@users.noreply.github.com>
Co-authored-by: James Braza <jamesbraza@gmail.com>
Co-authored-by: cinchen <eryue0220@gmail.com>
Co-authored-by: Mark Reed <markreed99@gmail.com>
Co-authored-by: John <jjmace01@gmail.com>
Co-authored-by: batracos <giulio.a@gmail.com>
Co-authored-by: Ziyang Hu <2103823+zh217@users.noreply.github.com>
Co-authored-by: Julius Brummack <133630819+jbrummack@users.noreply.github.com>
Co-authored-by: Julius Brummack <juliusbrummack@icloud.com>
Co-authored-by: Andrew Dirksen <2702854+bddap@users.noreply.github.com>
Co-authored-by: Christopher Yim <4638193+GoodKnight@users.noreply.github.com>
Co-authored-by: Britt <brittlewis12@gmail.com>
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@ashvardanian @GoodKnight