Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix segfault due to mismatched validity num and data buffer sizes #567

Merged
merged 2 commits into from
May 13, 2021
Merged

Fix segfault due to mismatched validity num and data buffer sizes #567

Show file tree
Hide file tree
Changes from 1 commit
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
e596914
Fix segfault due to mismatched validity num and data buffer sizes
ihnorton May 12, 2021
1582985
CI: Override SYSTEM variable to try to fix openssl build
ihnorton May 12, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions HISTORY.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
* Fixed incorrected error raised in .df[] indexer when pyarrow not installed [#554](https://github.com/TileDB-Inc/TileDB-Py/pull/554)
* Fixed `from_pandas(attr_filters=None, dim_filters=None)` (previously used internal defaults) [#564](https://github.com/TileDB-Inc/TileDB-Py/pull/554)
* Fixed `from_pandas` write bug due to incorrect classification of str/bytes columns [#562](https://github.com/TileDB-Inc/TileDB-Py/pull/562)
* Fix segfault due to mismatched validity num and data buffer sizes [#567](https://github.com/TileDB-Inc/TileDB-Py/pull/567)

# TileDB-Py 0.8.8 Release Notes

Expand Down
26 changes: 23 additions & 3 deletions tiledb/core.cc
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -703,6 +703,7 @@ class PyQuery {
(buf_nbytes < init_buffer_bytes_ || exact_init_bytes_)) {
buf_nbytes = init_buffer_bytes_;
offsets_num = init_buffer_bytes_ / sizeof(uint64_t);
validity_num = init_buffer_bytes_ / cell_nbytes;
}

buffers_order_.push_back(name);
Expand Down Expand Up @@ -757,10 +758,25 @@ class PyQuery {
}

void update_read_elem_num() {
for (const auto &read_info : query_->result_buffer_elements()) {
#if TILEDB_VERSION_MAJOR >= 2 && TILEDB_VERSION_MINOR >= 3
// needs https://github.com/TileDB-Inc/TileDB/pull/2238
auto result_elements = query_->result_buffer_elements_nullable();
#else
auto result_elements = query_->result_buffer_elements_nullable();
auto result_offsets_tmp = query_->result_buffer_elements();
#endif

for (const auto &read_info : result_elements) {
auto name = read_info.first;
uint64_t offset_elem_num = 0, data_vals_num = 0, validity_vals_num = 0;
std::tie(offset_elem_num, data_vals_num) = read_info.second;
uint64_t offset_elem_num = 0, data_vals_num = 0, validity_elem_num = 0;
std::tie(offset_elem_num, data_vals_num, validity_elem_num) =
read_info.second;

#if TILEDB_VERSION_MAJOR >= 2 && TILEDB_VERSION_MINOR < 3
// we need to fix-up the offset count b/c incorrect before 2.3
// (https://github.com/TileDB-Inc/TileDB/pull/2238)
offset_elem_num = result_offsets_tmp[name].first;
#endif

BufferInfo &buf = buffers_.at(name);

Expand All @@ -787,6 +803,7 @@ class PyQuery {

buf.data_vals_read += data_vals_num;
buf.offsets_read += offset_elem_num;
buf.validity_vals_read += validity_elem_num;
}
}

Expand Down Expand Up @@ -868,12 +885,14 @@ class PyQuery {

auto final_data_nbytes = buf.data_vals_read * buf.elem_nbytes;
auto final_offsets_count = buf.offsets_read + arrow_offset_size;
auto final_validity_count = buf.validity_vals_read;

assert(final_data_nbytes <= buf.data.size());
assert(final_offsets_count <= buf.offsets.size() + arrow_offset_size);

buf.data.resize({final_data_nbytes});
buf.offsets.resize({final_offsets_count});
buf.validity.resize({final_validity_count});

if (use_arrow_) {
if (retries_ > 0) {
Expand All @@ -885,6 +904,7 @@ class PyQuery {
// reset bytes-read so that set_buffers uses the full buffer size
buf.data_vals_read = 0;
buf.offsets_read = 0;
buf.validity_vals_read = 0;
}
}
if (use_arrow_) {
Expand Down