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Fix computation of GZip filter overhead. #5296

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merged 7 commits into from
Sep 11, 2024
Merged

Fix computation of GZip filter overhead. #5296

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c18b216
Add regression test for 48428
davisp May 29, 2024
8f40e9d
Fix computation of GZip filter overhead.
teo-tsirpanis Sep 10, 2024
5dd93b6
Fail when GZip compression output buffer is not large enough.
teo-tsirpanis Sep 10, 2024
d350260
Clean-up.
teo-tsirpanis Sep 10, 2024
b130ed0
Address PR feedback and replace deprecated data type.
teo-tsirpanis Sep 10, 2024
0fb5439
Add some unit tests for the GZip compressor.
teo-tsirpanis Sep 10, 2024
13c50c4
Update tiledb/sm/compressors/test/unit_gzip_compressor.cc
KiterLuc Sep 11, 2024
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1 change: 1 addition & 0 deletions test/regression/CMakeLists.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,7 @@ if (TILEDB_CPP_API)
list(APPEND SOURCES targets/sc-35424.cc)
list(APPEND SOURCES targets/sc-36372.cc)
list(APPEND SOURCES targets/sc-38300.cc)
list(APPEND SOURCES targets/sc-48428.cc)
list(APPEND SOURCES targets/sc-52975.cc)
list(APPEND SOURCES targets/sc-53334.cc)
list(APPEND SOURCES targets/sc-53791.cc)
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86 changes: 86 additions & 0 deletions test/regression/targets/sc-48428.cc
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Original file line number Diff line number Diff line change
@@ -0,0 +1,86 @@
#include <climits>

#include <tiledb/tiledb>
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Let's add a comment somewhere that explains that this adds a var sized attribute encoded with the GZIP filter and that we write data that will result in a 0 sized var tile.

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that will result in a 0 sized var tile

On second look this is quite non-apparent. How about I remove this regression test and write a targeted unit test for compressing a zero-sized buffer with the GZip filter?

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Let's keep the regression test in place and just add a quick comment.

But you are right, we should probably add a separate unit test as well.

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Updated the test's title, hope that's sufficient.

#include <tiledb/tiledb_experimental>

#include <test/support/tdb_catch.h>

using namespace tiledb;

static void create_array(Context& ctx, const std::string& array_uri);
static void write_array(Context& ctx, const std::string& array_uri);
static void read_array(Context& ctx, const std::string& array_uri);

TEST_CASE("Empty write breaks reads", "[hilbert][bug][sc48428]") {
Context ctx;
std::string array_uri = "test_empty_write";

// Test setup
create_array(ctx, array_uri);
write_array(ctx, array_uri);
read_array(ctx, array_uri);
}

void create_array(Context& ctx, const std::string& array_uri) {
auto obj = Object::object(ctx, array_uri);
if (obj.type() != Object::Type::Invalid) {
Object::remove(ctx, array_uri);
}

auto dim = Dimension::create<uint8_t>(ctx, "d", {{69, 105}}, 1);

Domain dom(ctx);
dom.add_dimension(dim);

auto filter = Filter(ctx, TILEDB_FILTER_GZIP);
auto flist = FilterList(ctx).add_filter(filter);

auto attr = Attribute::create(ctx, "a", TILEDB_STRING_UCS2)
.set_cell_val_num(std::numeric_limits<uint32_t>::max())
.set_filter_list(flist);

auto schema = ArraySchema(ctx, TILEDB_DENSE)
.set_cell_order(TILEDB_ROW_MAJOR)
.set_tile_order(TILEDB_COL_MAJOR)
.set_domain(dom)
.add_attribute(attr);

Array::create(array_uri, schema);
}

void write_array(Context& ctx, const std::string& array_uri) {
auto data = std::vector<uint16_t>();
auto offsets = std::vector<uint64_t>();
offsets.push_back(0);

Array array(ctx, array_uri, TILEDB_WRITE);
auto subarray = Subarray(ctx, array);
uint8_t start = 97;
uint8_t end = 97;
subarray.add_range(0, start, end);

Query query(ctx, array, TILEDB_WRITE);

query.set_layout(TILEDB_ROW_MAJOR)
.set_subarray(subarray)
.set_data_buffer("a", (void*)data.data(), data.size())
.set_offsets_buffer("a", offsets.data(), offsets.size());
REQUIRE(query.submit() == Query::Status::COMPLETE);
}

void read_array(Context& ctx, const std::string& array_uri) {
Array array(ctx, array_uri, TILEDB_READ);
auto subarray = Subarray(ctx, array);
uint8_t start = 97;
uint8_t end = 97;
subarray.add_range(0, start, end);

std::vector<uint16_t> a(1000000);
std::vector<uint64_t> offsets(256);
Query query(ctx, array, TILEDB_READ);
query.set_layout(TILEDB_ROW_MAJOR)
.set_subarray(subarray)
.set_data_buffer("a", (void*)a.data(), a.size())
.set_offsets_buffer("a", offsets);
REQUIRE(query.submit() == Query::Status::COMPLETE);
}
16 changes: 12 additions & 4 deletions tiledb/sm/compressors/gzip_compressor.cc
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Expand Up @@ -88,8 +88,13 @@ void GZip::compress(
(void)deflateEnd(&strm);

// Return
if (ret == Z_STREAM_ERROR || strm.avail_in != 0)
throw GZipException("Cannot compress with GZIP");
if (ret != Z_STREAM_END || strm.avail_in != 0) {
if (ret == Z_OK) {
throw GZipException("Cannot compress with GZIP; output buffer too small");
}
throw GZipException(
"Cannot compress with GZIP; error code " + std::to_string(ret));
}

// Set size of compressed data
uint64_t compressed_size = output_buffer->free_space() - strm.avail_out;
Expand Down Expand Up @@ -143,8 +148,11 @@ void GZip::decompress(
}

uint64_t GZip::overhead(uint64_t buffer_size) {
return 6 + 5 * uint64_t((std::ceil(buffer_size / 16834.0)));
// The zlib encoding adds 6 bytes (we don't use compression dictionary)
// and the overhead of deflate was taken from
// https://stackoverflow.com/a/23578269.
return 6 + 5 * uint64_t(std::floor(buffer_size / 16834.0) + 1);
}

}; // namespace sm
} // namespace sm
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Let's take the opportunity to change this to tiledb::sm above instead of having the two seperated.

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Done.

} // namespace tiledb
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