Skip to content

[FIX] Adjust allocation sizes #526

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

Open
panau161 wants to merge 4 commits into
base: main
Choose a base branch
from
Open

[FIX] Adjust allocation sizes #526

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
3567612
[FIX] Adjust allocation sizes
panau161 Oct 1, 2025
184ce80
[FIX] Add minimum query length check to FPGA checks
panau161 Oct 2, 2025
38c3017
[MISC] automatic linting
seqan-actions Oct 2, 2025
88abc25
Merge branch 'main' into adjust_malloc_sizes
panau161 Nov 3, 2025
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
23 changes: 12 additions & 11 deletions include/raptor/search/fpga/min_ibf_fpga_oneapi.hpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -80,8 +80,8 @@ class min_ibf_fpga_oneapi
size_t numberOfQueries;
std::vector<std::string> ids;

unique_utilities_ptr<char> queries_host; // size: currentBufferSize
unique_utilities_ptr<HostSizeType> querySizes_host; // size: numberOfQueries
unique_utilities_ptr<char> queries_host;
unique_utilities_ptr<HostSizeType> querySizes_host;
unique_utilities_ptr<Chunk> results_host;

std::vector<sycl::event> kernelEvents;
Expand Down Expand Up @@ -240,12 +240,14 @@ class min_ibf_fpga_oneapi
std::ofstream outputStream(output_path, std::ios::app);
std::string result_string{};

size_t const max_numberOfQueries = bufferSizeBytes / MIN_QUERY_LENGTH;
size_t const chunks_per_result = technical_bins / chunk_bits;

for (buffer_data & state : double_buffer)
{
// TODO bufferSizeBytes is a way too high upper bound
state.queries_host = malloc_host_utilities<char>(bufferSizeBytes);
state.querySizes_host = malloc_host_utilities<HostSizeType>(bufferSizeBytes);
state.results_host = malloc_host_utilities<Chunk>(bufferSizeBytes);
state.querySizes_host = malloc_host_utilities<HostSizeType>(max_numberOfQueries);
state.results_host = malloc_host_utilities<Chunk>(max_numberOfQueries * chunks_per_result);

state.kernelEvents.reserve(numberOfKernelCopys * 2 + 2); // +2: Distributor, Collector
state.numberOfQueries = 0;
Expand Down Expand Up @@ -308,21 +310,20 @@ class min_ibf_fpga_oneapi

result_string.clear();

size_t const elements_per_query = technical_bins / 64;
size_t const chunks_per_query = seqan::hibf::divide_and_ceil(technical_bins, chunk_bits);
size_t const elements_per_result = technical_bins / 64;
size_t const elements_per_chunk = chunk_bits / 64;

if (elements_per_chunk * chunks_per_query != elements_per_query)
throw std::runtime_error("outputResults: elements_per_query/chunks_per_query mismatch");
if (elements_per_chunk * chunks_per_result != elements_per_result)
throw std::runtime_error("outputResults: elements_per_result/chunks_per_result mismatch");

for (size_t queryIndex = 0; queryIndex < state.ids.size(); queryIndex++)
{
// TODO: Use string view?
result_string += state.ids.at(queryIndex).substr(1, std::string::npos) + '\t';

for (size_t chunkOffset = 0; chunkOffset < chunks_per_query; ++chunkOffset)
for (size_t chunkOffset = 0; chunkOffset < chunks_per_result; ++chunkOffset)
{
Chunk & chunk = state.results_host.get()[queryIndex * chunks_per_query + chunkOffset];
Chunk & chunk = state.results_host.get()[queryIndex * chunks_per_result + chunkOffset];

for (size_t elementOffset = 0; elementOffset < elements_per_chunk; ++elementOffset)
{
Expand Down
7 changes: 5 additions & 2 deletions src/argument_parsing/search_parsing.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ void fpga_check_kernel(search_arguments const & arguments)
# undef RAPTOR_TOSTRING
}

void fpga_checks(search_arguments const & arguments, size_t const max_query_length)
void fpga_checks(search_arguments const & arguments, size_t const max_query_length, size_t const min_query_length)
{
if (!arguments.use_fpga)
return;
Expand All @@ -76,6 +76,9 @@ void fpga_checks(search_arguments const & arguments, size_t const max_query_leng
if (max_query_length > 250u)
throw sharg::parser_error{"The query length is too long. The maximum is 250."};

if (min_query_length < 50u)
throw sharg::parser_error{"The query length is too short. The minimum is 50."};

fpga_check_kernel(arguments);
}

Expand Down Expand Up @@ -319,7 +322,7 @@ void search_parsing(sharg::parser & parser)
}

#if RAPTOR_FPGA
fpga_checks(arguments, max_query_length);
fpga_checks(arguments, max_query_length, min_query_length);
#endif

// ==========================================
Expand Down