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Enable GPU-accelerated nucleotide ungapped prefilter #1081

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36 changes: 27 additions & 9 deletions src/prefiltering/ungappedprefilter.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -51,10 +51,17 @@ void runFilterOnGpu(Parameters & par, BaseMatrix * subMat,
std::vector<hit_t> shortResults;
std::vector<Matcher::result_t> resultsAln;

// GPU PSSM always uses 21 rows (ConvertAA_20 encoding)
const bool isNucl = Parameters::isEqualDbtype(querySeqType, Parameters::DBTYPE_NUCLEOTIDES);
const int gpuAlphabetSize = 21;
// NucleotideMatrix encoding → ConvertAA_20 row index
// A(0)→0, C(1)→1, T(2)→16, G(3)→5, X(4)→20
static const int nuclToAA20[5] = {0, 1, 16, 5, 20};

size_t profileBufferLength = par.maxSeqLen;
int8_t* profile = NULL;
if (Parameters::isEqualDbtype(querySeqType, Parameters::DBTYPE_HMM_PROFILE) == false) {
profile = (int8_t*)malloc(subMat->alphabetSize * profileBufferLength * sizeof(int8_t));
profile = (int8_t*)malloc(gpuAlphabetSize * profileBufferLength * sizeof(int8_t));
}

std::string resultBuffer;
Expand Down Expand Up @@ -142,7 +149,7 @@ void runFilterOnGpu(Parameters & par, BaseMatrix * subMat,
int32_t maxTargetLength = lengths.back();
Marv::AlignmentType type = (par.prefMode == Parameters::PREF_MODE_UNGAPPED_AND_GAPPED) ?
Marv::AlignmentType::GAPLESS_SMITH_WATERMAN : Marv::AlignmentType::GAPLESS;
marv = new Marv(tdbr->getSize(), subMat->alphabetSize, maxTargetLength,
marv = new Marv(tdbr->getSize(), gpuAlphabetSize, maxTargetLength,
par.maxResListLen, type);
void* h = marv->loadDb(
tdbr->getDataForFile(0), offsetData, lengthData, tdbr->getDataSizeForFile(0)
Expand Down Expand Up @@ -174,7 +181,7 @@ void runFilterOnGpu(Parameters & par, BaseMatrix * subMat,
} else {
if ((size_t)qSeq.L >= profileBufferLength) {
profileBufferLength = (size_t)qSeq.L * 1.5;
profile = (int8_t*)realloc(profile, subMat->alphabetSize * profileBufferLength * sizeof(int8_t));
profile = (int8_t*)realloc(profile, gpuAlphabetSize * profileBufferLength * sizeof(int8_t));
}
if (compositionBias != NULL) {
if ((size_t)qSeq.L >= compBufferSize) {
Expand All @@ -184,13 +191,24 @@ void runFilterOnGpu(Parameters & par, BaseMatrix * subMat,
}
SubstitutionMatrix::calcLocalAaBiasCorrection(subMat, qSeq.numSequence, qSeq.L, compositionBias, par.compBiasCorrectionScale);
}
for (size_t j = 0; j < (size_t)subMat->alphabetSize; ++j) {
for (size_t i = 0; i < (size_t)qSeq.L; ++i) {
short bias = 0;
if (compositionBias != NULL) {
bias = static_cast<short>((compositionBias[i] < 0.0) ? (compositionBias[i] - 0.5) : (compositionBias[i] + 0.5));
if (isNucl) {
// Zero-fill all 21 rows, then place nucleotide scores at ConvertAA_20 positions
memset(profile, 0, gpuAlphabetSize * qSeq.L * sizeof(int8_t));
for (size_t j = 0; j < (size_t)subMat->alphabetSize; ++j) {
int aa20Row = nuclToAA20[j];
for (size_t i = 0; i < (size_t)qSeq.L; ++i) {
profile[aa20Row * qSeq.L + i] = subMat->subMatrix[j][qSeq.numSequence[i]];
}
}
} else {
for (size_t j = 0; j < (size_t)subMat->alphabetSize; ++j) {
for (size_t i = 0; i < (size_t)qSeq.L; ++i) {
short bias = 0;
if (compositionBias != NULL) {
bias = static_cast<short>((compositionBias[i] < 0.0) ? (compositionBias[i] - 0.5) : (compositionBias[i] + 0.5));
}
profile[j * qSeq.L + i] = subMat->subMatrix[j][qSeq.numSequence[i]] + bias;
}
profile[j * qSeq.L + i] = subMat->subMatrix[j][qSeq.numSequence[i]] + bias;
}
}
}
Expand Down
4 changes: 2 additions & 2 deletions src/workflow/Search.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -593,8 +593,8 @@ int search(int argc, const char **argv, const Command& command) {
FileUtil::writeFile(program.c_str(), translated_search_sh, translated_search_sh_len);
}else if(searchMode & Parameters::SEARCH_MODE_FLAG_QUERY_NUCLEOTIDE &&
searchMode & Parameters::SEARCH_MODE_FLAG_TARGET_NUCLEOTIDE){
if (par.gpu != 0) {
Debug(Debug::ERROR) << "No GPU support in nucleotide search\n";
if (par.gpu != 0 && par.prefMode == Parameters::PREF_MODE_UNGAPPED_AND_GAPPED) {
Debug(Debug::ERROR) << "GPU nucleotide search only supports ungapped prefilter mode\n";
EXIT(EXIT_FAILURE);
}
FileUtil::writeFile(tmpDir + "/blastn.sh", blastn_sh, blastn_sh_len);
Expand Down