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MICA-SE.c
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MICA-SE.c
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//
// MICA.c
//
// Copyright (C) 2013, HKU
//
// This program is free software; you can redistribute it and/or
// modify it under the terms of the GNU General Public License
// as published by the Free Software Foundation; either version 2
// of the License, or (at your option) any later version.
//
// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License
// along with this program; if not, write to the Free Software
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
//
// Modification History
//
// Date : 4th June 2013
// Changes : Correctly distribute the bucket. Currently the numReadPerCore for each core is
// hardcoded causing inefficient load balancing while the number of reads is not
// a multiple of the numReadPerCore.
//
// Date : 6th June 2013
// Changes : Add Occurrence Collector to gather output but discard them to avoid IO
//
// To-do : 1. Construct the BWT structure outside the pragma offload.
// 2. Don't need inout saCount everytime
//
///////////////////////////////////////////////////////////////////////////////////////////////
#include "MICA-SE.h"
#include "Release.h"
#define MIC_MAIN_NON_INPUT_VALUE 99999999
#define MIC_BATCH_SIZE 20000
#define SRA_READ_SKIP_INVALID 0
#define SRA_READ_REPLACE_INVALID 1
//-----------------------------------
// DEBUG FLAGS
//-----------------------------------
// Define to print output statistics
//#define MIC_DEBUG_PRINT_OUTPUT_COUNTS
// Declaration of Global Variables
// Global Variables should NEVER be referenced outside of
// this file though they can be.
__attribute__((target(mic)))
int InputNumOfMICThreads = 240;
int InputNumOfCPUThreads = 1;
char ReadFileName[MAX_FILENAME_LEN+1] = "";
char OutputFileName[MAX_FILENAME_LEN+1] = "*.out";
char DatabaseName[MAX_FILENAME_LEN+1] = "";
char InputSaValueFileName[MAX_FILENAME_LEN+1] = ".sa8";
char InputCPUSaValueFileName[MAX_FILENAME_LEN+1] = ".sa";
int InputSRAInvalidReadHandling = SRA_READ_SKIP_INVALID;
int InputQueryStrand = QUERY_BOTH_STRAND;
int InputAlignmentModel = SRA_MODEL_8G;
int InputMaxNumOfAlignment = -1;
int InputMaxError = 0;
int InputMaxNBMismatch = MIC_MAIN_NON_INPUT_VALUE;
int InputErrorType = MIC_MAIN_NON_INPUT_VALUE;
int InputOutputFileName = MIC_MAIN_NON_INPUT_VALUE;
int OutputFormat = MIC_MAIN_NON_INPUT_VALUE;
unsigned int InputMemoryCPUMaxUsageMBytes = -1;
unsigned int InputMemoryMICMaxUsageMBytes = 3600;
void PrintHelp();
dictionary *ParseInput(int argc, char** argv);
void ParseIniFile(char *iniFileName);
void SRAFillCharMap(unsigned char * charMap);
void PrintAlignmentSettings(SRAArguments * sArgs);
void SRAGetFileSuffix(int threadId, char * suffixStr);
// GetBatchSizing function takes the number of reads and
// calculates required number of cores; and the number of reads assigned to each core.
// The output number (batchSize * numThreads) can be greater than (totalNumRead).
void GetBatchSizing(unsigned int totalNumRead,
unsigned int maxNumThreads, unsigned int minBatchSize,
unsigned int * batchSize, unsigned int * numThreads) {
// If totalNumRead is empty, the output should all be zero
// i.e. 0 number of CPU and 0 read in each core
if (totalNumRead==0) {
(*batchSize) = 0;
(*numThreads) = 0;
return;
}
// If totalNumRead is smaller than the number of threads available,
// each core gets at most 1 read.
if (totalNumRead<=maxNumThreads) {
(*batchSize) = 1;
(*numThreads) = totalNumRead;
return;
}
// Otherwise, distribute the big bucket of reads to the cores
unsigned int tmp = (totalNumRead + (maxNumThreads - 1)) / maxNumThreads;
(*batchSize) = tmp;
(*numThreads) = maxNumThreads;
return;
}
int main(int argc, char** argv) {
printf("\n%s v%d.%d.%d (%s)\n",PROJECT_NAME,PROJECT_MAJOR,PROJECT_MINOR,PROJECT_REV,PROJECT_SPECIAL);
////////////////////////////////////////////////////////////
// Declaration of Variables
////////////////////////////////////////////////////////////
// Program input
dictionary *programInput;
double startTime, lastEventTime, timestamp;
startTime = setStartTime();
lastEventTime = 0;
unsigned long long i,j,k;
unsigned int u,v,w;
unsigned char charMap[256];
unsigned char complementMap[256];
char dummyQuality[SRA_MAX_READ_LENGTH];
memset(dummyQuality,0,sizeof(int)*SRA_MAX_READ_LENGTH);
//Initial Environmental Parameters for Intel MIC
MICSetParameters();
////////////////////////////////////////////////////////////
// Ini Configuration
////////////////////////////////////////////////////////////
char iniFilename[MAX_FILENAME_LEN];
sprintf(iniFilename, "%s.ini", argv[0]);
ParseIniFile(iniFilename);
// Command Argument - Override
programInput = ParseInput(argc, argv);
////////////////////////////////////////////////////////////
// Index Handling
////////////////////////////////////////////////////////////
printf("Loading index %s ... ",DatabaseName); fflush(stdout);
Idx2BWT * idx2BWT = BWTLoad2BWT(DatabaseName,InputSaValueFileName);
char LookupTableFileName[MAX_FILENAME_LEN+1];
char RevLookupTableFileName[MAX_FILENAME_LEN+1];
strcpy(LookupTableFileName,DatabaseName);
strcpy(RevLookupTableFileName,DatabaseName);
strcat(LookupTableFileName,".lkt");
strcat(RevLookupTableFileName,".rev.lkt");
LT * lookup = LTLoad(LookupTableFileName);
LT * rev_lookup = LTLoad(RevLookupTableFileName);
BWT * bwt = idx2BWT->bwt;
BWT * rev_bwt = idx2BWT->rev_bwt;
HSP * hsp = idx2BWT->hsp;
printf("DONE\n\n");
// Timestamp'ed -----------
timestamp = getElapsedTime(startTime);
printf("(Elapsed time (Index Loading) : %9.4f seconds)\n\n", timestamp - lastEventTime);
lastEventTime = timestamp;
// ------------------------
////////////////////////////////////////////////////////////
// CPU Allocation of Memory Frame
////////////////////////////////////////////////////////////
unsigned int numReadPerCore = MIC_BATCH_SIZE;
unsigned int memsize_readNameBufferFrame = MAX_SEQ_NAME_LENGTH*numReadPerCore*InputNumOfMICThreads;
unsigned int memsize_readBodyBufferFrame = SRA_MAX_READ_LENGTH*numReadPerCore*InputNumOfMICThreads;
unsigned int memsize_outputBufferFrame = MIC_SRA_OUTPUT_SIZE_PER_THREAD*InputNumOfMICThreads;
unsigned int memsize_outputBufferMeta = MIC_SRA_OUTPUT_META_PER_THREAD*InputNumOfMICThreads;
unsigned int memsize_bufferPerRead = numReadPerCore*InputNumOfMICThreads;
char * readNameBufferFrame = (char*) MEMManMalloc(sizeof(char)*memsize_readNameBufferFrame,MEMORY_TYPE_CPU);
unsigned char * readBodyBufferFrame = (unsigned char*) MEMManMalloc(sizeof(unsigned char)*memsize_readBodyBufferFrame,MEMORY_TYPE_SHARED);
char * readQualityBufferFrame = (char*) MEMManMalloc(sizeof(char)*memsize_readBodyBufferFrame,MEMORY_TYPE_SHARED);;
uint16_t * readLengthBufferFrame = (uint16_t*) MEMManMalloc(sizeof(uint16_t)*memsize_bufferPerRead,MEMORY_TYPE_SHARED);
int * uncertaintyNumberBufferFrame = (int*) MEMManMalloc(sizeof(int)*memsize_bufferPerRead,MEMORY_TYPE_SHARED);
unsigned int * threadAlgmt = (unsigned int*) MEMManMalloc(sizeof(unsigned int)*InputNumOfMICThreads,MEMORY_TYPE_SHARED);
uint16_t * occCount = (uint16_t*) MEMManMalloc(sizeof(uint16_t)*memsize_bufferPerRead,MEMORY_TYPE_SHARED);
unsigned int * outputBufferFrame = (unsigned int*) MEMManMalloc(sizeof(unsigned int)*memsize_outputBufferFrame,MEMORY_TYPE_SHARED);
uint8_t * outputBufferStatus = (uint8_t*) MEMManMalloc(sizeof(uint8_t)*memsize_bufferPerRead,MEMORY_TYPE_SHARED);
MICSRAOccMetadata * outputBufferMeta = (MICSRAOccMetadata*) MEMManMalloc(sizeof(MICSRAOccMetadata)*memsize_outputBufferMeta,MEMORY_TYPE_SHARED);
CPTSRAModel * cpModels = (CPTSRAModel*) MEMManMalloc(sizeof(CPTSRAModel) * SRA_MAX_READ_LENGTH,MEMORY_TYPE_SHARED);
printf("[INFO] Total Shared Working Memory allocated = %9.2f Mbytes\n",MEMManGetUsage(MEMORY_TYPE_SHARED)/1024.0/1024.0);
if (InputMemoryMICMaxUsageMBytes!=-1 && MEMManGetUsage(MEMORY_TYPE_SHARED)>(unsigned long long) InputMemoryMICMaxUsageMBytes*1024*1024) {
printf("[ERROR] Exceeded defined MIC limitation of %u MBytes\n",InputMemoryMICMaxUsageMBytes);
}
printf("[INFO] Total CPU Working Memory allocated = %9.2f Mbytes\n",MEMManGetUsage(MEMORY_TYPE_CPU)/1024.0/1024.0);
if (InputMemoryCPUMaxUsageMBytes!=-1 && MEMManGetUsage(MEMORY_TYPE_CPU)>(unsigned long long) InputMemoryCPUMaxUsageMBytes*1024*1024) {
printf("[ERROR] Exceeded defined CPU limitation of %u MBytes\n",InputMemoryMICMaxUsageMBytes);
}
printf("\n");
// Timestamp'ed -----------
timestamp = getElapsedTime(startTime);
printf("(Elapsed time (CPU Memory Allocation) : %9.4f seconds)\n\n", timestamp - lastEventTime);
lastEventTime = timestamp;
// ------------------------
////////////////////////////////////////////////////////////
// MIC Memory Allocation
////////////////////////////////////////////////////////////
// Forward BWT
unsigned int bwtCodeLengthInFile = BWTFileSizeInWord(bwt->textLength);
unsigned int bwtTextLength = bwt->textLength;
unsigned int bwtOccSizeInWord = bwt->occSizeInWord;
unsigned int bwtInverseSa0 = bwt->inverseSa0;
unsigned int * bwtBwtCode = bwt->bwtCode;
unsigned int * bwtCumulativeFreq = bwt->cumulativeFreq;
unsigned int * bwtOccValue = bwt->occValue;
unsigned int * bwtOccValueMajor = bwt->occValueMajor;
unsigned int * micOccValue = bwt->micOccValue;
unsigned int micBwtSaValueSizeInWord = bwt->saValueSizeInWord;
unsigned int * micBwtSaValue = bwt->saValue;
#pragma offload target(mic) \
nocopy(bwt:length(1) alloc_if(1) free_if(0) align(2*1024*1024)) \
nocopy(bwtBwtCode:length(bwtCodeLengthInFile) alloc_if(1) free_if(0) align(2*1024*1024)) \
nocopy(bwtCumulativeFreq:length(ALPHABET_SIZE+1) alloc_if(1) free_if(0) align(2*1024*1024)) \
nocopy(bwtOccValue:length(bwt->occSizeInWord) alloc_if(1) free_if(0) align(2*1024*1024)) \
nocopy(bwtOccValueMajor:length(bwt->occMajorSizeInWord) alloc_if(1) free_if(0) align(2*1024*1024)) \
nocopy(micBwtSaValue:length(micBwtSaValueSizeInWord) alloc_if(1) free_if(0) align(2*1024*1024)) \
nocopy(micOccValue:length(bwt->micOccSizeInWord) alloc_if(1) free_if(0) align(2*1024*1024))
{}
// Reverse BWT
unsigned int rbwtCodeLengthInFile = BWTFileSizeInWord(rev_bwt->textLength);
unsigned int rbwtTextLength = rev_bwt->textLength;
unsigned int rbwtOccSizeInWord = rev_bwt->occSizeInWord;
unsigned int rbwtInverseSa0 = rev_bwt->inverseSa0;
unsigned int * rbwtBwtCode = rev_bwt->bwtCode;
unsigned int * rbwtCumulativeFreq = rev_bwt->cumulativeFreq;
unsigned int * rbwtOccValue = rev_bwt->occValue;
unsigned int * rbwtOccValueMajor = rev_bwt->occValueMajor;
unsigned int * rmicOccValue = rev_bwt->micOccValue;
#pragma offload target(mic) \
nocopy(rev_bwt:length(1) alloc_if(1) free_if(0) align(2*1024*1024)) \
nocopy(rbwtBwtCode:length(rbwtCodeLengthInFile) alloc_if(1) free_if(0) align(2*1024*1024)) \
nocopy(rbwtCumulativeFreq:length(ALPHABET_SIZE+1) alloc_if(1) free_if(0) align(2*1024*1024)) \
nocopy(rbwtOccValue:length(rev_bwt->occSizeInWord) alloc_if(1) free_if(0) align(2*1024*1024)) \
nocopy(rbwtOccValueMajor:length(rev_bwt->occMajorSizeInWord) alloc_if(1) free_if(0) align(2*1024*1024)) \
nocopy(rmicOccValue:length(rev_bwt->micOccSizeInWord) alloc_if(1) free_if(0) align(2*1024*1024))
{}
// Input and Output Data
#pragma offload target(mic) \
nocopy(readBodyBufferFrame:length(memsize_readBodyBufferFrame) alloc_if(1) free_if(0) align(2*1024*1024)) \
nocopy(readLengthBufferFrame:length(memsize_bufferPerRead) alloc_if(1) free_if(0) align(2*1024*1024)) \
\
nocopy(cpModels:length(SRA_MAX_READ_LENGTH) alloc_if(1) free_if(0) align(2*1024*1024)) \
nocopy(occCount:length(memsize_bufferPerRead) alloc_if(1) free_if(0) align(2*1024*1024)) \
nocopy(threadAlgmt:length(InputNumOfMICThreads) alloc_if(1) free_if(0) align(2*1024*1024)) \
\
nocopy(outputBufferFrame:length(memsize_outputBufferFrame) alloc_if(1) free_if(0) align(2*1024*1024)) \
nocopy(outputBufferMeta:length(memsize_outputBufferMeta) alloc_if(1) free_if(0) align(2*1024*1024)) \
nocopy(outputBufferStatus:length(memsize_bufferPerRead) alloc_if(1) free_if(0) align(2*1024*1024))
{}
// Timestamp'ed -----------
timestamp = getElapsedTime(startTime);
printf("(Elapsed time (MIC Memory Allocation) : %9.4f seconds)\n\n", timestamp - lastEventTime);
lastEventTime = timestamp;
// ------------------------
////////////////////////////////////////////////////////////
// MIC Memory Copy
////////////////////////////////////////////////////////////
// Forward BWT
#pragma offload target(mic) \
in(bwt:length(1) alloc_if(0) free_if(0)) \
in(bwtBwtCode:length(bwtCodeLengthInFile) alloc_if(0) free_if(0)) \
in(bwtCumulativeFreq:length(ALPHABET_SIZE+1) alloc_if(0) free_if(0)) \
in(bwtOccValue:length(bwt->occSizeInWord) alloc_if(0) free_if(0)) \
in(bwtOccValueMajor:length(bwt->occMajorSizeInWord) alloc_if(0) free_if(0)) \
in(micBwtSaValue:length(micBwtSaValueSizeInWord) alloc_if(0) free_if(0)) \
in(micOccValue:length(bwt->micOccSizeInWord) alloc_if(0) free_if(0))
{
bwt->cumulativeFreq = bwtCumulativeFreq;
bwt->bwtCode = bwtBwtCode;
bwt->occValue = bwtOccValue;
bwt->occValueMajor = bwtOccValueMajor;
bwt->saValue = micBwtSaValue;
bwt->micOccValue = micOccValue;
}
// Reverse BWT
#pragma offload target(mic) \
in(rev_bwt:length(1) alloc_if(0) free_if(0)) \
in(rbwtBwtCode:length(rbwtCodeLengthInFile) alloc_if(0) free_if(0)) \
in(rbwtCumulativeFreq:length(ALPHABET_SIZE+1) alloc_if(0) free_if(0)) \
in(rbwtOccValue:length(rev_bwt->occSizeInWord) alloc_if(0) free_if(0)) \
in(rbwtOccValueMajor:length(rev_bwt->occMajorSizeInWord) alloc_if(0) free_if(0)) \
in(rmicOccValue:length(rev_bwt->micOccSizeInWord) alloc_if(0) free_if(0))
{
rev_bwt->cumulativeFreq = rbwtCumulativeFreq;
rev_bwt->bwtCode = rbwtBwtCode;
rev_bwt->occValue = rbwtOccValue;
rev_bwt->occValueMajor = rbwtOccValueMajor;
rev_bwt->micOccValue = rmicOccValue;
}
// Timestamp'ed -----------
timestamp = getElapsedTime(startTime);
printf("(Elapsed time (MIC Memory Copy) : %9.4f seconds)\n\n", timestamp - lastEventTime);
lastEventTime = timestamp;
// ------------------------
////////////////////////////////////////////////////////////
// CPU Index Re-Loading
////////////////////////////////////////////////////////////
char saFilename[MAX_INDEX_FILENAME_LENGTH];
strcpy(saFilename,DatabaseName);
strcat(saFilename,InputCPUSaValueFileName);
printf("Loading Full Suffix-Array for CPU %s ... ",saFilename); fflush(stdout);
BWTSAFree(idx2BWT->mmPool,idx2BWT->bwt);
BWTSALoad(idx2BWT->mmPool,idx2BWT->bwt,saFilename,NULL);
printf("DONE\n\n");
// Timestamp'ed -----------
timestamp = getElapsedTime(startTime);
printf("(Elapsed time (Index Loading) : %9.4f seconds)\n\n", timestamp - lastEventTime);
lastEventTime = timestamp;
// ------------------------
SRAArguments * sraArgs = SRAARGConstruct();
// Setting up SRA Indexes
SRAIndexPopulate(sraArgs->AlgnmtIndex,idx2BWT->bwt,idx2BWT->rev_bwt,idx2BWT->hsp,NULL,lookup,rev_lookup);
// Setting up SRA Settings
sraArgs->AlgnmtSetting->MaxError = InputMaxError;
sraArgs->AlgnmtSetting->MaxResult= InputMaxNumOfAlignment;
// Setting up output file
bam_header_t samOutputHeader;
SAMOutputHeaderConstruct(&samOutputHeader,hsp);
sraArgs->AlgnmtOutput->occCollector = SRAOCCCreate(SRAOCC_FLOOD_TYPE_EXPAND);
sraArgs->AlgnmtOutput->OutFileFormat = SRA_OUTPUT_FORMAT_SAM;
sraArgs->AlgnmtSetting->OutputFormat = SRA_OUTPUT_FORMAT_SAM;
sraArgs->AlgnmtOutput->SAMOutFilePtr = samopen("out","wh",&samOutputHeader);
SRAArguments * sraArgs_neg = SRAARGMakeSlave(sraArgs);
SRAModelSet * sraModelSet = SRAModelSetConstruct(
sraArgs->AlgnmtSetting,
sraArgs->AlgnmtIndex,
SRA_MODEL_16G,
SRA_MIN_READ_LENGTH,
SRA_MAX_READ_LENGTH);
//Printing Settings
PrintAlignmentSettings(sraArgs);
UTBFRBuffer * readQueryBuffer = UTBFRLoad(ReadFileName);
HSPFillCharMap(charMap);
if (InputSRAInvalidReadHandling == SRA_READ_REPLACE_INVALID) SRAFillCharMap(charMap);
HSPFillComplementMap(complementMap);
SRAOCCCollector * occCollector = sraArgs->AlgnmtOutput->occCollector;
double processingTime = 0;
double alignmentTime = 0;
double outputTime = 0;
double readLoadTime = 0;
double modelTime = 0;
unsigned int queryInBatch = 1;
unsigned long long consSaCount = 0;
unsigned long long cpuConsSaCount = 0;
unsigned long long queryHandled = 0;
#ifdef MIC_DEBUG_PRINT_OUTPUT_COUNTS
unsigned int numOfClosed = 0;
unsigned int numOfSaReq = 0;
unsigned int numOfSaContent = 0;
unsigned int numOfOccContent = 0;
#endif
while (queryInBatch!=0) {
// Read in the query for the buckets for all threads
// The current stamp is being retrieved
queryInBatch = SRAQueryAndNameGetBatchFromFASTAQLength(readQueryBuffer,
charMap,
numReadPerCore * InputNumOfMICThreads,
MAX_SEQ_NAME_LENGTH,
readNameBufferFrame,
SRA_MAX_READ_LENGTH,
readBodyBufferFrame,
readQualityBufferFrame,
readLengthBufferFrame,
uncertaintyNumberBufferFrame);
if (queryInBatch == 0) break;
// Timestamp'ed -----------
timestamp = getElapsedTime(startTime);
//printf("(Elapsed time (Read Loading) : %9.4f seconds)\n\n", timestamp - lastEventTime);
readLoadTime += timestamp - lastEventTime;
processingTime += timestamp - lastEventTime;
lastEventTime = timestamp;
// ------------------------
// Build up the SRA Model in case there are new read lengths
for (i=0;i<queryInBatch;i++) {
unsigned int readLength = readLengthBufferFrame[i];
SRAModel * sraModels = SRAModelSetGetModel(sraModelSet,readLength,QUERY_POS_STRAND);
if (sraModels==NULL) {
SRAModelConstruct(sraModelSet,readLength);
sraModels = SRAModelSetGetModel(sraModelSet,readLength,QUERY_POS_STRAND);
MICSRA2BWTModelPopulate(&(cpModels[readLength]),sraModels);
//Print the SRAModel for Debug Purposes
// DebugPrintModel(sraModels,stdout);
// MICSRADebugPrintModel(&cpModels[readLength],stdout);
}
}
// Timestamp'ed -----------
timestamp = getElapsedTime(startTime);
//printf("(Elapsed time (Read Loading) : %9.4f seconds)\n\n", timestamp - lastEventTime);
modelTime += timestamp - lastEventTime;
processingTime += timestamp - lastEventTime;
lastEventTime = timestamp;
// ------------------------
/*#pragma offload target(mic) \
in(readBodyBufferFrame:length(memsize_readBodyBufferFrame) alloc_if(0) free_if(0)) \
in(readLengthBufferFrame:length(memsize_bufferPerRead) alloc_if(0) free_if(0))
{}
// Timestamp'ed -----------
timestamp = getElapsedTime(startTime);
printf("(Elapsed time (MIC Read Copy) : %9.4f seconds)\n\n", timestamp - lastEventTime);
lastEventTime = timestamp;
// ------------------------*/
unsigned int batchSize, numThreads;
GetBatchSizing(queryInBatch,InputNumOfMICThreads,1,&batchSize,&numThreads);
memset(threadAlgmt,0,sizeof(unsigned int)*InputNumOfMICThreads);
memset(occCount,0,sizeof(uint16_t)*memsize_bufferPerRead);
memset(outputBufferStatus,MIC_OUTPUT_STATUS_OPEN,sizeof(unsigned char)*memsize_bufferPerRead);
printf("MIC Core initiated (%u) ... ",numThreads); fflush(stdout);
////////////////////////////////////////////////////////////
// Alignment Body
////////////////////////////////////////////////////////////
#pragma offload target(mic) \
nocopy(bwt:length(1) alloc_if(0) free_if(0)) \
nocopy(rev_bwt:length(1) alloc_if(0) free_if(0)) \
\
in(readBodyBufferFrame:length(memsize_readBodyBufferFrame) alloc_if(0) free_if(0)) \
in(readLengthBufferFrame:length(memsize_bufferPerRead) alloc_if(0) free_if(0)) \
in(cpModels:length(SRA_MAX_READ_LENGTH) alloc_if(0) free_if(0)) \
\
inout(threadAlgmt:length(InputNumOfMICThreads) alloc_if(0) free_if(0)) \
inout(occCount:length(memsize_bufferPerRead) alloc_if(0) free_if(0)) \
\
out(outputBufferFrame:length(memsize_outputBufferFrame) alloc_if(0) free_if(0)) \
out(outputBufferMeta:length(memsize_outputBufferMeta) alloc_if(0) free_if(0)) \
inout(outputBufferStatus:length(memsize_bufferPerRead) alloc_if(0) free_if(0))
#pragma omp parallel for private(i,j) num_threads(InputNumOfMICThreads)
for (i=0;i<numThreads;i++) {
unsigned int offset = i * batchSize;
int charIdx;
unsigned char c;
uint16_t metaCount;
// Shared in core
unsigned int * outputPtr = &outputBufferFrame[i*MIC_SRA_OUTPUT_SIZE_PER_THREAD];
MICSRAOccMetadata * metaPtr = &outputBufferMeta[i*MIC_SRA_OUTPUT_META_PER_THREAD];
unsigned int outputVacancy = MIC_SRA_OUTPUT_SIZE_PER_THREAD;
unsigned int metaVacancy = MIC_SRA_OUTPUT_META_PER_THREAD;
// Multiple cell per read
unsigned char * patternPtr = &readBodyBufferFrame[offset*SRA_MAX_READ_LENGTH];
MICSRAArguments * micArgs = MICSRAARGConstruct();
// ATTENTION. BWT is hacked into MICSRAArgs before
// proper implementation of MICSRAMdl.
micArgs->outputType = SRA_REPORT_ALL;
micArgs->bwt = bwt;
micArgs->rev_bwt = rev_bwt;
#pragma ivdep
for (j=0;j<batchSize;j++) {
// One per read
uint16_t patternLen = readLengthBufferFrame[offset + j];
uint8_t * outputStatus = &outputBufferStatus[offset + j];
uint16_t * _occCount = &occCount[offset + j];
metaCount = 0;
////////////////////////////////////////////
// READ
////////////////////////////////////////////
if (outputVacancy<MIC_SRA_OUTPUT_MAX_ALIGNMENT) {
//Skip if the global output buffer is flooded
(*outputStatus) = MIC_OUTPUT_STATUS_UNHANDLE;
} else if (metaVacancy<MIC_SRA_OUTPUT_MAX_META) {
//Skip if the global output buffer is flooded
(*outputStatus) = MIC_OUTPUT_STATUS_UNHANDLE;
} else if (patternLen==0) {
//Skip if the read is an invalid read
(*outputStatus) = MIC_OUTPUT_STATUS_SKIPPED;
} else {
micArgs->seedLength = patternLen;
micArgs->readLength = patternLen;
micArgs->readCode = patternPtr;
micArgs->outputStatus = outputStatus;
micArgs->outputBlock = outputPtr;
micArgs->occCount = _occCount;
micArgs->metaBlock = metaPtr;
micArgs->metaCount = &metaCount;
// Calling the model aligner
threadAlgmt[i] += MICProcessReadDoubleStrand(micArgs,&(cpModels[patternLen]),&(cpModels[patternLen]));
// This is equivelance to if (*outputStatus == MIC_OUTPUT_STATUS_OPEN) then (*outputStatus) = MIC_OUTPUT_STATUS_COMPLETE
(*outputStatus) |= MIC_OUTPUT_STATUS_COMPLETE * (*outputStatus == MIC_OUTPUT_STATUS_OPEN);
}
patternPtr += SRA_MAX_READ_LENGTH;
outputPtr += (*_occCount);
outputVacancy -= (*_occCount);
metaPtr += (metaCount);
metaVacancy -= (metaCount);
}
MICSRAARGFree(micArgs);
}
printf("DONE\n");
// Timestamp'ed -----------
timestamp = getElapsedTime(startTime);
alignmentTime += timestamp - lastEventTime;
processingTime += timestamp - lastEventTime;
lastEventTime = timestamp;
// ------------------------
for (i=0;i<numThreads;i++) {
consSaCount += threadAlgmt[i];
}
////////////////////////////////////////////////////////////
// Produce Statistics of Output
////////////////////////////////////////////////////////////
#ifdef MIC_DEBUG_PRINT_OUTPUT_COUNTS
for (i=0;i<queryInBatch;i++) {
if ( outputBufferStatus[i] == MIC_OUTPUT_STATUS_CLOSE) {
numOfClosed++;
printf("Closed Item size = %u\n",occCount[i]);
}
unsigned int * outputPtr = &outputBufferFrame[i*MIC_SRA_OUTPUT_SIZE_PER_THREAD];
numOfOccContent+=occCount[i];
}
printf("[STATISTICS] Number of Occurrences found = %u\n",numOfOccContent);
printf("[STATISTICS] Number of Closed Output Collector = %u\n",numOfClosed);
#endif
////////////////////////////////////////////////////////////
// Handling Output
// This following pick results from MIC and output with CPU
////////////////////////////////////////////////////////////
unsigned char negPattern[SRA_MAX_READ_LENGTH];
for (i=0;i<numThreads;i++) {
unsigned int offset = i * batchSize;
unsigned int * outputPtr = &outputBufferFrame[i*MIC_SRA_OUTPUT_SIZE_PER_THREAD];
MICSRAOccMetadata * metaPtr = &outputBufferMeta[i*MIC_SRA_OUTPUT_META_PER_THREAD];
unsigned int metaCount = metaPtr->numPayload;
for (j=0;j<batchSize;j++) {
unsigned int bufferIdx = offset + j;
unsigned int readIdx = queryHandled + bufferIdx;
unsigned char * patternPtr = &readBodyBufferFrame[bufferIdx*SRA_MAX_READ_LENGTH];
char * patternName = &readNameBufferFrame[bufferIdx*MAX_SEQ_NAME_LENGTH];
uint16_t patternLen = readLengthBufferFrame[bufferIdx];
SRAFlipPattern(charMap,patternPtr,patternLen,negPattern);
SRAQueryInfoPopulate(sraArgs->QueryInfo,readIdx,patternName,patternLen,patternPtr,patternPtr,QUERY_POS_STRAND,dummyQuality);
SRAQueryInfoPopulate(sraArgs_neg->QueryInfo,readIdx,patternName,patternLen,negPattern,patternPtr,QUERY_NEG_STRAND,dummyQuality);
SRAModel * sraModels = SRAModelSetGetModel(sraModelSet,patternLen,QUERY_POS_STRAND);
if ( outputBufferStatus[bufferIdx] == MIC_OUTPUT_STATUS_CLOSE) {
printf("[INFO] Unaligned closed read - MIC unaligned - %s!\n",patternName);
// In this case the output buffer is flooded as the number of output
// generated is larger than the MIC_SRA_OUTPUT_MAX_ALIGNMENT; or the number of header
// generated is larger than MIC_SRA_OUTPUT_MAX_META. MIC was not
// able to handle all the alignment result hence declared the read
// unaligned on MIC.
cpuConsSaCount += ProcessReadDoubleStrand(sraArgs,sraArgs_neg,sraModels,sraModels);
} else if ( outputBufferStatus[bufferIdx] == MIC_OUTPUT_STATUS_UNHANDLE) {
printf("[INFO] Unhandled read - MIC unaligned - %s!\n",patternName);
// In this case the entire core shared output buffer is flooded as the number of output
// generated is larger than the MIC_SRA_OUTPUT_SIZE_PER_THREAD. MIC was not
// able to handle all the reads in the input read block hence declared all consecutive read
// unaligned on MIC.
cpuConsSaCount += ProcessReadDoubleStrand(sraArgs,sraArgs_neg,sraModels,sraModels);
} else if ( outputBufferStatus[bufferIdx] == MIC_OUTPUT_STATUS_SKIPPED) {
if ( bufferIdx < queryInBatch ) {
printf("[INFO] Skipped read - MIC unaligned - %s!\n",patternName);
}
// In this case the MIC actively skipped the alignment of this read. Reason being the
// read contains invalid character or unknown reason. CPU should also skip it.
// These sample code gives output when these reads are found from the output block and attempt to process it.
// cpuConsSaCount += ProcessReadDoubleStrand(sraArgs,sraArgs_neg,sraModels,sraModels);
} else if ( outputBufferStatus[bufferIdx] == MIC_OUTPUT_STATUS_OPEN) {
printf("[ERROR] Skipped read - MIC still open - %s!\n",patternName);
// In this case the MIC actively skipped the alignment of this read. For unknown reason.
cpuConsSaCount += ProcessReadDoubleStrand(sraArgs,sraArgs_neg,sraModels,sraModels);
} else if (occCount[bufferIdx]==0) {
OCCReportNoAlignment(sraArgs);
} else {
if (occCount[bufferIdx]>0) {
for (k=0;k<occCount[bufferIdx];k++) {
if (metaCount==0) {
metaPtr++;
metaCount = metaPtr->numPayload;
}
OCCAddTextPositionToCache(sraArgs,SRAOCC_TYPE_AWAIT_TRANSLATE,
outputPtr[k], (metaPtr->strand + 1),
patternLen, metaPtr->numOfErr, 0,
metaPtr->errors);
metaCount--;
}
}
}
outputPtr += occCount[bufferIdx];;
OCCFlushCache(sraArgs);
}
}
queryHandled+=queryInBatch;
// Timestamp'ed -----------
timestamp = getElapsedTime(startTime);
//printf("(Elapsed time (Output) : %9.4f seconds)\n\n", timestamp - lastEventTime);
outputTime += timestamp - lastEventTime;
processingTime += timestamp - lastEventTime;
lastEventTime = timestamp;
// ------------------------
printf("Number of Query Handled = %llu\n",queryHandled);
printf("Consolidated SA Count (MIC-Accm) = %llu\n",consSaCount);
printf("Consolidated SA Count (CPU-Accm) = %llu\n",cpuConsSaCount);
printf("Read Loading Time = %9.4f seconds\n",readLoadTime);
printf("Model Building Time = %9.4f seconds\n",modelTime);
printf("Alignment Time = %9.4f seconds\n",alignmentTime);
printf("Output Time = %9.4f seconds\n",outputTime);
printf("Processing (Total) Time = %9.4f seconds\n",processingTime);
printf("\n");
printf("\n");
}
SRAModelSetFree(sraModelSet);
UTBFRFree(readQueryBuffer);
SRAARGFree(sraArgs);
SRAARGSlaveFree(sraArgs_neg);
SAMOutputHeaderDestruct(&samOutputHeader);
////////////////////////////////////////////////////////////
// Free MIC Memory Allocated
////////////////////////////////////////////////////////////
#pragma offload target(mic) \
nocopy(bwt:length(1) alloc_if(0) free_if(1)) \
nocopy(bwtBwtCode:length(bwtCodeLengthInFile) alloc_if(0) free_if(1)) \
nocopy(bwtCumulativeFreq:length(ALPHABET_SIZE+1) alloc_if(0) free_if(1)) \
nocopy(bwtOccValue:length(bwt->occSizeInWord) alloc_if(0) free_if(1)) \
nocopy(bwtOccValueMajor:length(bwt->occMajorSizeInWord) alloc_if(0) free_if(1)) \
nocopy(micBwtSaValue:length(micBwtSaValueSizeInWord) alloc_if(0) free_if(1)) \
nocopy(micOccValue:length(bwt->micOccSizeInWord) alloc_if(0) free_if(1))
{}
#pragma offload target(mic) \
nocopy(rev_bwt:length(1) alloc_if(0) free_if(1)) \
nocopy(rbwtBwtCode:length(rbwtCodeLengthInFile) alloc_if(0) free_if(1)) \
nocopy(rbwtCumulativeFreq:length(ALPHABET_SIZE+1) alloc_if(0) free_if(1)) \
nocopy(rbwtOccValue:length(rev_bwt->occSizeInWord) alloc_if(0) free_if(1)) \
nocopy(rbwtOccValueMajor:length(rev_bwt->occMajorSizeInWord) alloc_if(0) free_if(1)) \
nocopy(rmicOccValue:length(rev_bwt->micOccSizeInWord) alloc_if(0) free_if(1))
{}
// Input and Output Data
#pragma offload target(mic) \
nocopy(readBodyBufferFrame:length(memsize_readBodyBufferFrame) alloc_if(0) free_if(1)) \
nocopy(readLengthBufferFrame:length(memsize_bufferPerRead) alloc_if(0) free_if(1)) \
\
nocopy(cpModels:length(SRA_MAX_READ_LENGTH) alloc_if(0) free_if(1)) \
nocopy(occCount:length(memsize_bufferPerRead) alloc_if(0) free_if(1)) \
nocopy(threadAlgmt:length(InputNumOfMICThreads) alloc_if(0) free_if(1)) \
\
nocopy(outputBufferFrame:length(memsize_outputBufferFrame) alloc_if(0) free_if(1)) \
nocopy(outputBufferMeta:length(memsize_outputBufferMeta) alloc_if(0) free_if(1)) \
nocopy(outputBufferStatus:length(memsize_bufferPerRead) alloc_if(0) free_if(1))
{}
////////////////////////////////////////////////////////////
// Free Memory Allocated
////////////////////////////////////////////////////////////
printf("\nFree index ... ");
fflush(stdout);
LTFree(lookup);
LTFree(rev_lookup);
BWTFree2BWT(idx2BWT);
printf("DONE\n");
free(readNameBufferFrame);
free(readBodyBufferFrame);
free(readLengthBufferFrame);
free(threadAlgmt);
free(occCount);
free(outputBufferFrame);
free(outputBufferStatus);
free(outputBufferMeta);
free(cpModels);
return 0;
}
void PrintAlignmentSettings(SRAArguments * sArgs) {
SRASetting * sraSettings = sArgs->AlgnmtSetting;
SRAIndex * sraIndex = sArgs->AlgnmtIndex;
switch (sraSettings->OutputType) {
case SRA_REPORT_UNIQUE_BEST:
printf("Report = Unique Best Alignment.\n");
break;
case SRA_REPORT_RANDOM_BEST:
printf("Report = Random Best Alignment.\n");
break;
case SRA_REPORT_BEST_QUALITY:
printf("Report = Best Quality Alignment.\n");
break;
case SRA_REPORT_ALL_BEST:
if (sraSettings->MaxResult==-1) {
printf("Report = All Best Alignment (All).\n");
} else {
printf("Report = All Best Alignment (#<=%d).\n",sraSettings->MaxResult);
}
break;
case SRA_REPORT_ALL:
if (sraSettings->MaxResult==-1) {
printf("Report = All Alignment (All).\n");
} else {
printf("Report = All Alignment (#<=%d).\n",sraSettings->MaxResult);
}
break;
case SRA_REPORT_DETAIL:
printf("Report = Unique Best Alignment /w Detail (For SNP Analysis).\n");
break;
}
if (sraSettings->ErrorType==SRA_TYPE_MISMATCH_ONLY) {
printf("Max #Mismatch = %d\n",sraSettings->MaxError);
} else if (sraSettings->ErrorType==SRA_TYPE_EDIT_DISTANCE) {
printf("Max #Edit = %d\n",sraSettings->MaxError);
}
printf("Max #NBMism = %d\n",sraSettings->MaxNBMismatch);
printf("Ref.Seq Length = %u\n",sraIndex->bwt->textLength);
printf("Strand = ");
switch (sraSettings->ReadStrand) {
case QUERY_POS_STRAND:
printf("Positive\n");
break;
case QUERY_NEG_STRAND:
printf("Negative\n");
break;
case QUERY_BOTH_STRAND:
printf("Both\n");
break;
}
printf("Threads = %d / %d\n",InputNumOfCPUThreads,InputNumOfMICThreads);
/*
printf("Pre-Align Trim = ");
if (TrimPrealignRead>0) {
printf("Enabled (trimming=%u%c)\n",TrimPrealignRead ,'%');
} else {
printf("Disabled\n");
}
printf("2-Pass = ");
if (SRASecondPassEnabled) {
printf("Enabled (trimming=%u%c loosen=%d forceIndel=%d)\n",TrimUnalignRead,'%',LooseCriteriaUnalignRead,ForceIndelUnalignedRead);
} else {
printf("Disabled\n");
}
printf("SGA Seed Rvy = ");
if (InputSGASeedEnhancement) {
printf("%.2f / %.2f\n",InputSGASeedLength, InputSGASeedLengthOverlap);
printf(" = loosen=%d\n",InputSGASeedLooseCriteria);
if (InputSGASeedOccLimitation!=-1)
printf(" = limit'd=%d\n",InputSGASeedOccLimitation);
} else {
printf("Disabled\n");
}*/
switch (sraSettings->OutputFormat) {
case SRA_OUTPUT_FORMAT_PLAIN:
printf("Output Format = Succinct (Plain).\n");
break;
case SRA_OUTPUT_FORMAT_SAM:
printf("Output Format = SAM v1.4 (Plain).\n");
break;
case SRA_OUTPUT_FORMAT_BAM:
printf("Output Format = BAM v1.4 (Binary).\n");
break;
}
printf("\n");
}
void ParseIniFile(char *iniFileName) {
dictionary *ini;
printf("Loading %s ..", iniFileName);
ini = iniparser_load(iniFileName, FALSE);
if (ini == NULL) {
printf("not found.\n");
return;
}
printf("done.\n");
// Memory parameters
InputMemoryMICMaxUsageMBytes = iniparser_getuint(ini, "Memory:MemoryMICMaxUsageMBytes", InputMemoryMICMaxUsageMBytes);
InputMemoryCPUMaxUsageMBytes = iniparser_getuint(ini, "Memory:MemoryCPUMaxUsageMBytes", InputMemoryCPUMaxUsageMBytes);
// Database parameters
iniparser_copystring(ini, "Database:SaValueFileName", InputSaValueFileName, InputSaValueFileName, MAX_FILENAME_LEN);
iniparser_copystring(ini, "Database:CPUSaValueFileName", InputCPUSaValueFileName, InputCPUSaValueFileName, MAX_FILENAME_LEN);
//Query Parameters
InputNumOfMICThreads = iniparser_getuint(ini, "MultipleThreading:NumOfMICThreads", InputNumOfMICThreads );
InputNumOfCPUThreads = iniparser_getuint(ini, "MultipleThreading:NumOfCPUThreads", InputNumOfCPUThreads );
// Short Read Alignement Parameters
char tmp[10];
iniparser_copystring(ini, "AlignmentModel:AlignmentModel", tmp, tmp, 4);
if (strcmp(tmp,"16G")==0) {
InputAlignmentModel = SRA_MODEL_16G;
} else {
InputAlignmentModel = SRA_MODEL_8G;
}
// Read input handling
iniparser_copystring(ini, "AlignmentModel:InvalidReadHandling", tmp, tmp, 8);
if (strcmp(tmp,"REPLACE")==0) {
InputSRAInvalidReadHandling = SRA_READ_REPLACE_INVALID;
} else {
InputSRAInvalidReadHandling = SRA_READ_SKIP_INVALID;
}
InputMaxNumOfAlignment = iniparser_getdouble(ini, "SingleEnd:MaxNumOfAlignment", InputMaxNumOfAlignment );
iniparser_freedict(ini);
}
dictionary *ParseInput(int argc, char** argv) {
dictionary *programInput;
char t1[3] = "-c"; // specify that this is a boolean type parameter; no following argument
char t2[3] = "-U"; // specify that this is a boolean type parameter; no following argument
char t3[3] = "-A"; // specify that this is a boolean type parameter; no following argument
char *d[3];
char *tempString;
int len;
int i;
d[0] = t1;
d[1] = t2;
d[2] = t3;
programInput = paraparser_load(argc, argv, 3, d); // 4 parameters are boolean type
if (argc<4) {
PrintHelp();
exit(1);