// Store objects with their propterties as QJsonObjects
// This way, every object can have custom properties, without creating special object classes
// The objects and its properties also may be saved to file in a human readable and modifiable format
bool ObjectContainer::add(ObjectType type, QJsonObject& data)
{
if (!verifyData(data)) return false;
ObjectItem* item = new ObjectItem(data["name"].toString());
item->setData(data);
m_model.appendRow(item);
return true;
}
void onBlock(int rank, ADIOS_FILE* f, ADIOS_VARINFO* v, int i, int j, int blockCounter, FastBitDataType ft)
{
char bmsVarName[100];
char keyVarName[100];
char offsetName[100];
int64_t var_ids_bms[v->nblocks[i]];
int64_t var_ids_key[v->nblocks[i]];
int64_t var_ids_offset[v->nblocks[i]];
sprintf(bmsVarName, "bms-%d-%d-%d", v->varid, i, j);
sprintf(keyVarName, "key-%d-%d-%d", v->varid, i, j);
sprintf(offsetName, "offset-%d-%d-%d", v->varid, i, j);
uint64_t blockSize = fastbit_adios_util_getBlockSize(v, i, j);
uint64_t blockDataByteSize = adios_type_size (v->type, v->value) * blockSize;
char notes[100];
logTime(NULL); logTimeMillis(NULL);
sprintf(notes, " reading data from adios on varid=%d, time=%d, block: %d, size=%ld bytes=%ld", v->varid, i, j, blockSize, blockDataByteSize);
logTime(notes); logTimeMillis(notes);
localtime(&indexRefresh);
//printf(" %d th block / (%d), size= %" PRIu64 " bytes=%" PRIu64, j, blockSize, blockCounter, blockDataByteSize);
void* data = malloc (blockDataByteSize);
ADIOS_SELECTION* blockSel = adios_selection_writeblock(j);
//adios_selcton_writeblock(num), 0 <= num < nblocks[timestep]
//ADIOS_SELECTION* blockSel = adios_selection_writeblock(blockCounter);
int err = adios_schedule_read_byid(f, blockSel, v->varid, i, 1, data);
if (!err) {
err = adios_perform_reads(f, 1);
} else {
printf("Unable to read block %d at timestep: %d \n", j, i);
return;
//break;
}
//fastbit_adios_util_printData(data, v->type, blockSize);
char selName[20];
sprintf(selName, "block-%d", j);
processData(data, blockSize, rank, i, selName, ft, v);
//processData(void* data, uint64_t dataCount, int rank, int timestep, char* selName, FastBitDataType ft, ADIOS_VARINFO* v)
adios_selection_delete(blockSel);
verifyData(f, v, blockCounter, i);
} // onblock
void FullRun::perform() {
Run::perform(); // process common data
verifyData();
setup();
loadPTable(pTableFile);
Interface::instance() << Interface::SEPARATOR << endl;
Interface::instance().showLog(true);
progress();
Interface::instance() << Interface::SEPARATOR << endl;
Interface::instance().showLog(true);
if (!cloAllBpCalculated && !cloNoBpCalculated && !cloNo3sRecFile) {
/* We calculate breakpoints for the best triplets */
for (unsigned long i = 0; i < childDataset->getSize(); i++) {
Genome* child = childDataset->getGenome(i);
Triplet* bestRecTriplet = child->getBestRecombinantTriplet();
if (bestRecTriplet != NULL) {
recordRecombinantTriplet(bestRecTriplet);
}
}
}
if (isRandomMode && randomLoopNum > 1) {
Interface::instance() << "Recombination sensitivity: "
<< recombinationSensitivity << "/" << randomLoopNum << "\n";
Interface::instance().showOutput(true);
} else {
displayResult();
Interface::instance() << Interface::SEPARATOR << endl;
Interface::instance().showLog(true);
savePValHistogram();
}
/* Close all files */
if (fileSkippedTriplets)
fileSkippedTriplets->close();
if (fileRecombinants)
fileRecombinants->close();
if (fileLongRecombinants != NULL)
fileLongRecombinants->close();
}
void AplusPopup::receiveEvent(MSEvent &event_)
{
if (event_.type() == AplusEvent::symbol())
{
if (dbg_tmstk) cout << "Received UpdateEvent in AplusPopup" << endl;
redraw();
}
if (event_.type() == AplusVerifyEvent::symbol())
{
if (dbg_tmstk) cout << "Received VerifyEvent in AplusPopup" << endl;
AplusVerifyEvent *ave = (AplusVerifyEvent *) &event_;
ave->result(verifyData(ave->aplusVar(), ave->a()));
}
}
bool ObjectContainer::modify(QJsonObject& data)
{
if (!verifyData(data)) return false;
ObjectItem * item = getItem(data["id"].toInt());
if (!item)
{
StaticLogger::logit("WARNING: Object not modified! The object with id '" + QString::number(data["id"].toInt()) + "' does not exist.");
return false;
}
item->setData(data["name"].toString(), Qt::DisplayRole); // Modify name in gui
item->setData(data); // Modify object data ( UserRole + 1)
return true;
}
int ProcessSearchProductInfo(int new_sock)
{
int ErrorCode;
int i;
PRODUCTINFO_REQ_T Request;
PRODUCTINFO_RES_T *Result;
printLog(HEAD, "==[MSG_GET_PRODUCT_INFO_REQ]==\n");
if((ErrorCode = ReadProductInfoReq(new_sock, &Request)) == FAIL) {
if(Request.ReqCount > 0 && Request.RequestList != (PRODUCTID_USERID_T *) NULL) {
free(Request.RequestList);
}
return ErrorCode;
}
if((Result = (PRODUCTINFO_RES_T *) malloc(sizeof(PRODUCTINFO_RES_T)*Request.ReqCount)) == NULL) {
printLog(HEAD, "ERR: Memory Allocation Error... size(%d)\n", sizeof(PRODUCTINFO_RES_T)*Request.ReqCount);
if(Request.ReqCount > 0 && Request.RequestList != (PRODUCTID_USERID_T *) NULL) {
free(Request.RequestList);
}
return FAIL;
}
memset(Result, 0, sizeof(PRODUCTINFO_RES_T)*Request.ReqCount);
if((ErrorCode = verifyData(Request)) == TRUE) {
ErrorCode = processProductInfoGet(Request, Result);
}
WriteProductInfoMulti("MSG_GET_PRODUCT_INFO_REQ", MSG_GET_PRODUCT_INFO_REQ, MSG_PDA_ERROR, Request.ReqCount, Result, ErrorCode, new_sock);
if(Request.ReqCount > 0 && Request.RequestList != (PRODUCTID_USERID_T *) NULL) {
free(Request.RequestList);
}
for(i = 0; i < Request.ReqCount; i++) {
if(Result[i].ResCount > 0 && Result[i].ResultData != (PRODUCTINFO_DATA_T *) NULL) {
free(Result[i].ResultData);
}
}
if(Request.ReqCount && Result != (PRODUCTINFO_RES_T *)NULL)
free(Result);
return TRUE;
}
void AplusScrolledWindow::receiveEvent(MSEvent &event_)
{
if (event_.type()==MSIndexedEvent::symbol())
{
MSIndexedEvent &ev=(MSIndexedEvent&)event_;
update(ev.index());
}
else if (event_.type()==MSNullEvent::symbol())
update(MSIndexVector::nullVector());
else if (event_.type() == AplusEvent::symbol())
{
if (dbg_tmstk) cout << "Received UpdateEvent in AplusScrolledWindow" << endl;
redraw();
}
if (event_.type() == AplusVerifyEvent::symbol())
{
if (dbg_tmstk) cout << "Received VerifyEvent in AplusScrolledWindow" << endl;
AplusVerifyEvent *ave = (AplusVerifyEvent *) &event_;
ave->result(verifyData(ave->aplusVar(), ave->a()));
}
}
/*
** Main function.
*/
int main(void)
{
volatile char originalData[260] = {0};
volatile char readFlash[260] = {0};
unsigned int retVal = 0;
unsigned char choice;
/* Initializes the UART Instance for serial communication. */
UARTStdioInit();
UARTPuts("Welcome to SPI EDMA application.\r\n", -1);
UARTPuts("Here the SPI controller on the SoC communicates with", -1);
UARTPuts(" the SPI Flash present on the SoM.\r\n\r\n", -1);
/* Initializes the EDMA3 Instance. */
EDMA3Initialize();
/* Initializes the SPI1 Instance. */
SPIInitialize();
/* Request EDMA3CC for Tx and Rx channels for SPI1. */
RequestEDMA3Channels();
/* Enable SPI communication. */
SPIEnable(SOC_SPI_1_REGS);
/* Enable the SPI Flash for writing to it. */
WriteEnable();
UARTPuts("Do you want to erase a sector of the flash before writing to it ?.", -1);
UARTPuts("\r\nInput y(Y)/n(N) to proceed.\r\n", -1);
choice = UARTGetc();
UARTPutc(choice);
if(('y' == choice) || ('Y' == choice))
{
/* Erasing the specified sector of SPI Flash. */
FlashSectorErase();
}
WriteEnable();
/* Program a specified Page of the SPI Flash. */
FlashPageProgram(originalData);
/* Read the contents of the page that was previously written to. */
ReadFromFlash(readFlash);
/* Verify whether the written and the read contents are equal. */
retVal = verifyData(&originalData[4], &readFlash[4], 256);
if(TRUE == retVal)
{
UARTPuts("\r\nThe data in the Flash and the one written ", -1);
UARTPuts("to it are equal.\r\n", -1);
}
else
{
UARTPuts("\r\n\r\nThe data in the Flash and the one written to it", -1);
UARTPuts(" are not equal.\r\n", -1);
}
while(1);
}
void
KeyChain::onCertificateData(const ptr_lib::shared_ptr<const Interest> &interest, const ptr_lib::shared_ptr<Data> &data, ptr_lib::shared_ptr<ValidationRequest> nextStep)
{
// Try to verify the certificate (data) according to the parameters in nextStep.
verifyData(data, nextStep->onVerified_, nextStep->onVerifyFailed_, nextStep->stepCount_);
}
void GuiInspectorField::setData( const char* data, bool callbacks )
{
if( mField == NULL )
return;
if( verifyData( data ) )
{
String strData = data;
const U32 numTargets = mInspector->getNumInspectObjects();
if( callbacks && numTargets > 1 )
{ mInspector->onBeginCompoundEdit_callback(); }
for( U32 i = 0; i < numTargets; ++ i )
{
SimObject* target = mInspector->getInspectObject( i );
String oldValue = target->getDataField( mField->pFieldname, mFieldArrayIndex);
// For numeric fields, allow input expressions.
String newValue = strData;
S32 type= mField->type;
if( type == TypeS8 || type == TypeS32 || type == TypeF32 )
{
char buffer[ 2048 ];
expandEscape( buffer, newValue );
newValue = Con::evaluatef( "%%f = \"%s\"; return ( %s );", oldValue.c_str(), buffer );
}
else if( type == TypeS32Vector
|| type == TypeF32Vector
|| type == TypeColorI
|| type == TypeColorF
|| type == TypePoint2I
|| type == TypePoint2F
|| type == TypePoint3F
|| type == TypePoint4F
|| type == TypeRectI
|| type == TypeRectF
|| type == TypeMatrixPosition
|| type == TypeMatrixRotation
|| type == TypeBox3F
|| type == TypeRectUV )
{
//TODO: we should actually take strings into account and not chop things up between quotes
U32 numNewUnits = StringUnit::getUnitCount( newValue, " \t\n\r" );
StringBuilder strNew;
bool isFirst = true;
for( U32 n = 0; n < numNewUnits; ++ n )
{
char oldComponentVal[ 1024 ];
StringUnit::getUnit( oldValue, n, " \t\n\r", oldComponentVal, sizeof( oldComponentVal ) );
char newComponentExpr[ 1024 ];
StringUnit::getUnit( newValue, n, " \t\n\r", newComponentExpr, sizeof( newComponentExpr ) );
char buffer[ 2048 ];
expandEscape( buffer, newComponentExpr );
const char* newComponentVal = Con::evaluatef( "%%f = \"%s\"; %%v = \"%s\"; return ( %s );",
oldComponentVal, oldValue.c_str(), buffer );
if( !isFirst )
strNew.append( ' ' );
strNew.append( newComponentVal );
isFirst = false;
}
newValue = strNew.end();
}
target->inspectPreApply();
// Fire callback single-object undo.
if( callbacks )
{
mInspector->onInspectorFieldModified_callback(
target->getIdString(),
mField->pFieldname,
mFieldArrayIndex ? mFieldArrayIndex : "(null)",
oldValue.c_str(),
newValue.c_str() );
}
target->setDataField( mField->pFieldname, mFieldArrayIndex, newValue );
// Give the target a chance to validate.
target->inspectPostApply();
}
if( callbacks && numTargets > 1 )
{ mInspector->onEndCompoundEdit_callback(); }
}
// Force our edit to update
updateValue();
}
int main (int argc, char** argv)
{
fastbit_init(0);
fastbit_set_verbose_level(0);
ADIOS_FILE * f;
//MPI_Comm comm_dummy = 0; // MPI_Comm is defined through adios_read.h
MPI_Comm comm_dummy = MPI_COMM_WORLD;
int rank, size;
MPI_Init (&argc, &argv);
MPI_Comm_rank (comm_dummy, &rank);
MPI_Comm_size (comm_dummy, &size);
adios_init_noxml (comm_dummy);
if (argc < 2) {
printf("Usage: index_fastbit fileName (attrName)");
return 0;
}
f = adios_read_open_file (argv[1], ADIOS_READ_METHOD_BP, comm_dummy);
if (f == NULL) {
printf ("::%s\n", adios_errmsg());
return -1;
}
/*
adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, (f->file_size)*2/1048576 + 5); // +5MB for extra room in buffer
adios_declare_group (&gAdios_group, gGroupNameFastbitIdx, "", adios_flag_yes);
adios_select_method (gAdios_group, "MPI", "", "");
*/
gIdxFileName = fastbit_adios_util_getFastbitIndexFileName(argv[1]);
unlink(gIdxFileName);
adios_allocate_buffer (ADIOS_BUFFER_ALLOC_NOW, 500); // +5MB for extra room in buffer
adios_declare_group (&gAdios_group, gGroupNameFastbitIdx, "", adios_flag_yes);
adios_select_method (gAdios_group, "MPI", "", "");
adios_open (&gAdios_write_file, gGroupNameFastbitIdx, gIdxFileName, "w", MPI_COMM_WORLD);
#ifdef MULTI_BLOCK
int testid = adios_define_var (gAdios_group, "pack", "", adios_integer , 0, 0, 0);
#endif
#ifdef BOX
int testid = adios_define_var (gAdios_group, "elements", "", adios_integer , 0, 0, 0);
#endif
//uint64_t estimatedbytes = (nb+nk+no)*adios_type_size(adios_double, NULL);
int jobCounter = getJobCounter(f);
uint64_t estimatedbytes = getByteEstimationOnFile(f, rank);
if (size > 1) {
int maxJobsPP = jobCounter/size + 1;
estimatedbytes = estimatedbytes * maxJobsPP /jobCounter +1048576;
}
estimatedbytes += 1048576;
uint64_t adios_totalsize; // adios_group_size needs to be call before any write_byid, Otherwise write_byid does nothing
adios_group_size (gAdios_write_file, estimatedbytes , &adios_totalsize);
printf("=> .. adios open output file: %s, rank %d allocated %" PRIu64 " bytes... \n", gIdxFileName, rank, adios_totalsize);
// IMPORTANT:
// can only call open/close once in a process
// otherwise data is tangled or only the data in the last open/close call is recorded
#ifdef MULTI_BLOCK
adios_write_byid(gAdios_write_file, testid, &pack);
#endif
#ifdef BOX
adios_write_byid(gAdios_write_file, testid, &recommended_index_ele);
#endif
sumLogTime(-1);
sumLogTimeMillis(-1);
if (argc >= 3) {
int i=2;
while (i<argc) {
const char* varName = argv[i];
if(strstr(varName, "<binning prec") != NULL) {
if (gBinningOption == NULL) {
gBinningOption = argv[i];
}
if (argc == 3) {
buildIndexOnAllVar(f, rank, size);
break;
}
i++;
continue;
} else {
ADIOS_VARINFO * v = adios_inq_var(f, varName);
if (v == NULL) {
printf("No such variable: %s\n", varName);
return 0;
}
printf("building fastbit index on variable: %s\n", varName);
buildIndex_mpi(f, v, rank, size);
adios_free_varinfo(v);
i++;
}
}
} else {
buildIndexOnAllVar(f, rank, size);
}
sumLogTime(0);
sumLogTimeMillis(0);
adios_close(gAdios_write_file);
adios_read_close(f);
//
// writing file clean up
//
// read back:
f = adios_read_open_file (gIdxFileName, ADIOS_READ_METHOD_BP, comm_dummy);
if (f == NULL) {
printf("No such file: %s \n", gIdxFileName);
return 0;
}
int numVars = f->nvars;
int i=0;
int k=0;
int j=0;
for (i=0; i<numVars; i++) {
char* varName = f->var_namelist[i];
ADIOS_VARINFO* v = adios_inq_var(f, varName);
adios_inq_var_blockinfo(f,v);
int timestep = 0;
for (k=0; k<v->sum_nblocks; k++) {
verifyData(f, v, k, timestep);
}
adios_free_varinfo(v);
}
adios_read_close(f);
if (rank == 0) {
printf(" ==> index file is at: %s\n", gIdxFileName);
}
// clean up
MPI_Barrier (comm_dummy);
adios_finalize (rank);
MPI_Finalize ();
free (gIdxFileName);
fastbit_cleanup();
return 0;
}
