unsigned long ntp::getInternetTime(){
unsigned long epoch;
int i=0;
int t=0;
sendNTPpacket();
delay(500);
epoch=receiveTime();
t=0; // count sent tries
while ((epoch == 0xFFFFFFFF) && (t<4)){
i=0; // count receve tries
while ((epoch == 0xFFFFFFFF) && (i<4)){
delay(500);
epoch=receiveTime();
i++;
}
if (epoch == 0xFFFFFFFF) {
sendNTPpacket();
t++;
}
}
internetEpoch=epoch;
arduinoShift=millis()/1000;
return (epoch);
}
int ReceiveUnpreparedSpectraBatchFromRootProcess()
{
int batchSize;
MPI_Ssend( &g_pid, 1, MPI_INT, 0, 0xFF, MPI_COMM_WORLD );
string pack;
int len;
#ifdef MPI_DEBUG
cout << g_hostString << " is receiving a batch of unsequenced spectra." << endl;
Timer receiveTime(true);
#endif
MPI_Recv( &len, 1, MPI_INT, 0, 0x00, MPI_COMM_WORLD, &st );
pack.resize( len );
MPI_Recv( (void*) pack.data(), len, MPI_CHAR, 0, 0x01, MPI_COMM_WORLD, &st );
stringstream compressedStream( pack );
stringstream packStream;
boost::iostreams::filtering_ostream decompressorStream;
decompressorStream.push( boost::iostreams::zlib_decompressor() );
decompressorStream.push( packStream );
boost::iostreams::copy( compressedStream, decompressorStream );
decompressorStream.reset();
binary_iarchive packArchive( packStream );
try
{
packArchive & batchSize;
if( !batchSize )
{
#ifdef MPI_DEBUG
cout << g_hostString << " is informed that all spectra have been sequence tagged." << endl;
#endif
return 0; // do not expect another batch
}
#ifdef MPI_DEBUG
cout << g_hostString << " finished receiving a batch of " << batchSize << " unsequenced spectra; " <<
receiveTime.End() << " seconds elapsed." << endl;
#endif
for( int j=0; j < batchSize; ++j )
{
Spectrum* s = new Spectrum;
packArchive & *s;
spectra.push_back( s );
}
} catch( exception& e )
{
cerr << g_hostString << " had an error: " << e.what() << endl;
exit(1);
}
return 1; // expect another batch
}
int ReceiveProteinBatchFromRootProcess()
{
int batchSize;
MPI_Ssend( &g_pid, 1, MPI_INT, 0, 0xFF, MPI_COMM_WORLD );
MPI_Ssend( &g_numWorkers, 1, MPI_INT, 0, 0xFF, MPI_COMM_WORLD );
MPI_Recv( &batchSize, 1, MPI_INT, 0, 0x99, MPI_COMM_WORLD, &st );
if( !batchSize )
{
#ifdef MPI_DEBUG
cout << g_hostString << " is informed that all proteins have been searched." << endl;
#endif
return 0; // expect another batch
}
#ifdef MPI_DEBUG
cout << g_hostString << " is receiving " << batchSize << " proteins." << endl;
Timer receiveTime(true);
#endif
string pack;
int len;
MPI_Recv( &len, 1, MPI_INT, 0, 0x00, MPI_COMM_WORLD, &st );
pack.resize( len );
MPI_Recv( (void*) pack.data(), len, MPI_CHAR, 0, 0x01, MPI_COMM_WORLD, &st );
#ifdef MPI_DEBUG
cout << g_hostString << " finished receiving " << batchSize << " proteins; " <<
receiveTime.End() << " seconds elapsed." << endl;
#endif
stringstream packStream( pack );
binary_iarchive packArchive( packStream );
try
{
packArchive & g_rtConfig->ProteinIndexOffset;
string proteinString;
packArchive & proteinString;
shared_ptr<std::istream> proteinStream(new std::istringstream(proteinString));
Serializer_FASTA unpacker;
shared_ptr<ProteomeData> subsetProteinsPtr(new ProteomeData);
unpacker.read(proteinStream, *subsetProteinsPtr);
proteins = proteinStore(subsetProteinsPtr, g_rtConfig->DecoyPrefix, false);
} catch( exception& e )
{
cerr << g_hostString << " had an error: " << typeid(e).name() << " (" << e.what() << ")" << endl;
exit(1);
}
return 1; // don't expect another batch
}
// Message delivered through _msg
void _processInternalMessages() {
bool isMetric;
uint8_t type = _msg.type;
#if !defined(MY_DISABLE_REMOTE_RESET)
if (type == I_REBOOT) {
// Requires MySensors or other bootloader with watchdogs enabled
hwReboot();
} else
#endif
if (type == I_CONFIG) {
// Pick up configuration from controller (currently only metric/imperial)
// and store it in eeprom if changed
if (_msg.getString() == NULL) {
isMetric = true;
} else {
isMetric = _msg.getString()[0] == 'M';
}
_cc.isMetric = isMetric;
hwWriteConfig(EEPROM_CONTROLLER_CONFIG_ADDRESS, isMetric);
} else if (type == I_PRESENTATION) {
if (!mGetAck(_msg)) {
// Re-send node presentation to controller
#if defined(MY_RADIO_FEATURE)
transportPresentNode();
#endif
if (presentation)
presentation();
}
} else if (type == I_HEARTBEAT) {
sendHeartbeat();
} else if (type == I_TIME) {
// Deliver time to callback
if (receiveTime)
receiveTime(_msg.getULong());
}
#if defined(MY_REPEATER_FEATURE)
if (type == I_CHILDREN) {
if (_msg.getString()[0] == 'C') {
// Clears child relay data for this node
debug(PSTR("clear routing table\n"));
uint8_t i = 255;
do {
hwWriteConfig(EEPROM_ROUTES_ADDRESS+i, BROADCAST_ADDRESS);
} while (i--);
// Clear parent node id & distance to gw
hwWriteConfig(EEPROM_PARENT_NODE_ID_ADDRESS, AUTO);
hwWriteConfig(EEPROM_DISTANCE_ADDRESS, DISTANCE_INVALID);
// Find parent node
transportFindParentNode();
_sendRoute(build(_msg, _nc.nodeId, GATEWAY_ADDRESS, NODE_SENSOR_ID, C_INTERNAL, I_CHILDREN,false).set(""));
}
}
#endif
}
int ReceiveSpectraFromRootProcess()
{
int numSpectra;
int done;
#ifdef MPI_DEBUG
cout << g_hostString << " is receiving " << numSpectra << " unprepared spectra." << endl;
Timer receiveTime(true);
#endif
string pack;
int len;
MPI_Recv( &len, 1, MPI_INT, 0, 0x00, MPI_COMM_WORLD, &st );
pack.resize( len );
MPI_Recv( (void*) pack.data(), len, MPI_CHAR, 0, 0x01, MPI_COMM_WORLD, &st );
stringstream compressedStream( pack );
stringstream packStream;
boost::iostreams::filtering_ostream decompressorStream;
decompressorStream.push( boost::iostreams::zlib_decompressor() );
decompressorStream.push( packStream );
boost::iostreams::copy( compressedStream, decompressorStream );
decompressorStream.reset();
binary_iarchive packArchive( packStream );
try
{
//cout << g_hostString << " is unpacking spectra." << endl;
packArchive & numSpectra;
//cout << g_hostString << " has " << numSpectra << " spectra." << endl;
packArchive & done;
for( int j=0; j < numSpectra; ++j )
{
Spectrum* s = new Spectrum;
packArchive & *s;
spectra.push_back( s );
}
//cout << g_hostString << " is finished unpacking spectra." << endl;
} catch( exception& e )
{
cerr << g_hostString << " had an error: " << e.what() << endl;
exit(1);
}
#ifdef MPI_DEBUG
cout << g_hostString << " finished receiving " << numSpectra << " unprepared spectra; " <<
receiveTime.End() << " seconds elapsed." << endl;
#endif
return done;
}
void networkManage() {
uint16_t size;
if (sendClient.available()) {
// int size = sendClient.read((uint8_t *) buf2, BUFFER_SIZE);
size = readHttpFrame(sendClient);
#ifdef HMAC
if (!isTimeReady()) {
uint16_t endPos = strstrpos_P((char *) buf, DOUBLE_ENDL);
receiveTime((char *) &buf[endPos + 4]);
}
#endif
}
#ifdef HMAC
if (!isTimeReady() && sendClient.status() == SnSR::CLOSED && (lastFailTime == 0 || millis() - lastFailTime > dateFailRetryWait)) {
if (sendClient.connect(NotifyDstIp, notifyDstPort)) {
int len = clientBuildTimeQuery((char *) buf);
sendClient.write(buf, len);
} else {
lastFailTime = millis();
sendClient.stop();
}
}
#endif
if (!sendClient.connected()) {
sendClient.stop();
}
if (notification != 0 && sendClient.status() == SnSR::CLOSED) {
// there is a notif and we are not handling another one
if (lastFailTime == 0 || millis() - lastFailTime > notifFailRetryWait) {
if (sendClient.connect(NotifyDstIp, notifyDstPort)) {
int len = clientBuildNextQuery((char *) buf);
sendClient.write(buf, len);
} else {
lastFailTime = millis();
sendClient.stop();
}
}
}
EthernetClient client = server.available();
if (client) {
while (client.connected()) {
if (client.available()) {
size = readHttpFrame(client);
if (size > 0) {
buf[size] = 0;
size = handleWebRequest((char *) buf, 0, size);
buf[size] = 0;
client.println((const char *) buf);
}
delay(1);
client.stop();
}
}
}
if (needReboot) {
resetFunc();
}
}
int ReceiveResultsFromChildProcesses(bool firstBatch = false)
{
int numSpectra;
int sourceProcess;
Timer ResultsTime( true );
float totalResultsTime = 0.01f;
float lastUpdate = 0.0f;
for( int p=0; p < g_numChildren; ++p )
{
MPI_Recv( &sourceProcess, 1, MPI_INT, MPI_ANY_SOURCE, 0xEE, MPI_COMM_WORLD, &st );
#ifdef MPI_DEBUG
cout << g_hostString << " is receiving search results." << endl;
Timer receiveTime(true);
#endif
string pack;
int len;
MPI_Recv( &len, 1, MPI_INT, sourceProcess, 0x00, MPI_COMM_WORLD, &st );
pack.resize( len );
MPI_Recv( (void*) pack.data(), len, MPI_CHAR, sourceProcess, 0x01, MPI_COMM_WORLD, &st );
stringstream compressedStream( pack );
stringstream packStream;
boost::iostreams::filtering_ostream decompressorStream;
decompressorStream.push( boost::iostreams::zlib_decompressor() );
decompressorStream.push( packStream );
boost::iostreams::copy( compressedStream, decompressorStream );
decompressorStream.reset();
binary_iarchive packArchive( packStream );
try
{
SearchStatistics childSearchStats;
packArchive & numSpectra;
packArchive & childSearchStats;
if(firstBatch)
{
searchStatistics = searchStatistics + childSearchStats;
}
else
{
searchStatistics.numPeptidesGenerated += childSearchStats.numPeptidesGenerated;
searchStatistics.numVariantsGenerated += childSearchStats.numVariantsGenerated;
searchStatistics.numComparisonsDone += childSearchStats.numComparisonsDone;
searchStatistics.numPeptidesSkipped += childSearchStats.numPeptidesSkipped;
}
//cout << g_hostString << " is unpacking results for " << numSpectra << " spectra." << endl;
for( SpectraList::iterator sItr = spectra.begin(); sItr != spectra.end(); ++sItr )
{
Spectrum* childSpectrum = new Spectrum;
Spectrum* rootSpectrum = *sItr;
packArchive & *childSpectrum;
rootSpectrum->numTargetComparisons += childSpectrum->numTargetComparisons;
rootSpectrum->numDecoyComparisons += childSpectrum->numDecoyComparisons;
rootSpectrum->processingTime += childSpectrum->processingTime;
rootSpectrum->resultsByCharge.resize(childSpectrum->resultsByCharge.size());
for (size_t z=0; z < childSpectrum->resultsByCharge.size(); ++z)
{
Spectrum::SearchResultSetType& rootResults = rootSpectrum->resultsByCharge[z];
Spectrum::SearchResultSetType& childResults = childSpectrum->resultsByCharge[z];
BOOST_FOREACH(const Spectrum::SearchResultPtr& result, childResults)
rootResults.add( result );
if (childResults.bestFullySpecificTarget().get()) rootResults.add(childResults.bestFullySpecificTarget());
if (childResults.bestFullySpecificDecoy().get()) rootResults.add(childResults.bestFullySpecificDecoy());
if (childResults.bestSemiSpecificTarget().get()) rootResults.add(childResults.bestSemiSpecificTarget());
if (childResults.bestSemiSpecificDecoy().get()) rootResults.add(childResults.bestSemiSpecificDecoy());
if (childResults.bestNonSpecificTarget().get()) rootResults.add(childResults.bestNonSpecificTarget());
if (childResults.bestNonSpecificDecoy().get()) rootResults.add(childResults.bestNonSpecificDecoy());
}
for(flat_map<int,int>::iterator itr = childSpectrum->mvhScoreDistribution.begin(); itr != childSpectrum->mvhScoreDistribution.end(); ++itr)
rootSpectrum->mvhScoreDistribution[(*itr).first] += (*itr).second;
for(flat_map<int,int>::iterator itr = childSpectrum->mzFidelityDistribution.begin(); itr != childSpectrum->mzFidelityDistribution.end(); ++itr)
rootSpectrum->mzFidelityDistribution[(*itr).first] += (*itr).second;
rootSpectrum->scoreHistogram += childSpectrum->scoreHistogram;
delete childSpectrum;
}
//cout << g_hostString << " is finished unpacking results." << endl;
} catch( exception& e )
{
cerr << g_hostString << " had an error: " << e.what() << endl;
exit(1);
}
#ifdef MPI_DEBUG
cout << g_hostString << " finished receiving " << numSpectra << " search results; " <<
receiveTime.End() << " seconds elapsed.";
#endif
totalResultsTime = ResultsTime.TimeElapsed();
if( ( totalResultsTime - lastUpdate > g_rtConfig->StatusUpdateFrequency ) || p+1 == g_numChildren )
{
float nodesPerSec = float(p+1) / totalResultsTime;
float estimatedTimeRemaining = float(g_numChildren-p-1) / nodesPerSec;
cout << "Received results from " << p+1 << " of " << g_numChildren << " worker nodes; " << nodesPerSec <<
" per second, " << estimatedTimeRemaining << " seconds remaining." << endl;
lastUpdate = totalResultsTime;
}
}
return 0;
}
