void SSearchTest::runIndexedTest( int32_t index, UBool exec, const char* &name, char *params )
{
if (exec) logln("TestSuite SSearchTest: ");
switch (index) {
#if !UCONFIG_NO_BREAK_ITERATION
case 0: name = "searchTest";
if (exec) searchTest();
break;
case 1: name = "offsetTest";
if (exec) offsetTest();
break;
case 2: name = "monkeyTest";
if (exec) monkeyTest(params);
break;
case 3: name = "sharpSTest";
if (exec) sharpSTest();
break;
case 4: name = "goodSuffixTest";
if (exec) goodSuffixTest();
break;
case 5: name = "searchTime";
if (exec) searchTime();
break;
#endif
default: name = "";
break; //needed to end loop
}
}
int TransmitProteinsToChildProcesses()
{
int numProteins = (int) proteins.size();
vector< simplethread_handle_t > workerHandles;
int sourceProcess, batchSize;
bool IsFinished = false;
Timer searchTime( true );
float totalSearchTime = 0.01f;
float lastUpdate = 0.0f;
int i = 0;
int numChildrenFinished = 0;
while( numChildrenFinished < g_numChildren )
{
#ifdef MPI_DEBUG
cout << g_hostString << " is listening for a child process to offer to search some proteins." << endl;
#endif
// Listen for a process requesting proteins.
// Extract the number of CPUs available on the process.
MPI_Recv( &sourceProcess, 1, MPI_INT, MPI_ANY_SOURCE, 0xFF, MPI_COMM_WORLD, &st );
int sourceCPUs = 0;
MPI_Recv( &sourceCPUs, 1, MPI_INT, sourceProcess, 0xFF, MPI_COMM_WORLD, &st );
int pOffset = i;
// Scale the batchSize with the number of cpus in the requested process.
batchSize = min( numProteins-i, g_rtConfig->ProteinBatchSize*sourceCPUs );
stringstream packStream;
binary_oarchive packArchive( packStream );
try
{
packArchive & pOffset;
string proteinStream;
for( int j = i; j < i + batchSize; ++j )
{
proteinStream += ">" + proteins[j].getName() + " " + proteins[j].getDescription() + "\n"
+ proteins[j].getSequence() + "\n";
}
packArchive & proteinStream;
} catch( exception& e )
{
cerr << g_hostString << " had an error: " << e.what() << endl;
exit(1);
}
#ifdef MPI_DEBUG
cout << "Process #" << sourceProcess << " has " << sourceCPUs << " cpus. Sending " << batchSize << " proteins." << endl;
#endif
if( i < numProteins )
{
MPI_Ssend( &batchSize, 1, MPI_INT, sourceProcess, 0x99, MPI_COMM_WORLD );
#ifdef MPI_DEBUG
cout << g_hostString << " is sending " << batchSize << " proteins." << endl;
Timer sendTime(true);
#endif
string pack = packStream.str();
int len = (int) pack.length();
MPI_Send( &len, 1, MPI_INT, sourceProcess, 0x00, MPI_COMM_WORLD );
MPI_Send( (void*) pack.c_str(), len, MPI_CHAR, sourceProcess, 0x01, MPI_COMM_WORLD );
#ifdef MPI_DEBUG
cout << g_hostString << " finished sending " << batchSize << " proteins; " <<
sendTime.End() << " seconds elapsed." << endl;
#endif
i += batchSize;
} else
{
batchSize = 0;
MPI_Ssend( &batchSize, 1, MPI_INT, sourceProcess, 0x99, MPI_COMM_WORLD );
#ifdef MPI_DEBUG
cout << "Process #" << sourceProcess << " has been informed that all proteins have been searched." << endl;
#endif
++numChildrenFinished;
}
totalSearchTime = searchTime.TimeElapsed();
if( !IsFinished && ( ( totalSearchTime - lastUpdate > g_rtConfig->StatusUpdateFrequency ) || i+1 == numProteins ) )
{
if( i+1 == numProteins )
IsFinished = true;
float proteinsPerSec = float(i+1) / totalSearchTime;
bpt::time_duration estimatedTimeRemaining(0, 0, round((numProteins - i) / proteinsPerSec));
cout << "Searched " << i << " of " << numProteins << " proteins; "
<< round(proteinsPerSec) << " per second, "
<< format_date_time("%H:%M:%S", bpt::time_duration(0, 0, round(totalSearchTime))) << " elapsed, "
<< format_date_time("%H:%M:%S", estimatedTimeRemaining) << " remaining." << endl;
lastUpdate = totalSearchTime;
}
}
return 0;
}