Exemplo n.º 1
0
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
    }
}
Exemplo n.º 2
0
    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;
    }