static void WriteConfiguration(ConfigurationMgr mgr)
{
mgr.SmithWatermanSection.FastaFile = _fastaFile;
mgr.SmithWatermanSection.DistanceMatrixFile = _distanceFile;
mgr.SmithWatermanSection.IndexFile = _indexFile;
mgr.SmithWatermanSection.TimingFile = _timingFile;
mgr.SmithWatermanSection.SummaryFile = _summaryFile;
mgr.SmithWatermanSection.WriteFullMatrix = _writeFullResults;
mgr.SmithWatermanSection.WritePartialMatrix = _writePartialResults;
mgr.SmithWatermanSection.WriteAlignments = _writeAlignments;
mgr.SmithWatermanSection.WriteAlignmentsFile = _writeAlignmentFile;
mgr.SmithWatermanSection.NodeCount = _nodeCount;
mgr.SmithWatermanSection.ProcessPerNodeCount = _processPerNodeCount;
mgr.SmithWatermanSection.SequenceCount = _sequenceCount;
mgr.SmithWatermanSection.GapOpenPenalty = _gapOpen;
mgr.SmithWatermanSection.GapExtensionPenalty = _gapExtension;
mgr.SmithWatermanSection.AlignmentType = _alignmentType;
mgr.SmithWatermanSection.DistanceFunctionType = _distanceFunction;
mgr.SmithWatermanSection.ScoringMatrixName = _scoringMatrixName;
// Changes the MDS config
mgr.ManxcatSection.DataPoints = _sequenceCount;
mgr.ManxcatSection.DistanceMatrixFile = _distanceFile;
mgr.ManxcatSection.IndexFile = _indexFile;
// Changes the Pairwise config
mgr.PairwiseSection.DataPoints = _sequenceCount;
mgr.PairwiseSection.DistanceMatrixFile = _distanceFile;
mgr.PairwiseSection.IndexFile = _indexFile;
}
static void ReadConfiguration(ConfigurationMgr mgr)
{
_fastaFile = mgr.SmithWatermanSection.FastaFile;
_distanceFile = mgr.SmithWatermanSection.DistanceMatrixFile;
_indexFile = mgr.SmithWatermanSection.IndexFile;
_timingFile = mgr.SmithWatermanSection.TimingFile;
_summaryFile = mgr.SmithWatermanSection.SummaryFile;
_writeFullResults = mgr.SmithWatermanSection.WriteFullMatrix;
_writePartialResults = mgr.SmithWatermanSection.WritePartialMatrix;
_writeAlignments = mgr.SmithWatermanSection.WriteAlignments;
_writeAlignmentFile = mgr.SmithWatermanSection.WriteAlignmentsFile;
_nodeCount = mgr.SmithWatermanSection.NodeCount;
_processPerNodeCount = mgr.SmithWatermanSection.ProcessPerNodeCount;
_sequenceCount = 0;
_gapOpen = mgr.SmithWatermanSection.GapOpenPenalty;
_gapExtension = mgr.SmithWatermanSection.GapExtensionPenalty;
_alignmentType = mgr.SmithWatermanSection.AlignmentType;
_distanceFunction = mgr.SmithWatermanSection.DistanceFunctionType;
_scoringMatrixName = mgr.SmithWatermanSection.ScoringMatrixName;
_emailResultsTo = string.Join(",", mgr.GlobalSection.EmailAddresses);
}
static public void SavePath()
{
ConfigurationMgr.AddConfigurationElement(CustomDefine.configKey_StandealoneOutPath, strStandAloneOutPath);
ConfigurationMgr.AddConfigurationElement(CustomDefine.configKey_IOSOutPath, strIOSOutPath);
ConfigurationMgr.AddConfigurationElement(CustomDefine.configKey_AndroidOutPath, strAndroidOutPath);
ConfigurationMgr.AddConfigurationElement(CustomDefine.configKey_IOSGetPath, strIOSGetPath);
ConfigurationMgr.AddConfigurationElement(CustomDefine.configKey_AndroidGetPath, strStandAloneOutPath);
ConfigurationMgr.AddConfigurationElement(CustomDefine.configKey_StandealoneOutPath, strAndroidGetPath);
}
private void OnLoad(object sender, EventArgs e)
{
_configMgr = new ConfigurationMgr(ConfigFile);
Rectangle boundsTmp = Screen.GetBounds(Point.Empty);
_configMgr.Settings.StartPoint = Point.Empty;
_configMgr.Settings.EndPoint = new Point(boundsTmp.Width, boundsTmp.Height);
_optionsCtrl.SetObject(_configMgr.Settings);
}
private void OnLoad(object sender, EventArgs e)
{
_configMgr = new ConfigurationMgr();
_configMgr.LoadProfile(out _option);
_fileMonitor.Option = _option;
_optionsCtrl.SetObject(_option);
_refreshTimer = new Timer();
_refreshTimer.Tick += new EventHandler(OnTimer);
_refreshTimer.Enabled = false;
_refreshTimer.Interval = 1500;
}
static PathMgr()
{
strStandAloneOutPath = ConfigurationMgr.ReadConfigurationElement(CustomDefine.configKey_StandealoneOutPath);
strIOSOutPath = ConfigurationMgr.ReadConfigurationElement(CustomDefine.configKey_IOSOutPath);
strAndroidOutPath = ConfigurationMgr.ReadConfigurationElement(CustomDefine.configKey_AndroidOutPath);
strStandAloneGetPath = ConfigurationMgr.ReadConfigurationElement(CustomDefine.configKey_StandealoneGetPath);
strIOSGetPath = ConfigurationMgr.ReadConfigurationElement(CustomDefine.configKey_IOSGetPath);
strAndroidGetPath = ConfigurationMgr.ReadConfigurationElement(CustomDefine.configKey_AndroidGetPath);
}
static void Main(string[] args)
{
ConfigurationMgr configMgr = new ConfigurationMgr();
Console.WriteLine("***** appSettings before adding section, element and element items *****");
Console.WriteLine();
configMgr.ReadAllAppSettings();
configMgr.CreateAppSettings("appSettings", "KEY0", "VALUE0");
configMgr.CreateAppSettings("appSettings", "KEY1", "VALUE1");
configMgr.CreateAppSettings("appSettings", "KEY2", "VALUE2");
Console.WriteLine("***** appSettings after adding section, element and element items *****");
Console.WriteLine();
configMgr.ReadAllAppSettings();
Console.WriteLine("appSettings value for KEY0 is {0}", configMgr.GetAppSettingValue("KEY0"));
Console.WriteLine();
Console.ReadLine();
}
public MainDlg(ConfigurationMgr configMgr)
{
_configMgr = configMgr;
InitializeComponent();
}
public ConfigurationMgr()
{
if (m_Instance == null)
m_Instance = this;
}
static void Main(string[] args)
{
// Load the command line args into our helper class which allows us to name arguments
Arguments pargs = new Arguments(args);
pargs.Usage = "Usage: Salsa.SmithWatermanMPI.exe /configFile=<string> /nodeCount=<int>";
if (pargs.CheckRequired(new string[] { "configFile", "nodeCount" }) == false)
{
Console.WriteLine(pargs.Usage);
return;
}
using (MPI.Environment env = new MPI.Environment(ref args))
{
Stopwatch overallTimer = Stopwatch.StartNew();
_configFile = pargs.GetValue <string>("configFile");
_mgr = ConfigurationMgr.LoadConfiguration(_configFile, true);
ReadConfiguration(_mgr);
_jobId = Environment.GetEnvironmentVariable("%CCP_JOBID%");
_taskId = Environment.GetEnvironmentVariable("%CCP_TASKID%");
_nodeCount = pargs.GetValue <int>("nodeCount");
_processPerNodeCount = MPI.Intracommunicator.world.Size / _nodeCount;
// Read the fasta input file using our parser.
FastaSequenceParser parser = new FastaSequenceParser();
_sequences = parser.Parse(_fastaFile);
_sequenceCount = _sequences.Count;
Console.WriteLine("Read {0} sequence from Fasta File {1}", _sequenceCount, _fastaFile);
if ((_writeAlignments == true) && (!string.IsNullOrWhiteSpace(_writeAlignmentFile)))
{
string fileName = string.Format("{0}_{1}{2}", Path.GetFileNameWithoutExtension(_writeAlignmentFile), MPI.Intracommunicator.world.Rank, Path.GetExtension(_writeAlignmentFile));
string filePath = Path.Combine(Path.GetDirectoryName(_writeAlignmentFile), fileName);
_writeAlignmentsWriter = File.CreateText(filePath);
}
MPIComputeLowerTriangularBlocked computeAlignments = new MPIComputeLowerTriangularBlocked(_sequenceCount, ComputeBlock);
// Block Compute Section
MPI.Intracommunicator.world.Barrier();
Stopwatch computeTimer = Stopwatch.StartNew();
Console.WriteLine("Rank {0} Beginning Blocks Compute: {1}", MPI.Intracommunicator.world.Rank, DateTime.Now.ToString());
computeAlignments.Compute();
Console.WriteLine("Rank {0} Finished Blocks Compute: {1}", MPI.Intracommunicator.world.Rank, DateTime.Now.ToString());
MPI.Intracommunicator.world.Barrier();
_overallComputeTime = computeTimer.ElapsedMilliseconds;
computeTimer.Stop();
if (_writeAlignmentsWriter != null)
{
_writeAlignmentsWriter.Flush();
_writeAlignmentsWriter.Dispose();
return;
}
// MPI Scatter Section
MPI.Intracommunicator.world.Barrier();
Stopwatch mpiScatterTimer = Stopwatch.StartNew();
Console.WriteLine("Rank {0} Beginning Scatter Blocks: {1}", MPI.Intracommunicator.world.Rank, DateTime.Now.ToString());
computeAlignments.Scatter();
Console.WriteLine("Rank {0} Finished Scatter Blocks: {1}", MPI.Intracommunicator.world.Rank, DateTime.Now.ToString());
MPI.Intracommunicator.world.Barrier();
_overallMPIScatterTime = mpiScatterTimer.ElapsedMilliseconds;
mpiScatterTimer.Stop();
Stopwatch ioTimer = Stopwatch.StartNew();
Console.WriteLine("Rank {0} Beginning File IO: {1}", MPI.Intracommunicator.world.Rank, DateTime.Now.ToString());
{
if (_writePartialResults)
{
string partialDistanceFile = string.Format("{0}_{1}{2}", Path.GetFileNameWithoutExtension(_distanceFile), MPI.Intercommunicator.world.Rank, Path.GetExtension(_distanceFile));
partialDistanceFile = Path.Combine(Path.GetDirectoryName(_distanceFile), partialDistanceFile);
PartialMatrixBinaryWriter partialWriter = new PartialMatrixBinaryWriter();
partialWriter.Write(computeAlignments.PartialMatrix, partialDistanceFile);
}
// todo: saliya - Workaround code for issue with Tempest. Remove this once Tempest is healthy.
if (_writeFullResults)
{
computeAlignments.WriteFullMatrixOnRank0(_distanceFile);
}
// todo: saliya - This code doesn't work on Tempest with all cores for large data sizes.
// Something is wrong with MPI in Tempest probably. Till then we will use the
// code above.
/*
* if (_writeFullResults)
* {
* foreach (int minRankOnNode in MPI.Intracommunicator.world.GetMinRankOnAllNodes())
* {
* computeAlignments.WriteFullMatrix(minRankOnNode, _distanceFile);
* // Matrix<TDistance> fullMatrix = computeAlignments.GetFullMatrix(minRankOnNode);
*
* // if (MPI.Intracommunicator.world.Rank == minRankOnNode)
* // {
* // MatrixBinaryWriter fullWriter = new MatrixBinaryWriter();
* // fullWriter.Write(fullMatrix, _distanceFile);
* // Console.WriteLine("\tWrote Distance Matrix: {0}\t{1}", Environment.MachineName, _distanceFile);
* // }
* }
* }*/
}
Console.WriteLine("Rank {0} Finished File IO: {1}", MPI.Intracommunicator.world.Rank, DateTime.Now.ToString());
MPI.Intracommunicator.world.Barrier();
_overallDiskIOTime = ioTimer.ElapsedMilliseconds;
ioTimer.Stop();
_overallTime = overallTimer.ElapsedMilliseconds;
overallTimer.Stop();
_totalPairCount = MPI.Intercommunicator.world.Reduce <long>(computeAlignments.CellsComputed, MPI.Operation <long> .Add, 0);
_totalComputeTime = MPI.Intracommunicator.world.Reduce <long>(computeAlignments.BlockComputeTime, MPI.Operation <long> .Add, 0);
_totalMPIScatterTime = MPI.Intracommunicator.world.Reduce <long>(computeAlignments.MPIScatterTime, MPI.Operation <long> .Add, 0);
if (MPI.Intracommunicator.world.Rank == 0)
{
WriteIndexFile(_indexFile, _sequences);
WriteTimingFile(_timingFile);
WriteSummaryFile(_summaryFile);
WriteConfiguration(_mgr);
_mgr.SaveAs(_configFile);
}
}
}
