public static void SetupParallelism(ref string[] args)
{
// Set up MPI
DAVectorUtility.MPI_Environment = new MPI.Environment(ref args);
DAVectorUtility.MPI_communicator = Communicator.world; //initializing MPI world communicator
DAVectorUtility.MPI_Rank = DAVectorUtility.MPI_communicator.Rank; // Rank of this process
DAVectorUtility.MPI_Size = DAVectorUtility.MPI_communicator.Size; // Number of MPI Processes
// Set up MPI
DAVectorUtility.MPIperNodeCount = DAVectorUtility.MPI_Size / DAVectorUtility.NodeCount;
if ((DAVectorUtility.MPIperNodeCount * DAVectorUtility.NodeCount) != DAVectorUtility.MPI_Size)
{
Exception e = DAVectorUtility.SALSAError("Inconsistent MPI counts Nodes "
+ DAVectorUtility.NodeCount.ToString() + " Size " + DAVectorUtility.MPI_Size.ToString());
throw (e);
}
DAVectorUtility.ParallelPattern = "---------------------------------------------------------\nMachine:"
+ MPI.Environment.ProcessorName.ToString() + " " + DAVectorUtility.ThreadCount.ToString()
+ "x" + DAVectorUtility.MPIperNodeCount.ToString() + "x" + DAVectorUtility.NodeCount.ToString();
if (DAVectorUtility.MPI_Rank == 0)
{
DAVectorUtility.SALSAPrint(0, DAVectorUtility.ParallelPattern);
}
} // End SetupParallelism
} // End ReadDataFromFile
public static void ReadDataFromFile(string fname, int ClusterPosition, int[] InitialPointAssignment, int StartPointPosition)
{
char[] _sep = new[] { ' ', ',', '\t' };
int FirstPointPosition = 0;
int TotalNumberPointstoRead = 0;
FirstPointPosition = DAVectorUtility.PointStart_Process;
TotalNumberPointstoRead = DAVectorUtility.PointCount_Process;
int MinSplitSize = ClusterPosition + 1;
if (StartPointPosition >= 0)
{
MinSplitSize = Math.Max(MinSplitSize, StartPointPosition + Program.ParameterVectorDimension);
}
bool success = false;
string line = " Unset";
int CountLinesinFile = 0;
string stringtest = "";
try
{
StreamReader sr = null;
if (!string.IsNullOrEmpty(fname))
{
Stream stream = File.Open(fname, FileMode.Open, FileAccess.Read, FileShare.Read);
sr = new StreamReader(stream);
}
if (sr != null)
{
while (!sr.EndOfStream)
{
line = sr.ReadLine();
if (!string.IsNullOrEmpty(line))
{
string[] splits = line.Trim().Split(_sep, StringSplitOptions.RemoveEmptyEntries);
if (splits.Length < MinSplitSize)
{
DAVectorUtility.SALSAPrint(0, "Count " + CountLinesinFile.ToString() + " Illegal data length on Point file " + splits.Length.ToString()
+ " " + MinSplitSize.ToString() + " " + line);
continue;
} // Skip header lines
double junk;
if (!Double.TryParse(splits[StartPointPosition], out junk))
{
continue; // Skip header lines
}
if (CountLinesinFile < FirstPointPosition)
{
CountLinesinFile += 1;
continue;
}
int ActualPointPosition = CountLinesinFile - FirstPointPosition;
int label = 0;
if (StartPointPosition >= 0)
{
stringtest = "0 *" + splits[StartPointPosition];
Program.PointPosition[ActualPointPosition][0] = double.Parse(splits[StartPointPosition]);
stringtest = "1 *" + splits[StartPointPosition + 1];
Program.PointPosition[ActualPointPosition][1] = double.Parse(splits[StartPointPosition + 1]);
if (Program.ParameterVectorDimension > 2)
{
for (int VectorIndex = 2; VectorIndex < Program.ParameterVectorDimension; VectorIndex++)
{
stringtest = VectorIndex.ToString() + " *" + splits[StartPointPosition + VectorIndex];
Program.PointPosition[ActualPointPosition][VectorIndex] = double.Parse(splits[VectorIndex + StartPointPosition]);
}
}
}
if (ClusterPosition >= 0)
{
if (!Int32.TryParse(splits[ClusterPosition], out label))
{
label = 1;
}
InitialPointAssignment[ActualPointPosition] = label - 1;
}
++ActualPointPosition;
++CountLinesinFile;
if (CountLinesinFile >= (FirstPointPosition + TotalNumberPointstoRead))
{
break;
}
}
}
if (CountLinesinFile != (FirstPointPosition + TotalNumberPointstoRead))
{
Exception e = DAVectorUtility.SALSAError("Illegal count on Points file " + fname + " Rank " + DAVectorUtility.MPI_Rank.ToString()
+ " Lines in File " + CountLinesinFile.ToString() + " Number to Read " + TotalNumberPointstoRead.ToString());
throw (e);
}
success = true;
}
sr.Close();
}
catch (Exception e)
{
Console.WriteLine(stringtest + "* Failed reading Points data " + DAVectorUtility.MPI_Rank.ToString() + " " + CountLinesinFile.ToString() + " Start "
+ FirstPointPosition.ToString() + " Number " + TotalNumberPointstoRead.ToString() + " " + line + e);
throw (e);
}
if (!success)
{
Exception e = DAVectorUtility.SALSAError("DA Vector File read error " + fname);
throw (e);
}
} // End ReadDataFromFile
} // End ReadDataFromFile
public static void Read3DDataFromFile(string fname, int VectorSize, int StartPointPosition)
{
char[] _sep = new[] { ' ', ',', '\t' };
int FirstPointPosition = 0;
int TotalNumberPointstoRead = 0;
TotalNumberPointstoRead = DAVectorUtility.PointCount_Global;
int MinSplitSize = StartPointPosition + VectorSize;
bool success = false;
string line = " Unset";
int CountLinesinFile = 0;
try
{
StreamReader sr = null;
if (!string.IsNullOrEmpty(fname))
{
Stream stream = File.Open(fname, FileMode.Open, FileAccess.Read, FileShare.Read);
sr = new StreamReader(stream);
}
if (sr != null)
{
while (!sr.EndOfStream)
{
line = sr.ReadLine();
if (!string.IsNullOrEmpty(line))
{
string[] splits = line.Trim().Split(_sep);
if (splits.Length < MinSplitSize)
{
DAVectorUtility.SALSAPrint(0, "Count " + CountLinesinFile.ToString() + " Illegal data length on Point file " + splits.Length.ToString()
+ " " + MinSplitSize.ToString() + " " + line);
continue;
} // Skip header lines
double junk;
if (!Double.TryParse(splits[StartPointPosition], out junk))
{
continue; // Skip header lines
}
if (CountLinesinFile < FirstPointPosition)
{
CountLinesinFile += 1;
continue;
}
int ActualPointPosition = CountLinesinFile - FirstPointPosition;
if (StartPointPosition >= 0)
{
Program.FullPoint3DPosition[ActualPointPosition][0] = double.Parse(splits[StartPointPosition]);
Program.FullPoint3DPosition[ActualPointPosition][1] = double.Parse(splits[StartPointPosition + 1]);
if (VectorSize > 2)
{
for (int VectorIndex = 2; VectorIndex < VectorSize; VectorIndex++)
{
Program.FullPoint3DPosition[ActualPointPosition][VectorIndex] = double.Parse(splits[VectorIndex + StartPointPosition]);
}
}
}
++ActualPointPosition;
++CountLinesinFile;
if (CountLinesinFile >= (FirstPointPosition + TotalNumberPointstoRead))
{
break;
}
}
}
if (CountLinesinFile != (FirstPointPosition + TotalNumberPointstoRead))
{
Exception e = DAVectorUtility.SALSAError("Illegal count on Points file " + fname + " Rank " + DAVectorUtility.MPI_Rank.ToString()
+ " Lines in File " + CountLinesinFile.ToString() + " Number to Read " + TotalNumberPointstoRead.ToString());
throw (e);
}
success = true;
}
sr.Close();
}
catch (Exception e)
{
Console.WriteLine("Failed reading Points data " + DAVectorUtility.MPI_Rank.ToString() + " " + CountLinesinFile.ToString() + " Start "
+ FirstPointPosition.ToString() + " Number " + TotalNumberPointstoRead.ToString() + " " + line + e);
throw (e);
}
if (!success)
{
Exception e = DAVectorUtility.SALSAError("DA Vector File read error " + fname);
throw (e);
}
} // End Read3DDataFromFile
} // End ReadLabelsFromFile
// read point data from file to memory
// OutputFileType = 0 Harvard Format Cosmic Index mz RT Charge Peptide Peptide.id Mclust Medea
// OutputFileType = 1 Ingest output file: Index mz RT 0.0 Cluster#
public static void AnalyzeDataFromFile(string fname)
{
char[] _sep = new[] { ' ', '\t' };
int Maxcounts = 200;
int[] CountLabels = new int[Maxcounts];
for (int ChargeIndex = 0; ChargeIndex < Maxcounts; ChargeIndex++)
{
CountLabels[ChargeIndex] = 0;
}
int MinSplitSize = Program.ParameterVectorDimension + 3;
int SplitPosition = 1 + Program.ParameterVectorDimension;
if (Program.InputFileType == 1)
{
MinSplitSize = 5;
SplitPosition = 4;
}
bool success = false;
int count = 0;
try
{
StreamReader sr = null;
if (!string.IsNullOrEmpty(fname))
{
Stream stream = File.Open(fname, FileMode.Open, FileAccess.Read, FileShare.Read);
sr = new StreamReader(stream);
}
if (sr != null)
{
string line;
while (!sr.EndOfStream)
{
line = sr.ReadLine();
if (!string.IsNullOrEmpty(line))
{
string[] splits = line.Trim().Split(_sep);
if (splits.Length < MinSplitSize)
{
Exception e = DAVectorUtility.SALSAError("Count " + count.ToString() + "Illegal data length on Point file " + splits.Length.ToString()
+ " " + MinSplitSize.ToString() + " " + line);
throw (e);
}
int Charge = -101;
if (!Int32.TryParse(splits[SplitPosition], out Charge))
{
continue;
}
if ((Program.SelectedInputLabel < 0) && (Charge == -Program.SelectedInputLabel))
{
continue;
}
int position = 1 + Charge;
position = Math.Max(0, position);
position = Math.Min(Maxcounts - 1, position);
++CountLabels[position];
count++;
}
}
success = true;
if (Program.SelectedInputLabel >= 0)
{
DAVectorUtility.PointCount_Global = CountLabels[1 + Program.SelectedInputLabel];
}
else
{
DAVectorUtility.PointCount_Global = 0;
for (int selection = 0; selection < Maxcounts; selection++)
{
DAVectorUtility.PointCount_Global += CountLabels[selection];
}
}
DAVectorUtility.SALSAPrint(1, "File Analyzed " + fname + " Total " + count.ToString());
string label = "Charge";
if (Program.InputFileType == 1)
{
label = "Cluster";
}
if (CountLabels[0] > 0)
{
DAVectorUtility.SALSAPrint(1, "Negative " + label + "s " + CountLabels[0].ToString());
}
for (int LabelIndex = 1; LabelIndex < (Maxcounts - 1); LabelIndex++)
{
if (CountLabels[LabelIndex] > 0)
{
DAVectorUtility.SALSAPrint(1, label + " " + (LabelIndex - 1).ToString() + " Count " + CountLabels[LabelIndex].ToString());
}
}
if (CountLabels[Maxcounts - 1] > 0)
{
DAVectorUtility.SALSAPrint(1, "Overflow " + label + "s " + CountLabels[Maxcounts - 1].ToString());
}
}
sr.Close();
}
catch (Exception e)
{
Console.WriteLine("Failed reading Points data" + e);
throw (e);
}
if (!success)
{
Exception e = DAVectorUtility.SALSAError("DA Vector File Analyze error " + fname);
throw (e);
}
} // End AnalyzeDataFromFile