Add parallel parsing/serialization for Simple TSV
Doesn't give as much of a performance bonus as hoped
This commit is contained in:
Nathan McRae
parent
3727f8051b
commit
4ddb8dc44d
|
|
@ -644,6 +644,146 @@ public class SaneTsv
|
|||
return Encoding.UTF8.GetBytes(escapedString.ToString());
|
||||
}
|
||||
|
||||
public static byte[] SerializeSimpleTsvParallel(IList<string> header, IList<IList<string>> data)
|
||||
{
|
||||
var serialized = new List<byte>();
|
||||
var escapedString = new StringBuilder();
|
||||
|
||||
// Serialize header
|
||||
for (int i = 0; i < header.Count; i++)
|
||||
{
|
||||
if (header[i].Contains(':'))
|
||||
{
|
||||
throw new Exception($"Column {i} contains the character ':'");
|
||||
}
|
||||
|
||||
for (int j = i + 1; j < header.Count; j++)
|
||||
{
|
||||
if (header[i] == header[j])
|
||||
{
|
||||
throw new Exception("Column names in header must be unique");
|
||||
}
|
||||
}
|
||||
|
||||
for (int j = 0; j < header[i].Count(); j++)
|
||||
{
|
||||
if (header[i][j] == '\n')
|
||||
{
|
||||
escapedString.Append("\\n");
|
||||
}
|
||||
else if (header[i][j] == '\t')
|
||||
{
|
||||
escapedString.Append("\\t");
|
||||
}
|
||||
else if (header[i][j] == '\\')
|
||||
{
|
||||
escapedString.Append("\\\\");
|
||||
}
|
||||
else if (header[i][j] == '#')
|
||||
{
|
||||
escapedString.Append("\\#");
|
||||
}
|
||||
else
|
||||
{
|
||||
escapedString.Append(header[i][j]);
|
||||
}
|
||||
}
|
||||
|
||||
if (i == header.Count - 1)
|
||||
{
|
||||
escapedString.Append('\n');
|
||||
}
|
||||
else
|
||||
{
|
||||
escapedString.Append('\t');
|
||||
}
|
||||
}
|
||||
|
||||
serialized.AddRange(Encoding.UTF8.GetBytes(escapedString.ToString()));
|
||||
|
||||
// TODO: need to figure out where the crossover it
|
||||
// Complication: it probably depends on processor count
|
||||
if (data.Count < 100)
|
||||
{
|
||||
serialized.AddRange(Encoding.UTF8.GetBytes(SerializeSimpleTsvParallel(data, 0, data.Count)));
|
||||
}
|
||||
else
|
||||
{
|
||||
int tasks = Environment.ProcessorCount - 1;
|
||||
int splitCount = data.Count / tasks;
|
||||
byte[][] bytes = new byte[tasks][];
|
||||
Parallel.For(0, tasks, i =>
|
||||
{
|
||||
int endIndex;
|
||||
if (i == tasks - 1)
|
||||
{
|
||||
endIndex = data.Count;
|
||||
}
|
||||
else
|
||||
{
|
||||
endIndex = (i + 1) * splitCount;
|
||||
}
|
||||
string escapedString = SerializeSimpleTsvParallel(data, i * splitCount, endIndex);
|
||||
bytes[i] = Encoding.UTF8.GetBytes(escapedString);
|
||||
});
|
||||
|
||||
for (int i = 0; i < tasks; i++)
|
||||
{
|
||||
serialized.AddRange(bytes[i]);
|
||||
}
|
||||
}
|
||||
|
||||
return serialized.ToArray();
|
||||
}
|
||||
|
||||
public static string SerializeSimpleTsvParallel(IList<IList<string>> data, int startIndex, int endIndex)
|
||||
{
|
||||
var escapedString = new StringBuilder();
|
||||
|
||||
// Serialize data
|
||||
for (int i = startIndex; i < endIndex; i++)
|
||||
{
|
||||
for (int j = 0; j < data[i].Count; j++)
|
||||
{
|
||||
for (int k = 0; k < data[i][j].Length; k++)
|
||||
{
|
||||
if (data[i][j][k] == '\n')
|
||||
{
|
||||
escapedString.Append("\\n");
|
||||
}
|
||||
else if (data[i][j][k] == '\t')
|
||||
{
|
||||
escapedString.Append("\\t");
|
||||
}
|
||||
else if (data[i][j][k] == '\\')
|
||||
{
|
||||
escapedString.Append("\\\\");
|
||||
}
|
||||
else if (data[i][j][k] == '#')
|
||||
{
|
||||
escapedString.Append("\\#");
|
||||
}
|
||||
else
|
||||
{
|
||||
escapedString.Append(data[i][j][k]);
|
||||
}
|
||||
}
|
||||
|
||||
if (j < data[i].Count - 1)
|
||||
{
|
||||
escapedString.Append('\t');
|
||||
}
|
||||
else if (i < data.Count - 1)
|
||||
{
|
||||
escapedString.Append('\n');
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return escapedString.ToString();
|
||||
}
|
||||
|
||||
|
||||
public static (string[] columns, string[][] data) ParseSimpleTsv(byte[] inputBuffer)
|
||||
{
|
||||
string[] columnNames = null;
|
||||
|
|
@ -795,6 +935,225 @@ public class SaneTsv
|
|||
return (columnNames, records.ToArray());
|
||||
}
|
||||
|
||||
public static (string[] columns, string[][] data) ParseSimpleTsvParallel(byte[] inputBuffer)
|
||||
{
|
||||
string[] columnNames = null;
|
||||
var headers = new List<byte[]>();
|
||||
var fieldBytes = new List<byte>();
|
||||
int startOfData = -1;
|
||||
for (int i = 0; i < inputBuffer.Count(); i++)
|
||||
{
|
||||
if (inputBuffer[i] == '\\')
|
||||
{
|
||||
if (i + 1 == inputBuffer.Count())
|
||||
{
|
||||
throw new Exception($"Found '\\' at end of input");
|
||||
}
|
||||
if (inputBuffer[i + 1] == 'n')
|
||||
{
|
||||
fieldBytes.Add((byte)'\n');
|
||||
i++;
|
||||
}
|
||||
else if (inputBuffer[i + 1] == '\\')
|
||||
{
|
||||
fieldBytes.Add((byte)'\\');
|
||||
i++;
|
||||
}
|
||||
else if (inputBuffer[i + 1] == 't')
|
||||
{
|
||||
fieldBytes.Add((byte)'\t');
|
||||
i++;
|
||||
}
|
||||
else if (inputBuffer[i + 1] == '#')
|
||||
{
|
||||
fieldBytes.Add((byte)'#');
|
||||
i++;
|
||||
}
|
||||
else
|
||||
{
|
||||
throw new Exception($"Expected 'n', 't', '#', or '\\' after '\\' at line {1} column {i}");
|
||||
}
|
||||
}
|
||||
else if (inputBuffer[i] == '\t')
|
||||
{
|
||||
// end of field
|
||||
headers.Add(fieldBytes.ToArray());
|
||||
fieldBytes.Clear();
|
||||
}
|
||||
else if (inputBuffer[i] == '\n')
|
||||
{
|
||||
// This is the end of the header
|
||||
headers.Add(fieldBytes.ToArray());
|
||||
startOfData = i + 1;
|
||||
|
||||
columnNames = new string[headers.Count];
|
||||
fieldBytes.Clear();
|
||||
|
||||
for (int j = 0; j < headers.Count; j++)
|
||||
{
|
||||
string columnString;
|
||||
try
|
||||
{
|
||||
columnString = Encoding.UTF8.GetString(headers[j]);
|
||||
}
|
||||
catch (Exception e)
|
||||
{
|
||||
throw new Exception($"Column {headers.Count} name is not valid UTF-8", e);
|
||||
}
|
||||
|
||||
if (columnString.Contains(':'))
|
||||
{
|
||||
throw new Exception($"Header {headers.Count} contain ':', which is not allowed for column names");
|
||||
}
|
||||
|
||||
columnNames[j] = columnString;
|
||||
}
|
||||
|
||||
// Done parsing header
|
||||
break;
|
||||
}
|
||||
else if (inputBuffer[i] == '#')
|
||||
{
|
||||
throw new Exception($"Found unescaped '#' at line 1, column {i}");
|
||||
}
|
||||
else
|
||||
{
|
||||
fieldBytes.Add(inputBuffer[i]);
|
||||
}
|
||||
}
|
||||
|
||||
return (columnNames, ParseSimpleTsvParallel(inputBuffer, columnNames.Length, startOfData, inputBuffer.Length));
|
||||
}
|
||||
|
||||
public static string[][] ParseSimpleTsvParallel(byte[] inputBuffer, int numFields, int startIndex, int endIndex)
|
||||
{
|
||||
var fieldBytes = new List<byte>();
|
||||
var fields = new List<byte[]>();
|
||||
var records = new List<string[]>();
|
||||
|
||||
int line = 1;
|
||||
int currentLineStart = 0;
|
||||
|
||||
// Go back to the start of the current line
|
||||
int i = startIndex;
|
||||
while (inputBuffer[i] != '\n')
|
||||
{
|
||||
i--;
|
||||
}
|
||||
|
||||
// We want to start at the first byte of the current line
|
||||
i++;
|
||||
|
||||
for (; i < endIndex; i++)
|
||||
{
|
||||
if (inputBuffer[i] == '\\')
|
||||
{
|
||||
if (i + 1 == inputBuffer.Count())
|
||||
{
|
||||
throw new Exception($"Found '\\' at end of input");
|
||||
}
|
||||
if (inputBuffer[i + 1] == 'n')
|
||||
{
|
||||
fieldBytes.Add((byte)'\n');
|
||||
i++;
|
||||
}
|
||||
else if (inputBuffer[i + 1] == '\\')
|
||||
{
|
||||
fieldBytes.Add((byte)'\\');
|
||||
i++;
|
||||
}
|
||||
else if (inputBuffer[i + 1] == 't')
|
||||
{
|
||||
fieldBytes.Add((byte)'\t');
|
||||
i++;
|
||||
}
|
||||
else if (inputBuffer[i + 1] == '#')
|
||||
{
|
||||
fieldBytes.Add((byte)'#');
|
||||
i++;
|
||||
}
|
||||
else
|
||||
{
|
||||
throw new Exception($"Expected 'n', 't', '#', or '\\' after '\\' at line {line} column {i - currentLineStart}");
|
||||
}
|
||||
}
|
||||
else if (inputBuffer[i] == '\t')
|
||||
{
|
||||
// end of field
|
||||
fields.Add(fieldBytes.ToArray());
|
||||
fieldBytes.Clear();
|
||||
}
|
||||
else if (inputBuffer[i] == '\n')
|
||||
{
|
||||
fields.Add(fieldBytes.ToArray());
|
||||
fieldBytes.Clear();
|
||||
|
||||
if (numFields != fields.Count)
|
||||
{
|
||||
throw new Exception($"Expected {numFields} fields on line {line}, but found {fields.Count}");
|
||||
}
|
||||
else
|
||||
{
|
||||
var fieldStrings = new string[fields.Count];
|
||||
for (int j = 0; j < fields.Count; j++)
|
||||
{
|
||||
try
|
||||
{
|
||||
fieldStrings[j] = Encoding.UTF8.GetString(fields[j]);
|
||||
}
|
||||
catch (Exception e)
|
||||
{
|
||||
throw new Exception($"Line {line}, column {j} is not valid UTF-8", e);
|
||||
}
|
||||
}
|
||||
records.Add(fieldStrings);
|
||||
fields.Clear();
|
||||
}
|
||||
|
||||
line++;
|
||||
currentLineStart = i + 1;
|
||||
}
|
||||
else if (inputBuffer[i] == '#')
|
||||
{
|
||||
throw new Exception($"Found unescaped '#' at line {line}, column {i - currentLineStart}");
|
||||
}
|
||||
else
|
||||
{
|
||||
fieldBytes.Add(inputBuffer[i]);
|
||||
}
|
||||
}
|
||||
|
||||
fields.Add(fieldBytes.ToArray());
|
||||
|
||||
if (fields.Count == 0)
|
||||
{
|
||||
throw new Exception("Found 0 fields on last line. Possibly because of extra \\n after last record");
|
||||
}
|
||||
if (numFields != fields.Count)
|
||||
{
|
||||
throw new Exception($"Expected {numFields} fields on line {line}, but found {fields.Count}");
|
||||
}
|
||||
else
|
||||
{
|
||||
var fieldStrings = new string[fields.Count];
|
||||
for (int j = 0; j < fields.Count; j++)
|
||||
{
|
||||
try
|
||||
{
|
||||
fieldStrings[j] = Encoding.UTF8.GetString(fields[j]);
|
||||
}
|
||||
catch (Exception e)
|
||||
{
|
||||
throw new Exception($"Line {line}, column {j} is not valid UTF-8", e);
|
||||
}
|
||||
}
|
||||
records.Add(fieldStrings);
|
||||
fields.Clear();
|
||||
}
|
||||
|
||||
return records.ToArray();
|
||||
}
|
||||
|
||||
public static Type GetColumnFromType(Type type)
|
||||
{
|
||||
if (type == typeof(string))
|
||||
|
|
@ -893,7 +1252,7 @@ public class SaneTsv
|
|||
|
||||
public static byte[] SerializeSimpleTsv<T>(IList<T> data) where T : TsvRecord
|
||||
{
|
||||
return SerializeTsv<T>(data, FormatType.TYPED_TSV);
|
||||
return SerializeTsv<T>(data, FormatType.SIMPLE_TSV);
|
||||
}
|
||||
|
||||
public static byte[] SerializeTypedTsv<T>(IList<T> data) where T : TsvRecord
|
||||
|
|
@ -977,14 +1336,17 @@ public class SaneTsv
|
|||
}
|
||||
}
|
||||
|
||||
bytes.Add((byte)':');
|
||||
try
|
||||
if (tsvFormat != FormatType.SIMPLE_TSV)
|
||||
{
|
||||
bytes.AddRange(Encoding.UTF8.GetBytes(GetNameFromColumn(headerTypes[i])));
|
||||
}
|
||||
catch (Exception e)
|
||||
{
|
||||
throw new Exception($"Invalid header type for column {i}", e);
|
||||
bytes.Add((byte)':');
|
||||
try
|
||||
{
|
||||
bytes.AddRange(Encoding.UTF8.GetBytes(GetNameFromColumn(headerTypes[i])));
|
||||
}
|
||||
catch (Exception e)
|
||||
{
|
||||
throw new Exception($"Invalid header type for column {i}", e);
|
||||
}
|
||||
}
|
||||
|
||||
if (i == headerNames.Count - 1)
|
||||
|
|
|
|||
|
|
@ -101,6 +101,18 @@ internal class Program
|
|||
public double BinFloat { get; set; }
|
||||
}
|
||||
|
||||
public class StringTestRecord : SaneTsv.TsvRecord
|
||||
{
|
||||
[SaneTsv.TypedTsvColumn("column1")]
|
||||
public string Column1 { get; set; }
|
||||
|
||||
[SaneTsv.TypedTsvColumn]
|
||||
public string column2 { get; set; }
|
||||
|
||||
[SaneTsv.TypedTsvColumn("columnthree\nyep")]
|
||||
public string Column3 { get; set; }
|
||||
}
|
||||
|
||||
private static void Main(string[] args)
|
||||
{
|
||||
{
|
||||
|
|
@ -292,6 +304,160 @@ internal class Program
|
|||
}
|
||||
}
|
||||
|
||||
{
|
||||
string testName = "Timing comparison of simple parse methods and comparison of simple serialization methods";
|
||||
|
||||
int N = 1000000;
|
||||
var records = new StringTestRecord[N];
|
||||
var rand = new Random(1);
|
||||
|
||||
for (int i = 0; i < N; i++)
|
||||
{
|
||||
records[i] = new StringTestRecord()
|
||||
{
|
||||
Column1 = rand.Next().ToString(),
|
||||
column2 = rand.Next().ToString(),
|
||||
Column3 = rand.Next().ToString(),
|
||||
};
|
||||
}
|
||||
|
||||
string[][] recordStrings = records.Select(record => new string[] { record.Column1, record.column2, record.Column3 }).ToArray();
|
||||
|
||||
DateTime lastTime = DateTime.Now;
|
||||
byte[] serialized1 = SaneTsv.SerializeSimpleTsv<StringTestRecord>(records);
|
||||
|
||||
TimeSpan speccedSerializationTime = DateTime.Now - lastTime;
|
||||
Console.WriteLine($"Specced serialization time: {speccedSerializationTime}");
|
||||
lastTime = DateTime.Now;
|
||||
|
||||
byte[] serialized2 = SaneTsv.SerializeSimpleTsv(new string[] { "column1", "column2", "columnthree\nyep" }, recordStrings);
|
||||
|
||||
TimeSpan unspeccedSerializationTime = DateTime.Now - lastTime;
|
||||
Console.WriteLine($"Unspecced serialization time: {unspeccedSerializationTime}");
|
||||
lastTime = DateTime.Now;
|
||||
|
||||
Tsv<StringTestRecord> parsed = SaneTsv.ParseSimpleTsv<StringTestRecord>(serialized1);
|
||||
|
||||
TimeSpan speccedParseTime = DateTime.Now - lastTime;
|
||||
Console.WriteLine($"Specced parse time: {speccedParseTime}");
|
||||
lastTime = DateTime.Now;
|
||||
|
||||
(string[] columns, string[][] data) = SaneTsv.ParseSimpleTsv(serialized2);
|
||||
|
||||
TimeSpan unspeccedParseTime = DateTime.Now - lastTime;
|
||||
Console.WriteLine($"Unspecced parse time: {unspeccedParseTime}");
|
||||
}
|
||||
|
||||
{
|
||||
string testName = "Check parallel serialization";
|
||||
|
||||
int N = 100000;
|
||||
var records = new StringTestRecord[N];
|
||||
var rand = new Random(1);
|
||||
|
||||
for (int i = 0; i < N; i++)
|
||||
{
|
||||
records[i] = new StringTestRecord()
|
||||
{
|
||||
Column1 = rand.Next().ToString(),
|
||||
column2 = rand.Next().ToString(),
|
||||
Column3 = rand.Next().ToString(),
|
||||
};
|
||||
}
|
||||
|
||||
string[][] recordStrings = records.Select(record => new string[] { record.Column1, record.column2, record.Column3 }).ToArray();
|
||||
|
||||
DateTime lastTime = DateTime.Now;
|
||||
byte[] serialized1 = SaneTsv.SerializeSimpleTsv(new string[] { "column1", "column2", "columnthree\nyep" }, recordStrings);
|
||||
TimeSpan unparallelTime = DateTime.Now - lastTime;
|
||||
lastTime = DateTime.Now;
|
||||
byte[] serialized2 = SaneTsv.SerializeSimpleTsvParallel(new string[] { "column1", "column2", "columnthree\nyep" }, recordStrings);
|
||||
TimeSpan parallelTime = DateTime.Now - lastTime;
|
||||
|
||||
Console.WriteLine($"Unparallel serialization time: {unparallelTime}");
|
||||
Console.WriteLine($"Parallel serialization time: {parallelTime}");
|
||||
|
||||
bool matching = true;
|
||||
for (int i = 0; i < Math.Min(serialized1.Length, serialized2.Length); i++)
|
||||
{
|
||||
if (serialized1[i] != serialized2[i])
|
||||
{
|
||||
matching = false;
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
if (matching)
|
||||
{
|
||||
Console.WriteLine($"Passed {testName}");
|
||||
}
|
||||
else
|
||||
{
|
||||
Console.WriteLine($"Failed {testName}");
|
||||
}
|
||||
}
|
||||
|
||||
{
|
||||
string testName = "Check parallel parsing";
|
||||
|
||||
int N = 100000;
|
||||
var records = new StringTestRecord[N];
|
||||
var rand = new Random(1);
|
||||
|
||||
for (int i = 0; i < N; i++)
|
||||
{
|
||||
records[i] = new StringTestRecord()
|
||||
{
|
||||
Column1 = rand.Next().ToString(),
|
||||
column2 = rand.Next().ToString(),
|
||||
Column3 = rand.Next().ToString(),
|
||||
};
|
||||
}
|
||||
|
||||
byte[] serialized = SaneTsv.SerializeSimpleTsv<StringTestRecord>(records);
|
||||
|
||||
DateTime lastTime = DateTime.Now;
|
||||
(string[] headers2, string[][] data2) = SaneTsv.ParseSimpleTsv(serialized);
|
||||
TimeSpan unparallelTime = DateTime.Now - lastTime;
|
||||
lastTime = DateTime.Now;
|
||||
(string[] headers, string[][] data) = SaneTsv.ParseSimpleTsvParallel(serialized);
|
||||
TimeSpan parallelTime = DateTime.Now - lastTime;
|
||||
|
||||
Console.WriteLine($"Unparallel serialization time: {unparallelTime}");
|
||||
Console.WriteLine($"Parallel serialization time: {parallelTime}");
|
||||
|
||||
bool matching = true;
|
||||
for (int j = 0; j < Math.Min(headers2.Length, headers.Length); j++)
|
||||
{
|
||||
if (headers[j] != headers2[j])
|
||||
{
|
||||
matching = false;
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
for (int i = 0; i < Math.Min(data.Length, data2.Length) && matching; i++)
|
||||
{
|
||||
for (int j = 0; j < data[0].Length; j++)
|
||||
{
|
||||
if (data[i][j] != data2[i][j])
|
||||
{
|
||||
matching = false;
|
||||
break;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (matching)
|
||||
{
|
||||
Console.WriteLine($"Passed {testName}");
|
||||
}
|
||||
else
|
||||
{
|
||||
Console.WriteLine($"Failed {testName}");
|
||||
}
|
||||
}
|
||||
|
||||
Console.WriteLine("Done with tests");
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue
Block a user