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Merge pull request #29 from hgb-bin-proteomics/develop
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Implement integer matrix operations
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@michabirklbauer
michabirklbauer authored Feb 1, 2024
2 parents f5b2d6f + b218f83 commit 7891352
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961 changes: 961 additions & 0 deletions Archive/Experimental/findTopCandidatesCudaInt.cpp
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293 changes: 293 additions & 0 deletions DataLoader/Benchmark.cs
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using System.Diagnostics;
using System.Runtime.InteropServices;

namespace CandidateVectorSearch
{
public partial class DataLoader
{
public static int Benchmark(int nrCandidates, int nrSpectra, int topN, int batchSize, Random r)
{
// generate candidate vectors
var candidateValues = new int[nrCandidates * 100];
var candidatesIdx = new int[nrCandidates];
var csrRowoffsets = new int[nrCandidates + 1];
var csrIdx = new int[nrCandidates * 100];
var currentIdx = 0;
for (int i = 0; i < candidateValues.Length; i += 100)
{
candidatesIdx[currentIdx] = i;
csrRowoffsets[currentIdx] = i;
var tmpValues = new int[100];
for (int j = 0; j < tmpValues.Length; j++)
{
var val = r.Next(ENCODING_SIZE);
while (Array.Exists(tmpValues, x => x == val))
{
val = r.Next(ENCODING_SIZE);
}
tmpValues[j] = val;
}
Array.Sort(tmpValues);
for (int j = 0; j < tmpValues.Length; j++)
{
candidateValues[i + j] = tmpValues[j];
csrIdx[i + j] = tmpValues[j];
}
currentIdx++;
if (currentIdx % 5000 == 0)
{
Console.WriteLine($"Generated {currentIdx} candidates...");
}
}
// add the end of matrix as specified in CSR format
csrRowoffsets[currentIdx++] = nrCandidates * 100;

// generate spectra vectors
var spectraValues = new int[nrSpectra * 500];
var spectraIdx = new int[nrSpectra];
currentIdx = 0;
for (int i = 0; i < spectraValues.Length; i += 500)
{
spectraIdx[currentIdx] = i;
var tmpValues = new int[500];
for (int j = 0; j < tmpValues.Length; j++)
{
var val = r.Next(ENCODING_SIZE);
while (Array.Exists(tmpValues, x => x == val))
{
val = r.Next(ENCODING_SIZE);
}
tmpValues[j] = val;
}
Array.Sort(tmpValues);
for (int j = 0; j < tmpValues.Length; j++)
{
spectraValues[i + j] = tmpValues[j];
}
currentIdx++;
}

// get pointer addresses and call c++ function
var cValuesLoc = GCHandle.Alloc(candidateValues, GCHandleType.Pinned);
var cIdxLoc = GCHandle.Alloc(candidatesIdx, GCHandleType.Pinned);
var csrRowoffsetsLoc = GCHandle.Alloc(csrRowoffsets, GCHandleType.Pinned);
var csrIdxLoc = GCHandle.Alloc(csrIdx, GCHandleType.Pinned);
var sValuesLoc = GCHandle.Alloc(spectraValues, GCHandleType.Pinned);
var sIdxLoc = GCHandle.Alloc(spectraIdx, GCHandleType.Pinned);
var resultArrayEigen = new int[spectraIdx.Length * topN];
var resultArrayEigen2 = new int[spectraIdx.Length * topN];
var resultArrayEigen2Int = new int[spectraIdx.Length * topN];
var resultArrayEigenB = new int[spectraIdx.Length * topN];
var resultArrayEigenB2 = new int[spectraIdx.Length * topN];
var resultArrayEigenB2Int = new int[spectraIdx.Length * topN];
var resultArrayCuda = new int[spectraIdx.Length * topN];
var resultArrayCudaB = new int[spectraIdx.Length * topN];
var resultArrayCudaB2 = new int[spectraIdx.Length * topN];
var memStat = 1;
try
{
IntPtr cValuesPtr = cValuesLoc.AddrOfPinnedObject();
IntPtr cIdxPtr = cIdxLoc.AddrOfPinnedObject();
IntPtr csrRowoffsetsPtr = csrRowoffsetsLoc.AddrOfPinnedObject();
IntPtr csrIdxPtr = csrIdxLoc.AddrOfPinnedObject();
IntPtr sValuesPtr = sValuesLoc.AddrOfPinnedObject();
IntPtr sIdxPtr = sIdxLoc.AddrOfPinnedObject();

var sw1 = Stopwatch.StartNew();

IntPtr resultEigen = findTopCandidates(cValuesPtr, cIdxPtr, sValuesPtr, sIdxPtr,
candidateValues.Length, candidatesIdx.Length, spectraValues.Length, spectraIdx.Length,
topN, (float) 0.02, NORMALIZE, USE_GAUSSIAN, 0, 0);

Marshal.Copy(resultEigen, resultArrayEigen, 0, spectraIdx.Length * topN);

memStat = releaseMemory(resultEigen);

sw1.Stop();

Console.WriteLine("Time for candidate search Eigen SpM*SpV:");
Console.WriteLine(sw1.Elapsed.TotalSeconds.ToString());

var sw2 = Stopwatch.StartNew();

IntPtr resultEigen2 = findTopCandidates2(cValuesPtr, cIdxPtr, sValuesPtr, sIdxPtr,
candidateValues.Length, candidatesIdx.Length, spectraValues.Length, spectraIdx.Length,
topN, (float) 0.02, NORMALIZE, USE_GAUSSIAN, 0, 0);

Marshal.Copy(resultEigen2, resultArrayEigen2, 0, spectraIdx.Length * topN);

memStat = releaseMemory(resultEigen2);

sw2.Stop();

Console.WriteLine("Time for candidate search Eigen SpM*V:");
Console.WriteLine(sw2.Elapsed.TotalSeconds.ToString());

var sw2Int = Stopwatch.StartNew();

IntPtr resultEigen2Int = findTopCandidates2Int(cValuesPtr, cIdxPtr, sValuesPtr, sIdxPtr,
candidateValues.Length, candidatesIdx.Length, spectraValues.Length, spectraIdx.Length,
topN, (float) 0.02, NORMALIZE, USE_GAUSSIAN, 0, 0);

Marshal.Copy(resultEigen2Int, resultArrayEigen2Int, 0, spectraIdx.Length * topN);

memStat = releaseMemory(resultEigen2Int);

sw2Int.Stop();

Console.WriteLine("Time for candidate search Eigen SpM*V (int):");
Console.WriteLine(sw2Int.Elapsed.TotalSeconds.ToString());

var sw3 = Stopwatch.StartNew();

IntPtr resultEigenB = findTopCandidatesBatched(cValuesPtr, cIdxPtr, sValuesPtr, sIdxPtr,
candidateValues.Length, candidatesIdx.Length, spectraValues.Length, spectraIdx.Length,
topN, (float) 0.02, NORMALIZE, USE_GAUSSIAN, batchSize, 0, 0);

Marshal.Copy(resultEigenB, resultArrayEigenB, 0, spectraIdx.Length * topN);

memStat = releaseMemory(resultEigenB);

sw3.Stop();

Console.WriteLine("Time for candidate search Eigen SpM*SpM:");
Console.WriteLine(sw3.Elapsed.TotalSeconds.ToString());

var sw4 = Stopwatch.StartNew();

IntPtr resultEigenB2 = findTopCandidatesBatched2(cValuesPtr, cIdxPtr, sValuesPtr, sIdxPtr,
candidateValues.Length, candidatesIdx.Length, spectraValues.Length, spectraIdx.Length,
topN, (float) 0.02, NORMALIZE, USE_GAUSSIAN, batchSize, 0, 0);

Marshal.Copy(resultEigenB2, resultArrayEigenB2, 0, spectraIdx.Length * topN);

memStat = releaseMemory(resultEigenB2);

sw4.Stop();

Console.WriteLine("Time for candidate search Eigen SpM*M:");
Console.WriteLine(sw4.Elapsed.TotalSeconds.ToString());

var sw4Int = Stopwatch.StartNew();

IntPtr resultEigenB2Int = findTopCandidatesBatched2Int(cValuesPtr, cIdxPtr, sValuesPtr, sIdxPtr,
candidateValues.Length, candidatesIdx.Length, spectraValues.Length, spectraIdx.Length,
topN, (float) 0.02, NORMALIZE, USE_GAUSSIAN, batchSize, 0, 0);

Marshal.Copy(resultEigenB2Int, resultArrayEigenB2Int, 0, spectraIdx.Length * topN);

memStat = releaseMemory(resultEigenB2Int);

sw4Int.Stop();

Console.WriteLine("Time for candidate search Eigen SpM*M (int):");
Console.WriteLine(sw4Int.Elapsed.TotalSeconds.ToString());

var sw5 = Stopwatch.StartNew();

IntPtr resultCuda = findTopCandidatesCuda(csrRowoffsetsPtr, csrIdxPtr,
sValuesPtr, sIdxPtr,
csrRowoffsets.Length, csrIdx.Length,
spectraValues.Length, spectraIdx.Length,
topN, (float) 0.02, NORMALIZE, USE_GAUSSIAN, 0);

Marshal.Copy(resultCuda, resultArrayCuda, 0, spectraIdx.Length * topN);

memStat = releaseMemoryCuda(resultCuda);

sw5.Stop();

Console.WriteLine("Time for candidate search Cuda SpMV:");
Console.WriteLine(sw5.Elapsed.TotalSeconds.ToString());

var sw6 = Stopwatch.StartNew();

IntPtr resultCudaB2 = findTopCandidatesCudaBatched2(csrRowoffsetsPtr, csrIdxPtr,
sValuesPtr, sIdxPtr,
csrRowoffsets.Length, csrIdx.Length,
spectraValues.Length, spectraIdx.Length,
topN, (float) 0.02, NORMALIZE, USE_GAUSSIAN, batchSize, 0);

Marshal.Copy(resultCudaB2, resultArrayCudaB2, 0, spectraIdx.Length * topN);

memStat = releaseMemoryCuda(resultCudaB2);

sw6.Stop();

Console.WriteLine("Time for candidate search Cuda SpMM:");
Console.WriteLine(sw6.Elapsed.TotalSeconds.ToString());

var sw7 = Stopwatch.StartNew();

IntPtr resultCudaB = findTopCandidatesCudaBatched(csrRowoffsetsPtr, csrIdxPtr,
sValuesPtr, sIdxPtr,
csrRowoffsets.Length, csrIdx.Length,
spectraValues.Length, spectraIdx.Length,
topN, (float) 0.02, NORMALIZE, USE_GAUSSIAN, batchSize, 0);

Marshal.Copy(resultCudaB, resultArrayCudaB, 0, spectraIdx.Length * topN);

memStat = releaseMemoryCuda(resultCudaB);

sw7.Stop();

Console.WriteLine("Time for candidate search Cuda SpGEMM:");
Console.WriteLine(sw7.Elapsed.TotalSeconds.ToString());
}
catch (Exception ex)
{
Console.WriteLine("Something went wrong:");
Console.WriteLine(ex.ToString());
}
finally
{
if (cValuesLoc.IsAllocated) { cValuesLoc.Free(); }
if (cIdxLoc.IsAllocated) { cIdxLoc.Free(); }
if (csrRowoffsetsLoc.IsAllocated) { csrRowoffsetsLoc.Free(); }
if (csrIdxLoc.IsAllocated) { csrIdxLoc.Free(); }
if (sValuesLoc.IsAllocated) { sValuesLoc.Free(); }
if (sIdxLoc.IsAllocated) { sIdxLoc.Free(); }
}

Console.WriteLine($"Top 5 of the first spectrum:");

for (int i = 0; i < 5; i++)
{
Console.WriteLine($"eSpVf32: {resultArrayEigen[i]}");
Console.WriteLine($"eDnVf32: {resultArrayEigen2[i]}");
Console.WriteLine($"eDnVi32: {resultArrayEigen2Int[i]}");
Console.WriteLine($"eSpMf32: {resultArrayEigenB[i]}");
Console.WriteLine($"eDnMf32: {resultArrayEigenB2[i]}");
Console.WriteLine($"eDnMi32: {resultArrayEigenB2Int[i]}");
Console.WriteLine($"cDnVf32: {resultArrayCuda[i]}");
Console.WriteLine($"cSpMf32: {resultArrayCudaB[i]}");
Console.WriteLine($"cDnMf32: {resultArrayCudaB2[i]}");
Console.WriteLine("-----");
}

Console.WriteLine($"Top 5 of the last spectrum:");

for (int i = spectraIdx.Length * topN - topN; i < spectraIdx.Length * topN - topN + 5; i++)
{
Console.WriteLine($"eSpVf32: {resultArrayEigen[i]}");
Console.WriteLine($"eDnVf32: {resultArrayEigen2[i]}");
Console.WriteLine($"eDnVi32: {resultArrayEigen2Int[i]}");
Console.WriteLine($"eSpMf32: {resultArrayEigenB[i]}");
Console.WriteLine($"eDnMf32: {resultArrayEigenB2[i]}");
Console.WriteLine($"eDnMi32: {resultArrayEigenB2Int[i]}");
Console.WriteLine($"cDnVf32: {resultArrayCuda[i]}");
Console.WriteLine($"cSpMf32: {resultArrayCudaB[i]}");
Console.WriteLine($"cDnMf32: {resultArrayCudaB2[i]}");
Console.WriteLine("-----");
}

Console.WriteLine($"MemStat: {memStat}");

//
GC.Collect();
GC.WaitForPendingFinalizers();

return 0;
}
}
}
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