Merge pull request #3 from hgb-bin-proteomics/develop

fix compiler options
hgb-bin-proteomics · Jul 14, 2023 · 611df23 · 611df23
2 parents 22a27f1 + 0551f00
commit 611df23
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Showing 6 changed files with 23 additions and 15 deletions.
diff --git a/DataLoader/Eigen.cs b/DataLoader/Eigen.cs
@@ -7,8 +7,10 @@ public partial class DataLoader
     {
         const string dll = @"VectorSearch.dll";
         [DllImport(dll, CallingConvention = CallingConvention.Cdecl)]
-        private static extern IntPtr findTopCandidates(IntPtr cV, IntPtr cI, IntPtr sV, IntPtr sI,
-                                                       int cVL, int cIL, int sVL, int sIL,
+        private static extern IntPtr findTopCandidates(IntPtr cV, IntPtr cI, 
+                                                       IntPtr sV, IntPtr sI,
+                                                       int cVL, int cIL, 
+                                                       int sVL, int sIL,
                                                        int n, float tolerance);
 
         [DllImport(dll, CallingConvention = CallingConvention.Cdecl)]
@@ -87,9 +89,11 @@ public static int Eigen(int nrCandidates, int nrSpectra, int topN, Random r)
                 IntPtr sValuesPtr = sValuesLoc.AddrOfPinnedObject();
                 IntPtr sIdxPtr = sIdxLoc.AddrOfPinnedObject();
 
-                IntPtr result = findTopCandidates(cValuesPtr, cIdxPtr, sValuesPtr, sIdxPtr,
-                                                  candidateValues.Length, candidatesIdx.Length, spectraValues.Length, spectraIdx.Length,
-                                                  topN, (float)0.02);
+                IntPtr result = findTopCandidates(cValuesPtr, cIdxPtr, 
+                                                  sValuesPtr, sIdxPtr,
+                                                  candidateValues.Length, candidatesIdx.Length, 
+                                                  spectraValues.Length, spectraIdx.Length,
+                                                  topN, (float) 0.02);
 
                 Marshal.Copy(result, resultArray, 0, spectraIdx.Length * topN);
 

diff --git a/VectorSearch/VectorSearch.vcxproj b/VectorSearch/VectorSearch.vcxproj
@@ -31,30 +31,30 @@
     <UseDebugLibraries>true</UseDebugLibraries>
     <PlatformToolset>v143</PlatformToolset>
     <CharacterSet>Unicode</CharacterSet>
-    <CLRSupport>true</CLRSupport>
+    <CLRSupport>false</CLRSupport>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|Win32'" Label="Configuration">
     <ConfigurationType>DynamicLibrary</ConfigurationType>
     <UseDebugLibraries>false</UseDebugLibraries>
     <PlatformToolset>v143</PlatformToolset>
     <WholeProgramOptimization>true</WholeProgramOptimization>
     <CharacterSet>Unicode</CharacterSet>
-    <CLRSupport>true</CLRSupport>
+    <CLRSupport>false</CLRSupport>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Debug|x64'" Label="Configuration">
     <ConfigurationType>DynamicLibrary</ConfigurationType>
     <UseDebugLibraries>true</UseDebugLibraries>
     <PlatformToolset>v143</PlatformToolset>
     <CharacterSet>Unicode</CharacterSet>
-    <CLRSupport>true</CLRSupport>
+    <CLRSupport>false</CLRSupport>
   </PropertyGroup>
   <PropertyGroup Condition="'$(Configuration)|$(Platform)'=='Release|x64'" Label="Configuration">
     <ConfigurationType>DynamicLibrary</ConfigurationType>
     <UseDebugLibraries>false</UseDebugLibraries>
     <PlatformToolset>v143</PlatformToolset>
     <WholeProgramOptimization>true</WholeProgramOptimization>
     <CharacterSet>Unicode</CharacterSet>
-    <CLRSupport>true</CLRSupport>
+    <CLRSupport>false</CLRSupport>
   </PropertyGroup>
   <Import Project="$(VCTargetsPath)\Microsoft.Cpp.props" />
   <ImportGroup Label="ExtensionSettings">

diff --git a/VectorSearch/dllmain.cpp b/VectorSearch/dllmain.cpp
@@ -6,7 +6,7 @@
 #include <iostream>
 
 const int versionMajor = 1;
-const int versionMinor = 1;
+const int versionMinor = 2;
 const int versionFix = 0;
 
 #define METHOD_EXPORTS
@@ -23,8 +23,10 @@ const int APPROX_NNZ_PER_ROW = 100;
 const double ONE_OVER_SQRT_PI = 0.39894228040143267793994605993438;
 
 extern "C" {
-    EXPORT int* findTopCandidates(int*, int*, int*, int*, 
-                                  int, int, int, int, 
+    EXPORT int* findTopCandidates(int*, int*, 
+                                  int*, int*, 
+                                  int, int, 
+                                  int, int, 
                                   int, float);
 
     EXPORT int releaseMemory(int*);
@@ -47,8 +49,10 @@ float normpdf(float, float, float);
 /// <param name="n">How many of the best hits should be returned (int).</param>
 /// <param name="tolerance">Tolerance for peak matching (float).</param>
 /// <returns>An integer array of length sILength * n containing the indexes of the top n candidates for each spectrum.</returns>
-int* findTopCandidates(int* candidatesValues, int* candidatesIdx, int* spectraValues, int* spectraIdx, 
-                       int cVLength, int cILength, int sVLength, int sILength,
+int* findTopCandidates(int* candidatesValues, int* candidatesIdx, 
+                       int* spectraValues, int* spectraIdx, 
+                       int cVLength, int cILength, 
+                       int sVLength, int sILength,
                        int n, float tolerance) {
 
     std::cout << "Running Eigen vector search version " << versionMajor << "." << versionMinor << "." << versionFix << std::endl;
@@ -79,6 +83,7 @@ int* findTopCandidates(int* candidatesValues, int* candidatesIdx, int* spectraVa
         int startIter = spectraIdx[i];
         int endIter = i + 1 == sILength ? sVLength : spectraIdx[i + 1];
         auto* v = new Eigen::SparseVector<float, Eigen::ColMajor>(ENCODING_SIZE);
+        v->reserve(APPROX_NNZ_PER_ROW);
         for (int j = startIter; j < endIter; ++j) {
             auto currentPeak = spectraValues[j];
             auto minPeak = currentPeak - t > 0 ? currentPeak - t : 0;

diff --git a/VectorSearchCUDA/dllmain.cpp b/VectorSearchCUDA/dllmain.cpp
@@ -239,7 +239,6 @@ float normpdf(float x, float mu, float sigma) {
     return (ONE_OVER_SQRT_PI / sigma) * exp(-0.5 * squared((x - mu) / sigma));
 }
 
-
 BOOL APIENTRY DllMain( HMODULE hModule,
                        DWORD  ul_reason_for_call,
                        LPVOID lpReserved

diff --git a/dll/VectorSearch.dll b/dll/VectorSearch.dll
diff --git a/dll/VectorSearchCUDA.dll b/dll/VectorSearchCUDA.dll