rel2: code development

CMakeLists.txt

@@ -29,7 +29,7 @@ set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}")
 
 include_directories(include)
 
-set (BIOEM_ICC_FLAGS "-xHost -O3 -fno-alias -fno-fnalias -unroll -g0 -ipo")
+set (BIOEM_ICC_FLAGS "-O3 -fno-alias -fno-fnalias -unroll -g0 -ip")
 set (BIOEM_GCC_FLAGS "-O3 -march=native -fweb -mfpmath=sse -frename-registers -minline-all-stringops -ftracer -funroll-loops -fpeel-loops -fprefetch-loop-arrays -ffast-math -ggdb")
 
 if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
@@ -50,11 +50,6 @@ if (NOT FFTW_FOUND)
 endif()
 include_directories(${FFTW_INCLUDE_DIRS})
 
-find_package( Boost 1.43 REQUIRED COMPONENTS program_options )
-include_directories( ${Boost_INCLUDE_DIRS} )
-
-
-
 ###Find Optional Packages
 
 ###Find CUDA
@@ -163,7 +158,6 @@ if (FFTWF_LIBRARIES)
 else()
         target_link_libraries(bioEM -L${FFTW_LIBDIR} -lfftw3 -lfftw3f)
 endif()
-target_link_libraries(bioEM ${Boost_PROGRAM_OPTIONS_LIBRARY})
 
 if (MPI_FOUND)
         target_link_libraries(bioEM ${MPI_LIBRARIES})
@@ -172,7 +166,6 @@ endif()
 ###Show Status
 message(STATUS "Build Status")
 message(STATUS "FFTW library: ${FFTW_LIBDIR}")
-message(STATUS "Boost directory: ${Boost_LIBRARY_DIRS}")
 message(STATUS "FFTW includedir: ${FFTW_INCLUDEDIR}")
 message(STATUS "CUDA libraries:  ${CUDA_CUDA_LIBRARY}")
 message(STATUS "CUDART libraries:  ${CUDA_LIBRARIES}")

autotuner.cpp

+/* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+   < BioEM software for Bayesian inference of Electron Microscopy images>
+   Copyright (C) 2017 Pilar Cossio, Markus Rampp, Luka Stanisic and Gerhard
+   Hummer.
+   Max Planck Institute of Biophysics, Frankfurt, Germany.
+   Max Planck Computing and Data Facility, Garching, Germany.
+
+   Released under the GNU Public License, v3.
+   See license statement for terms of distribution.
+
+   ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
+
 #include "autotuner.h"
 
 void Autotuner::Reset()
@@ -16,64 +28,75 @@ void Autotuner::Reset()
   fb = 0.;
   fx = 0.;
 
-  if (algo == 3) workload = 50;
+  if (algo == 3)
+    workload = 50;
 }
 
 bool Autotuner::Needed(int iteration)
 {
-  if (stopTuning) return false;
+  if (stopTuning)
+    return false;
 
   switch (algo)
-    {
+  {
     case 1:
     case 3:
       return iteration % (stable + 1) == stable;
-    case 2: return (iteration == (int) stable / 2 ) || (iteration == stable);
+    case 2:
+      return (iteration == (int) stable / 2) || (iteration == stable);
     default: /* Should never happen */;
-    }
+  }
   return false;
 }
 
 bool Autotuner::Finished()
 {
   switch (algo)
-    {
+  {
     case 1:
       if (workload < 30)
-	{
-	  workload = best_workload;
-	  return stopTuning = true;
-	}
+      {
+        workload = best_workload;
+        return stopTuning = true;
+      }
       break;
     case 2:
-      if (best_workload != 0) return stopTuning = true;
+      if (best_workload != 0)
+        return stopTuning = true;
       break;
     case 3:
-      if ((c - b == limit) && (b - a == limit)) return stopTuning = true;
+      if ((c - b == limit) && (b - a == limit))
+        return stopTuning = true;
       break;
     default: /* Should never happen */;
-    }
+  }
   return false;
 }
 
 void Autotuner::Tune(double compTime)
 {
   switch (algo)
-    {
-    case 1: AlgoSimple(compTime); break;
-    case 2: AlgoRatio(compTime); break;
-    case 3: AlgoBisection(compTime); break;
+  {
+    case 1:
+      AlgoSimple(compTime);
+      break;
+    case 2:
+      AlgoRatio(compTime);
+      break;
+    case 3:
+      AlgoBisection(compTime);
+      break;
     default: /* Should never happen */;
-    }
+  }
 }
 
 void Autotuner::AlgoSimple(double compTime)
 {
   if (best_time == 0. || compTime < best_time)
-    {
-      best_time = compTime;
-      best_workload = workload;
-    }
+  {
+    best_time = compTime;
+    best_workload = workload;
+  }
 
   workload -= 5;
 }
@@ -81,46 +104,46 @@ void Autotuner::AlgoSimple(double compTime)
 void Autotuner::AlgoRatio(double compTime)
 {
   if (best_time == 0.)
-    {
-      best_time = compTime;
-      workload = 1;
-    }
+  {
+    best_time = compTime;
+    workload = 1;
+  }
   else
-    {
-      best_workload = (int) 100 * (compTime / (best_time + compTime));
-      workload = best_workload;
-    }
+  {
+    best_workload = (int) 100 * (compTime / (best_time + compTime));
+    workload = best_workload;
+  }
 }
 
 void Autotuner::AlgoBisection(double compTime)
 {
   if (fb == 0.)
-    {
-      fb = compTime;
-      x = 75;
-      workload = x;
-      return;
-    }
+  {
+    fb = compTime;
+    x = 75;
+    workload = x;
+    return;
+  }
 
   fx = compTime;
 
   if (fx < fb)
-    {
-      if (x < b)
-	c = b;
-      else
-	a = b;
-      b = x;
-      fb = fx;
-    }
+  {
+    if (x < b)
+      c = b;
+    else
+      a = b;
+    b = x;
+    fb = fx;
+  }
   else
-    {
-      if (x < b)
-	a = x;
-      else
-	c = x;
-    }
-
-  x = (c-b > b-a) ? (int)(b+(c-b)/2) : (int)(a+(b-a+1)/2);
+  {
+    if (x < b)
+      a = x;
+    else
+      c = x;
+  }
+
+  x = (c - b > b - a) ? (int) (b + (c - b) / 2) : (int) (a + (b - a + 1) / 2);
   workload = x;
 }

include/autotuner.h

 /* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
    < BioEM software for Bayesian inference of Electron Microscopy images>
-   Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp, 
-        Volker Lindenstruth and Gerhard Hummer.
+   Copyright (C) 2017 Pilar Cossio, Markus Rampp, Luka Stanisic and Gerhard
+   Hummer.
    Max Planck Institute of Biophysics, Frankfurt, Germany.
+   Max Planck Computing and Data Facility, Garching, Germany.
 
+   Released under the GNU Public License, v3.
    See license statement for terms of distribution.
 
    ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
@@ -11,52 +13,58 @@
 #ifndef AUTOTUNER_H
 #define AUTOTUNER_H
 
-class Autotuner {
+class Autotuner
+{
 
 public:
-	Autotuner() {stopTuning = true;}
+  Autotuner() { stopTuning = true; }
 
-	/* Setting variables to initial values */
-	inline void Initialize(int alg=3, int st=7) {algo = alg; stable=st; Reset(); }
+  /* Setting variables to initial values */
+  inline void Initialize(int alg = 3, int st = 7)
+  {
+    algo = alg;
+    stable = st;
+    Reset();
+  }
 
-	/* Resetting variables to initial values */
-	void Reset();
+  /* Resetting variables to initial values */
+  void Reset();
 
-	/* Check if autotuning is needed, depending on which comparison is finished */
-	bool Needed(int iteration);
+  /* Check if autotuning is needed, depending on which comparison is finished */
+  bool Needed(int iteration);
 
-	/* Check if optimal workload value has been computed */
-	bool Finished();
+  /* Check if optimal workload value has been computed */
+  bool Finished();
 
-	/* Set a new workload value to test, depending on the algorithm */
-	void Tune(double compTime);
+  /* Set a new workload value to test, depending on the algorithm */
+  void Tune(double compTime);
 
-	/* Return workload value */
-	inline int Workload() {return workload;}
+  /* Return workload value */
+  inline int Workload() { return workload; }
 
 private:
-	int algo;
-	int stable;
-
-	bool stopTuning;
-	int workload;
-
-	/* Variables needed for AlgoSimple and AlgoRatio */
-	double best_time;
-	int best_workload;
-
-	/* Variables needed for AlgoBisection */
-	int a;
-	int b;
-	int c;
-	int x;
-	int limit;
-	double fb, fx;
-
-	/* Autotuning algorithms */
-	void AlgoSimple(double compTime);
-	void AlgoRatio(double compTime);
-	void AlgoBisection(double compTime);
+  int algo;
+  int stable;
+
+  bool stopTuning;
+  int workload;
+
+  /* Variables needed for AlgoSimple and AlgoRatio */
+  double best_time;
+  int best_workload;
+
+  /* Variables needed for AlgoBisection */
+  int a;
+  int b;
+  int c;
+  int x;
+  int limit;
+  double fb, fx;
+
+  /* Autotuning algorithms */
+  void AlgoSimple(double compTime);
+  void AlgoRatio(double compTime);
+  void AlgoBisection(double compTime);
 };
 
 #endif

include/bioem.h

 /* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
    < BioEM software for Bayesian inference of Electron Microscopy images>
-   Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp, 
-        Volker Lindenstruth and Gerhard Hummer.
+   Copyright (C) 2017 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
+        Luka Stanisic, Volker Lindenstruth and Gerhard Hummer.
    Max Planck Institute of Biophysics, Frankfurt, Germany.
-   Frankfurt Institute for Advanced Studies, Goethe University Frankfurt, Germany.
-   Max Planck Computing and Data Facility, Garching, Germany. 
+   Frankfurt Institute for Advanced Studies, Goethe University Frankfurt,
+   Germany.
+   Max Planck Computing and Data Facility, Garching, Germany.
 
-   Released under the GNU Public License, v3. 
+   Released under the GNU Public License, v3.
    See license statement for terms of distribution.
 
    ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
@@ -14,66 +15,87 @@
 #ifndef BIOEM_H
 #define BIOEM_H
 
-#include "defs.h"
 #include "bioem.h"
-#include "model.h"
+#include "defs.h"
 #include "map.h"
+#include "model.h"
 #include "param.h"
 
 class bioem
 {
-	friend class bioem_RefMap;
-	friend class bioem_Probability;
+  friend class bioem_RefMap;
+  friend class bioem_Probability;
 
 public:
-	bioem();
-	virtual ~bioem();
-
-	int configure(int ac, char* av[]);
-	void cleanup(); //Cleanup everything happening during configure
-
-	int precalculate(); // Is it better to pass directly the input File names?
-	int dopreCalCrossCorrelation(int iRefMap, int iRefMapLocal);
-	int run();
-	int doProjections(int iMap);
-	int createConvolutedProjectionMap(int iOreint, int iMap, mycomplex_t* lproj, myfloat_t* Mapconv, mycomplex_t* localmultFFT, myfloat_t& sumC, myfloat_t& sumsquareC);
-
-	virtual int compareRefMaps(int iOrient, int iConv, myfloat_t amp, myfloat_t pha, myfloat_t env, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap = 0);
-
-	virtual void* malloc_device_host(size_t size);
-	virtual void free_device_host(void* ptr);
-	virtual void rebalance(int workload); //Rebalance GPUWorkload
-	void rebalanceWrapper(int workload); //Rebalance wrapper
-
-	int createProjection(int iMap, mycomplex_t* map);
-	int calcross_cor(myfloat_t* localmap, myfloat_t& sum, myfloat_t& sumsquare);
-	void calculateCCFFT(int iMap, int iOrient, int iConv, myfloat_t amp, myfloat_t pha, myfloat_t env, myfloat_t sumC, myfloat_t sumsquareC, mycomplex_t* localConvFFT, mycomplex_t* localCCT, myfloat_t* lCC);
-
-	bioem_Probability pProb;
-
-        string OutfileName;
-	bool yesoutfilename;
-
+  bioem();
+  virtual ~bioem();
+
+  void printOptions(myoption_t *myoptions, int myoptions_length);
+  int readOptions(int ac, char *av[]);
+  int configure(int ac, char *av[]);
+  void cleanup(); // Cleanup everything happening during configure
+
+  int precalculate(); // Is it better to pass directly the input File names?
+  inline int needToPrintModel() { return param.printModel; }
+  int printModel();
+  int run();
+  int doProjections(int iMap);
+  int createConvolutedProjectionMap(int iOreint, int iMap, mycomplex_t *lproj,
+                                    mycomplex_t *localmultFFT, myfloat_t &sumC,
+                                    myfloat_t &sumsquareC);
+  int createConvolutedProjectionMap_noFFT(mycomplex_t *lproj,
+                                          myfloat_t *Mapconv,
+                                          mycomplex_t *localmultFFT,
+                                          myfloat_t &sumC,
+                                          myfloat_t &sumsquareC);
+
+  virtual int compareRefMaps(int iPipeline, int iOrient, int iConv,
+                             int maxParallelConv, mycomplex_t *localmultFFT,
+                             myparam5_t *comp_params, const int startMap = 0);
+
+  virtual void *malloc_device_host(size_t size);
+  virtual void free_device_host(void *ptr);
+  virtual void rebalance(int workload); // Rebalance GPUWorkload
+  void rebalanceWrapper(int workload);  // Rebalance wrapper
+
+  int createProjection(int iMap, mycomplex_t *map);
+  int calcross_cor(myfloat_t *localmap, myfloat_t &sum, myfloat_t &sumsquare);
+  void calculateCCFFT(int iMap, mycomplex_t *localConvFFT,
+                      mycomplex_t *localCCT, myfloat_t *lCC);
+  void doRefMap_CPU_Parallel(int iRefMap, int iOrient, int iConv,
+                             myfloat_t *lCC, myparam5_t *comp_params,
+                             myblockCPU_t *comp_block);
+  void doRefMap_CPU_Reduce(int iRefMap, int iOrient, int iConvStart,
+                           int maxParallelConv, myparam5_t *comp_params,
+                           myblockCPU_t *comp_block);
+
+  bioem_Probability pProb;
+
+  string OutfileName;
 
 protected:
-	virtual int deviceInit();
-	virtual int deviceStartRun();
-	virtual int deviceFinishRun();
-
-	bioem_param param;
-	bioem_model Model;
-	bioem_RefMap RefMap;
-
-	int nReferenceMaps;			//Maps in memory at a time
-	int nReferenceMapsTotal;	//Maps in total
-
-	int nProjectionMaps;		//Maps in memory at a time
-	int nProjectionMapsTotal;	//Maps in total
-
-	int FFTAlgo;				//Use the FFT Algorithm (Default 1)
-	int DebugOutput;			//Debug Output Level (Default 2)
-	int nProjectionsAtOnce;		//Number of projections to do at once via OpenMP (Default 1)
-	bool Autotuning;				//Do the autotuning of the load-balancing between CPUs and GPUs
+  virtual int deviceInit();
+  virtual int deviceStartRun();
+  virtual int deviceFinishRun();
+
+  bioem_param param;
+  bioem_model Model;
+  bioem_RefMap RefMap;
+
+  int nReferenceMaps;      // Maps in memory at a time
+  int nReferenceMapsTotal; // Maps in total
+
+  int nProjectionMaps;      // Maps in memory at a time
+  int nProjectionMapsTotal; // Maps in total
+
+  int BioEMAlgo;          // BioEM algorithm used to do comparison (Default 1)
+  int CudaThreadCount;    // Number of CUDA threads used in each block (Default
+                          // depends on the BioEM algorithm)
+  int DebugOutput;        // Debug Output Level (Default 0)
+  int nProjectionsAtOnce; // Number of projections to do at once via OpenMP
+                          // (Default number of OMP threads)
+  bool Autotuning; // Do the autotuning of the load-balancing between CPUs and
+  // GPUs (Default 1, if GPUs are used and GPUWORKLOAD is not specified)
 };
 
 #endif

include/bioem_cuda.h

 /* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
    < BioEM software for Bayesian inference of Electron Microscopy images>
-   Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp, 
+   Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
         Volker Lindenstruth and Gerhard Hummer.
    Max Planck Institute of Biophysics, Frankfurt, Germany.
-   Frankfurt Institute for Advanced Studies, Goethe University Frankfurt, Germany.
-   Max Planck Computing and Data Facility, Garching, Germany. 
+   Frankfurt Institute for Advanced Studies, Goethe University Frankfurt,
+   Germany.
+   Max Planck Computing and Data Facility, Garching, Germany.
 
-   Released under the GNU Public License, v3. 
+   Released under the GNU Public License, v3.
    See license statement for terms of distribution.
 
    ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
@@ -16,6 +17,6 @@
 
 #include "bioem.h"
 
-extern bioem* bioem_cuda_create();
+extern bioem *bioem_cuda_create();
 
 #endif

include/bioem_cuda_internal.h

 /* ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
    < BioEM software for Bayesian inference of Electron Microscopy images>
-   Copyright (C) 2016 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp, 
-        Volker Lindenstruth and Gerhard Hummer.
+   Copyright (C) 2017 Pilar Cossio, David Rohr, Fabio Baruffa, Markus Rampp,
+        Luka Stanisic, Volker Lindenstruth and Gerhard Hummer.
    Max Planck Institute of Biophysics, Frankfurt, Germany.
-   Frankfurt Institute for Advanced Studies, Goethe University Frankfurt, Germany.
-   Max Planck Computing and Data Facility, Garching, Germany. 
+   Frankfurt Institute for Advanced Studies, Goethe University Frankfurt,
+   Germany.
+   Max Planck Computing and Data Facility, Garching, Germany.
 
-   Released under the GNU Public License, v3. 
+   Released under the GNU Public License, v3.
    See license statement for terms of distribution.
 
    ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
@@ -17,7 +18,7 @@
 #include <cuda.h>
 #include <cufft.h>
 
-//Hack to make nvcc compiler accept fftw.h, float128 is not used anyway
+// Hack to make nvcc compiler accept fftw.h, float128 is not used anyway
 #define __float128 double
 #include <fftw3.h>
 #undef __float128
@@ -27,51 +28,60 @@
 class bioem_cuda : public bioem
 {
 public:
-	bioem_cuda();
-	virtual ~bioem_cuda();
+  bioem_cuda();
+  virtual ~bioem_cuda();
 
-	virtual int compareRefMaps(int iOrient, int iConv, myfloat_t amp, myfloat_t pha, myfloat_t env, const myfloat_t* conv_map, mycomplex_t* localmultFFT, myfloat_t sumC, myfloat_t sumsquareC, const int startMap = 0);
-	virtual void* malloc_device_host(size_t size);
-	virtual void free_device_host(void* ptr);
-	virtual void rebalance(int workload); //Rebalance GPUWorkload
+  virtual int compareRefMaps(int iPipeline, int iOrient, int iConv,
+                             int maxParallelConv, mycomplex_t *localmultFFT,
+                             myparam5_t *comp_params, const int startMap = 0);
+  virtual void *malloc_device_host(size_t size);
+  virtual void free_device_host(void *ptr);
+  virtual void rebalance(int workload); // Rebalance GPUWorkload
 
 protected:
-	virtual int deviceInit();
-	virtual int deviceStartRun();
-	virtual int deviceFinishRun();
-	int deviceExit();
-	
+  virtual int deviceInit();
+  virtual int deviceStartRun();
+  virtual int deviceFinishRun();
+  int deviceExit();
+
 private:
-	int selectCudaDevice();
-
-	int deviceInitialized;
-
-	cudaStream_t cudaStream[3];
-	cudaEvent_t cudaEvent[3];
-	cudaEvent_t cudaFFTEvent[2];
-	bioem_RefMap_Mod* pRefMap_device_Mod;
-	bioem_RefMap* gpumap;
-	bioem_Probability* pProb_host;
-	bioem_Probability pProb_device;
-	void* pProb_memory;
-	myfloat_t* pConvMap_device[2];
-
-	mycomplex_t* pRefMapsFFT;
-	mycomplex_t* pConvMapFFT;
-	mycomplex_t* pConvMapFFT_Host;
-	mycuComplex_t* pFFTtmp2[2];
-	myfloat_t* pFFTtmp[2];
-	cufftHandle plan[2][2];
-
-	myfloat_t *maps, *sum, *sumsquare;
-
-	int GPUAlgo;		//GPU Algorithm to use, 0: parallelize over maps, 1: as 0 but work split in multiple kernels (better), 2: also parallelize over shifts (best)
-	int GPUAsync;		//Run GPU Asynchronously, do the convolutions on the host in parallel.
-	int GPUDualStream;	//Use two streams to improve paralelism
-	int GPUWorkload;	//Percentage of workload to perform on GPU. Default 100. Rest is done on processor in parallel.
-
-	int maxRef;
+  int selectCudaDevice();
+
+  int deviceInitialized;
+
+  cudaStream_t cudaStream[PIPELINE_LVL + 1]; // Streams are used for both
+                                             // PIPELINE and MULTISTREAM control
+  cudaEvent_t cudaEvent[PIPELINE_LVL + 1];
+  cudaEvent_t cudaFFTEvent[MULTISTREAM_LVL];
+  bioem_RefMap *gpumap;
+  bioem_Probability *pProb_host;
+  bioem_Probability pProb_device;
+  void *pProb_memory;
+
+  mycomplex_t *pRefMapsFFT;
+  mycomplex_t *pConvMapFFT;
+  mycomplex_t *pConvMapFFT_Host;
+  mycuComplex_t *pFFTtmp2[MULTISTREAM_LVL];
+  myfloat_t *pFFTtmp[MULTISTREAM_LVL];