From 02123bb1a6a6d0d35a4ea024350b714430a4b330 Mon Sep 17 00:00:00 2001
From: David Rohr <drohr@jwdt.org>
Date: Wed, 14 May 2014 09:36:37 +0200
Subject: [PATCH] improve async cuda transfer, improve cuda tracing
---
bioem.cpp | 33 ++++++++++++++++++++++++++++++++-
bioem_cuda.cu | 20 ++++++++++++++++++--
include/bioem_cuda_internal.h | 4 ++--
include/defs.h | 1 +
4 files changed, 53 insertions(+), 5 deletions(-)
diff --git a/bioem.cpp b/bioem.cpp
index 5531290..e92a222 100644
--- a/bioem.cpp
+++ b/bioem.cpp
@@ -2,7 +2,7 @@
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2014 Pilar Cossio, David Rohr and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
-
+
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
@@ -27,6 +27,29 @@
#include "model.h"
#include "map.h"
+#ifdef BIOEM_USE_NVTX
+#include "nvToolsExt.h"
+
+const uint32_t colors[] = { 0x0000ff00, 0x000000ff, 0x00ffff00, 0x00ff00ff, 0x0000ffff, 0x00ff0000, 0x00ffffff };
+const int num_colors = sizeof(colors)/sizeof(colors[0]);
+
+#define cuda_custom_timeslot(name,cid) { \
+ int color_id = cid; \
+ color_id = color_id%num_colors;\
+ nvtxEventAttributes_t eventAttrib = {0}; \
+ eventAttrib.version = NVTX_VERSION; \
+ eventAttrib.size = NVTX_EVENT_ATTRIB_STRUCT_SIZE; \
+ eventAttrib.colorType = NVTX_COLOR_ARGB; \
+ eventAttrib.color = colors[color_id]; \
+ eventAttrib.messageType = NVTX_MESSAGE_TYPE_ASCII; \
+ eventAttrib.message.ascii = name; \
+ nvtxRangePushEx(&eventAttrib); \
+}
+#define cuda_custom_timeslot_end nvtxRangePop();
+#else
+#define cuda_custom_timeslot(name,cid)
+#define cuda_custom_timeslot_end
+#endif
#include "bioem_algorithm.h"
using namespace boost;
@@ -440,6 +463,8 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
// ********************* and turns projection into Fourier space ************************
// **************************************************************************************
+ cuda_custom_timeslot("Projection", 0);
+
myfloat3_t RotatedPointsModel[Model.nPointsModel];
myfloat_t rotmat[3][3];
myfloat_t alpha, gam, beta;
@@ -516,6 +541,8 @@ int bioem::createProjection(int iMap, mycomplex_t* mapFFT)
// ********** Omp Critical is necessary with FFTW*******
myfftw_execute_dft_r2c(param.fft_plan_r2c_forward, localproj, mapFFT);
+ cuda_custom_timeslot_end;
+
return(0);
}
@@ -527,6 +554,8 @@ int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj
// *************** and Backtransforming it to real Space ********************************
// **************************************************************************************
+ cuda_custom_timeslot("Convolution", 1);
+
mycomplex_t* tmp = localCCT[omp_get_thread_num()];
// **** Multiplying FFTmap with corresponding kernel ****
@@ -559,6 +588,8 @@ int bioem::createConvolutedProjectionMap(int iMap, int iConv, mycomplex_t* lproj
sumC = sumC / norm2;
sumsquareC = sumsquareC / norm4;
+ cuda_custom_timeslot_end;
+
return(0);
}
diff --git a/bioem_cuda.cu b/bioem_cuda.cu
index e19a844..01e6d98 100644
--- a/bioem_cuda.cu
+++ b/bioem_cuda.cu
@@ -2,7 +2,7 @@
< BioEM software for Bayesian inference of Electron Microscopy images>
Copyright (C) 2014 Pilar Cossio, David Rohr and Gerhard Hummer.
Max Planck Institute of Biophysics, Frankfurt, Germany.
-
+
See license statement for terms of distribution.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++*/
@@ -176,7 +176,12 @@ int bioem_cuda::compareRefMaps(int iOrient, int iConv, const myfloat_t* conv_map
if (FFTAlgo)
{
memcpy(&pConvMapFFT_Host[(iConv & 1) * param.FFTMapSize], localmultFFT, param.FFTMapSize * sizeof(mycomplex_t));
- checkCudaErrors(cudaMemcpyAsync(&pConvMapFFT[(iConv & 1) * param.FFTMapSize], &pConvMapFFT_Host[(iConv & 1) * param.FFTMapSize], param.FFTMapSize * sizeof(mycomplex_t), cudaMemcpyHostToDevice, cudaStream[0]));
+ checkCudaErrors(cudaMemcpyAsync(&pConvMapFFT[(iConv & 1) * param.FFTMapSize], &pConvMapFFT_Host[(iConv & 1) * param.FFTMapSize], param.FFTMapSize * sizeof(mycomplex_t), cudaMemcpyHostToDevice, cudaStream[GPUAsync ? 2 : 0]));
+ if (GPUAsync)
+ {
+ checkCudaErrors(cudaEventRecord(cudaEvent[2], cudaStream[2]));
+ checkCudaErrors(cudaStreamWaitEvent(cudaStream[0], cudaEvent[2], 0));
+ }
if (GPUDualStream)
{
checkCudaErrors(cudaEventRecord(cudaFFTEvent[0], cudaStream[0]));
@@ -310,6 +315,11 @@ int bioem_cuda::deviceInit()
checkCudaErrors(cudaEventCreate(&cudaFFTEvent[i]));
checkCudaErrors(cudaMalloc(&pConvMap_device[i], sizeof(myfloat_t) * RefMap.refMapSize));
}
+ if (GPUAsync)
+ {
+ checkCudaErrors(cudaStreamCreate(&cudaStream[2]));
+ checkCudaErrors(cudaEventCreate(&cudaEvent[2]));
+ }
if (FFTAlgo)
{
@@ -358,6 +368,12 @@ int bioem_cuda::deviceExit()
{
cudaFree(pRefMap_device_Mod);
}
+ if (GPUAsync)
+ {
+ cudaStreamDestroy(cudaStream[2]);
+ cudaEventDestroy(cudaEvent[2]);
+ }
+
delete gpumap;
cudaThreadExit();
diff --git a/include/bioem_cuda_internal.h b/include/bioem_cuda_internal.h
index d3816f9..e3fec06 100644
--- a/include/bioem_cuda_internal.h
+++ b/include/bioem_cuda_internal.h
@@ -29,8 +29,8 @@ protected:
int deviceInitialized;
- cudaStream_t cudaStream[2];
- cudaEvent_t cudaEvent[2];
+ cudaStream_t cudaStream[3];
+ cudaEvent_t cudaEvent[3];
cudaEvent_t cudaFFTEvent[2];
bioem_RefMap_Mod* pRefMap_device_Mod;
bioem_RefMap* gpumap;
diff --git a/include/defs.h b/include/defs.h
index 83ba1bf..8049a0e 100644
--- a/include/defs.h
+++ b/include/defs.h
@@ -69,6 +69,7 @@ struct myfloat3_t
#define CUDA_BLOCK_COUNT 1024 * 16
#define CUDA_MAX_SHIFT_REDUCE 1024
#define CUDA_FFTS_AT_ONCE 1024
+//#define BIOEM_USE_NVTX
static inline void* mallocchk(size_t size)
{
--
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