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L13: Application Case Studies CS6235. Outline Application Case Studies – Advanced MRI Reconstruction Reading: Kirk and Hwu, Chapter 8 or From the sample.

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Presentation on theme: "L13: Application Case Studies CS6235. Outline Application Case Studies – Advanced MRI Reconstruction Reading: Kirk and Hwu, Chapter 8 or From the sample."— Presentation transcript:

1 L13: Application Case Studies CS6235

2 Outline Application Case Studies – Advanced MRI Reconstruction Reading: Kirk and Hwu, Chapter 8 or From the sample book http://courses.ece.illinois.edu/ece498/al/textbook/C hapter7-MRI-Case-Study.pdf http://courses.ece.illinois.edu/ece498/al/textbook/C hapter7-MRI-Case-Study.pdf 2 L12: Application Case Studies

3 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign 3 Reconstructing MR Images Cartesian Scan DataSpiral Scan Data Gridding FFTLS Cartesian scan data + FFT: Slow scan, fast reconstruction, images may be poor Cartesian Scan - straightforward implementation on Scanners Spiral Scan -reduced sensibility to patient motion, better ability to provide self calibration,

4 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign 4 Reconstructing MR Images Cartesian Scan DataSpiral Scan Data Gridding FFTLeast-Squares (LS) Spiral scan data + LS Superior images at expense of significantly more computation

5 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign 5 Least-Squares Reconstruction Compute Q for F H F Acquire Data Compute F H d Find ρ Q : a data structure that allows us to compute F H F Q depends only on scanner configuration F H d depends on scan data Aim: find ρ; using linear solver Accelerate Q and F H d on GPU – Q: 1-2 days on CPU – F H d: 6-7 hours on CPU – ρ: 1.5 minutes on CPU d:data samples on scanner F: matrix that models the physics of the imaging process W:matrix that incorporates anatomical differences p: vector that contains reconstructed voxel values f H d: computed for every image acquisition - reduce time to mins calculating p uses the CG algo Q:once for every trajectory

6 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign 6 for (m = 0; m < M; m++) { phiMag[m] = rPhi[m]*rPhi[m] + iPhi[m]*iPhi[m]; for (n = 0; n < N; n++) { expQ = 2*PI*(kx[m]*x[n] + ky[m]*y[n] + kz[m]*z[n]); rQ[n] +=phiMag[m]*cos(expQ); iQ[n] +=phiMag[m]*sin(expQ); } (a) Q computation for (m = 0; m < M; m++) { rMu[m] = rPhi[m]*rD[m] + iPhi[m]*iD[m]; iMu[m] = rPhi[m]*iD[m] – iPhi[m]*rD[m]; for (n = 0; n < N; n++) { expFhD = 2*PI*(kx[m]*x[n] + ky[m]*y[n] + kz[m]*z[n]); cArg = cos(expFhD); sArg = sin(expFhD); rFhD[n] += rMu[m]*cArg – iMu[m]*sArg; iFhD[n] += iMu[m]*cArg + rMu[m]*sArg; } }(b) F H d computation Q v.s. F H D Same structure for Q and fHd Q: matrix to matrix Fhd: matrix and vector

7 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign 7 for (m = 0; m < M; m++) { rMu[m] = rPhi[m]*rD[m] + iPhi[m]*iD[m]; iMu[m] = rPhi[m]*iD[m] – iPhi[m]*rD[m]; for (n = 0; n < N; n++) { expFhD = 2*PI*(kx[m]*x[n] + ky[m]*y[n] + kz[m]*z[n]); cArg = cos(expFhD); sArg = sin(expFhD); rFhD[n] += rMu[m]*cArg – iMu[m]*sArg; iFhD[n] += iMu[m]*cArg + rMu[m]*sArg; } Algorithms to Accelerate Scan data – M = # scan points – kx, ky, kz = 3D scan data Pixel data – N = # pixels – x, y, z = input 3D pixel data – rFhD, iFhD= output pixel data Complexity is O(MN) Inner loop – 13 FP MUL or ADD ops – 2 FP trig ops – 12 loads, 2 stores - inner and outer loop can be done in parallel - inner loop: depends on previous calculation in loop - ratio of fp to mem: 3:1 best; worst 1:1

8 Step 1. Consider Parallelism to Evaluate Partitioning Options for (m = 0; m < M; m++) { rMu[m] = rPhi[m]*rD[m] + iPhi[m]*iD[m]; iMu[m] = rPhi[m]*iD[m] – iPhi[m]*rD[m]; for (n = 0; n < N; n++) { expFhD = 2*PI*(kx[m]*x[n] + ky[m]*y[n] + kz[m]*z[n]); cArg = cos(expFhD); sArg = sin(expFhD); rFhD[n] += rMu[m]*cArg – iMu[m]*sArg; iFhD[n] += iMu[m]*cArg + rMu[m]*sArg; } What about M total threads? Note: M is O(millions) (Step 2) What happens to data accesses with this strategy? - map outer loop to threads - then each processes inside

9 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign 8 __global__ void cmpFHd(float* rPhi, iPhi, phiMag, kx, ky, kz, x, y, z, rMu, iMu, int N) { int m = blockIdx.x * FHD_THREADS_PER_BLOCK + threadIdx.x; rMu[m] = rPhi[m]*rD[m] + iPhi[m]*iD[m]; iMu[m] = rPhi[m]*iD[m] – iPhi[m]*rD[m]; for (n = 0; n < N; n++) { expFhD = 2*PI*(kx[m]*x[n] + ky[m]*y[n] + kz[m]*z[n]); cArg = cos(expFhD); sArg = sin(expFhD); rFhD[n] += rMu[m]*cArg – iMu[m]*sArg; iFhD[n] += iMu[m]*cArg + rMu[m]*sArg; } One Possibility

10 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign 8 __global__ void cmpFHd(float* rPhi, iPhi, phiMag, kx, ky, kz, x, y, z, rMu, iMu, int N) { int m = blockIdx.x * FHD_THREADS_PER_BLOCK + threadIdx.x; rMu[m] = rPhi[m]*rD[m] + iPhi[m]*iD[m]; iMu[m] = rPhi[m]*iD[m] – iPhi[m]*rD[m]; for (n = 0; n < N; n++) { expFhD = 2*PI*(kx[m]*x[n] + ky[m]*y[n] + kz[m]*z[n]); cArg = cos(expFhD); sArg = sin(expFhD); rFhD[n] += rMu[m]*cArg – iMu[m]*sArg; iFhD[n] += iMu[m]*cArg + rMu[m]*sArg; } One Possibility Major flaw: This code does not work correctly! The accumulation needs to use atomic operation.

11 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign 9 Back to the Drawing Board – Maybe map the n loop to threads? for (m = 0; m < M; m++) { rMu[m] = rPhi[m]*rD[m] + iPhi[m]*iD[m]; iMu[m] = rPhi[m]*iD[m] – iPhi[m]*rD[m]; for (n = 0; n < N; n++) { expFhD = 2*PI*(kx[m]*x[n] + ky[m]*y[n] + kz[m]*z[n]); cArg = cos(expFhD); sArg = sin(expFhD); rFhD[n] += rMu[m]*cArg – iMu[m]*sArg; iFhD[n] += iMu[m]*cArg + rMu[m]*sArg; }

12 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign 10 for (m = 0; m < M; m++) { rMu[m] = rPhi[m]*rD[m] + iPhi[m]*iD[m]; iMu[m] = rPhi[m]*iD[m] – iPhi[m]*rD[m]; for (n = 0; n < N; n++) { expFhD = 2*PI*(kx[m]*x[n] + ky[m]*y[n] + kz[m]*z[n]); cArg = cos(expFhD); sArg = sin(expFhD); rFhD[n] += rMu[m]*cArg – iMu[m]*sArg; iFhD[n] += iMu[m]*cArg + rMu[m]*sArg; } (a) F H d computation for (m = 0; m < M; m++) { rMu[m] = rPhi[m]*rD[m] + iPhi[m]*iD[m]; iMu[m] = rPhi[m]*iD[m] – iPhi[m]*rD[m]; } for (m = 0; m < M; m++) { for (n = 0; n < N; n++) { expFhD = 2*PI*(kx[m]*x[n] + ky[m]*y[n] + kz[m]*z[n]); cArg = cos(expFhD); sArg = sin(expFhD); rFhD[n] += rMu[m]*cArg – iMu[m]*sArg; iFhD[n] += iMu[m]*cArg + rMu[m]*sArg; } }(b) after loop fission Loop Fission

13 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana- Champaign 11 __global__ void cmpMu(float* rPhi, iPhi, rD, iD, rMu, iMu) { int m = blockIdx.x * MU_THREAEDS_PER_BLOCK + threadIdx.x; rMu[m] = rPhi[m]*rD[m] + iPhi[m]*iD[m]; iMu[m] = rPhi[m]*iD[m] – iPhi[m]*rD[m]; } A Separate cmpMu Kernel After loop fission –computation is in 2 steps –2 parallel kernels executed one after the other –first step implemented below:

14 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007- 2009 University of Illinois, Urbana-Champaign 12 for (m = 0; m < M; m++) { for (n = 0; n < N; n++) { expFhD = 2*PI*(kx[m]*x[n] + ky[m]*y[n] + kz[m]*z[n]); cArg = cos(expFhD); sArg = sin(expFhD); rFhD[n] += rMu[m]*cArg – iMu[m]*sArg; iFhD[n] += iMu[m]*cArg + rMu[m]*sArg; } } (a) before loop interchange Figure 7.9 Loop interchange of the F H D computation Loop Interchange Parallelizing second loop Options: –1. one thread for each inner loop N * M threads –2. loop interchange each outer loop processes an rFhD[n] and iFhD[n]

15 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007- 2009 University of Illinois, Urbana-Champaign 12 for (m = 0; m < M; m++) { for (n = 0; n < N; n++) { expFhD = 2*PI*(kx[m]*x[n] + ky[m]*y[n] + kz[m]*z[n]); cArg = cos(expFhD); sArg = sin(expFhD); rFhD[n] += rMu[m]*cArg – iMu[m]*sArg; iFhD[n] += iMu[m]*cArg + rMu[m]*sArg; } } (a) before loop interchange for (n = 0; n < N; n++) { for (m = 0; m < M; m++) { expFhD = 2*PI*(kx[m]*x[n] + ky[m]*y[n] + kz[m]*z[n]); cArg = cos(expFhD); sArg = sin(expFhD); rFhD[n] += rMu[m]*cArg – iMu[m]*sArg; iFhD[n] += iMu[m]*cArg + rMu[m]*sArg; } } (b) after loop interchange Figure 7.9 Loop interchange of the F H D computation Loop Interchange Possible since all iterations of both level are independent

16 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign 13 __global__ void cmpFHd(float*kx,ky,kz, x,y,z, rMu,iMu, int M){ int n = blockIdx.x * FHD_THREADS_PER_BLOCK + threadIdx.x; for (m = 0; m < M; n++) { float expFhD = 2*PI*(kx[m]*x[n]+ky[m]*y[n]+kz[m]*z[n]); float cArg = cos(expFhD); float sArg = sin(expFhD); rFhD[n] += rMu[m]*cArg – iMu[m]*sArg; iFhD[n] += iMu[m]*cArg + rMu[m]*sArg; } 6 Step 2. New FHd kernel

17 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007- 2009 University of Illinois, Urbana-Champaign 14 __global__ void cmpFHd(float* rPhi, iPhi, phiMag, kx, ky, kz, x, y, z, rMu, iMu, int M) { int n = blockIdx.x * FHD_THREADS_PER_BLOCK + threadIdx.x; float xn_r = x[n]; float yn_r = y[n]; float zn_r = z[n]; float rFhDn_r = rFhD[n]; float iFhDn_r = iFhD[n]; for (m = 0; m < M; m++) { float expFhD = 2*PI*(kx[m]*xn_r+ky[m]*yn_r+kz[m]*zn_r); float cArg = cos(expFhD); float sArg = sin(expFhD); rFhDn_r += rMu[m]*cArg – iMu[m]*sArg; iFhDn_r += iMu[m]*cArg + rMu[m]*sArg; } rFhD[n] = rFhD_r; iFhD[n] = iFhD_r; } Step 3. Using Registers to Reduce Global Memory Traffic Still too much stress on memory! Note that kx, ky and kz are read-only and based on m - only for loop n can we move into register - there should be way for m, they are read only - goal: access ratio of 10:1 - m is independent of n => al threads will be accessing same ks -each time something is accessed from cache it is broadcasted to every thread in warp => no conflicts - constant memory is only 64KB => we need tiling

18 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007- 2009 University of Illinois, Urbana-Champaign 15 Tiling of Scan Data LS recon uses multiple grids – Each grid operates on all pixels – Each grid operates on a distinct subset of scan data – Each thread in the same grid operates on a distinct pixel for (m = 0; m < M/32; m++) { exQ = 2*PI*(kx[m]*x[n] + ky[m]*y[n] + kz[m]*z[n]) rQ[n] += phi[m]*cos(exQ) iQ[n] += phi[m]*sin(exQ) } 12 Thread n operates on pixel n:

19 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign 16 __constant__ float kx_c[CHUNK_SIZE], ky_c[CHUNK_SIZE], kz_c[CHUNK_SIZE]; … __ void main() { int i; for (i = 0; i < M/CHUNK_SIZE; i++); cudaMemcpyToSymbol(kx_c,&kx[i*CHUNK_SIZE],4*CHUNK_SIZE); cudaMemcpyToSymbol(ky_c,&ky[i*CHUNK_SIZE],4*CHUNK_SIZE); cudaMemcpyToSymbol(kz_c,&ky[i*CHUNK_SIZE],4*CHUNK_SIZE); … cmpFHD >> (rPhi, iPhi, phiMag, x, y, z, rMu, iMu, int M); } /* Need to call kernel one more time if M is not */ /* perfect multiple of CHUNK SIZE */ } Tiling k-space data to fit into constant memory each processes a chunk that fits in 64K memory

20 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007- 2009 University of Illinois, Urbana-Champaign 17 __global__ void cmpFHd(float*x, y, z, rMu, iMu, int M) { int n = blockIdx.x * FHD_THREADS_PER_BLOCK + threadIdx.x; float xn_r = x[n]; float yn_r = y[n]; float zn_r = z[n]; float rFhDn_r = rFhD[n]; float iFhDn_r = iFhD[n]; for (m = 0; m < M; m++) { float expFhD = 2*PI*(kx_c[m]*xn_r+ky_c[m]*yn_r+kz_c[m]*zn_r); float cArg = cos(expFhD); float sArg = sin(expFhD); rFhDn_r += rMu[m]*cArg – iMu[m]*sArg; iFhDn_r += iMu[m]*cArg + rMu[m]*sArg; } rFhD[n] = rFhD_r; iFhD[n] = iFhD_r; } Revised Kernel for Constant Memory

21 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007- 2009 University of Illinois, Urbana-Champaign 18 Sidebar: Cache-Conscious Data Layout kx, ky, kz, and phi components of same scan point have spatial and temporal locality –Prefetching –Caching Old layout does not fully leverage that locality New layout does fully leverage that locality

22 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign 19 struct kdata { float x, float y, float z; } k; __constant__ struct kdata k_c[CHUNK_SIZE]; … __ void main() { int i; for (i = 0; i < M/CHUNK_SIZE; i++); cudaMemcpyToSymbol(k_c, k, 12*CHUNK_SIZE); cmpFHD >> (...); } Adjusting K-space Data Layout

23 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign 20 __global__ void cmpFHd(float* rPhi, iPhi, phiMag, x, y, z, rMu, iMu, int M) { int n = blockIdx.x * FHD_THREADS_PER_BLOCK + threadIdx.x; float xn_r = x[n]; float yn_r = y[n]; float zn_r = z[n]; float rFhDn_r = rFhD[n]; float iFhDn_r = iFhD[n]; for (m = 0; m < M; m++) { float expFhD = 2*PI*(k[m].x*xn_r+k[m].y*yn_r+k[m].z*zn_r); float cArg = cos(expFhD); float sArg = sin(expFhD); rFhDn_r += rMu[m]*cArg – iMu[m]*sArg; iFhDn_r += iMu[m]*cArg + rMu[m]*sArg; } rFhD[n] = rFhD_r; iFhD[n] = iFhD_r; } Figure 7.16 Adjusting the k-space data memory layout in the F H d kernel

24 21 Overcoming Mem BW Bottlenecks Old bottleneck: off-chip BW –Solution: constant memory –FP arithmetic to off-chip loads: 421 to 1 Performance –22.8 GFLOPS (F H d) New bottleneck: trig operations © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign

25 22 Using Super Function Units Old bottleneck: trig operations –Solution: SFUs Performance –92.2 GFLOPS (F H d) New bottleneck: overhead of branches and address calculations © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign

26 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign 23 Sidebar: Effects of Approximations Avoid temptation to measure only absolute error (I 0 – I) –Can be deceptively large or small Metrics –PSNR: Peak signal-to-noise ratio –SNR: Signal-to-noise ratio Avoid temptation to consider only the error in the computed value –Some apps are resistant to approximations; others are very sensitive 20 A.N. Netravali and B.G. Haskell, Digital Pictures: Representation, Compression, and Standards (2nd Ed), Plenum Press, New York, NY (1995).

27 24 Step 4: Overcoming Bottlenecks (Overheads) Old bottleneck: Overhead of branches and address calculations –Solution: Loop unrolling and experimental tuning Performance –145 GFLOPS (F H d) 21 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign

28 © David Kirk/NVIDIA and Wen-mei W. Hwu, 2007-2009 University of Illinois, Urbana-Champaign Summary of Results QFHdFHdTotal ReconstructionRun Time (m)GFLOPRun Time (m) GFLOPLinear Solver (m) Recon. Time (m) Gridding + FFT (CPU, DP) N/A 0.39 LS (CPU, DP)4009.00.3518.00.41.59519.59 LS (CPU, SP)2678.70.5342.30.71.61343.91 LS (GPU, Naïve)260.25.141.05.41.6542.65 LS (GPU, CMem)72.018.69.822.81.5711.37 LS (GPU, CMem, SFU) 13.698.22.492.21.604.00 LS (GPU, CMem, SFU, Exp) 7.5178.91.5144.51.693.19 108X228X 357X

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