Solving ODEs with GPUs

Transcript

1. VexCL Rapid development of scientific code for GPUs Denis Demidov Institute of System Analysis / Russian Academy of Sciences, Kazan Federal University March 2018,
2. Why GPUs? November 2017: Top500 - 6 out of top 10 systems use accelerators/GPUs Green500 - 6 out of top 10 systems use GPUs PizDaint system (No 3 in Top500) CPU GPU Model Intel Xeon E5-2690 v3 NVIDIA Tesla P100 16GB Peak performance 500 GFLOPS 4.7 TFLOPS Memory bandwidth 68 GB/s 732 GB/s Price $2000 $5700 Max power consumption 135 W 250 W
3. Peak performance for CPUs and GPUs1 1https://www.karlrupp.net/2013/06/cpu-gpu-and-mic-hardware-characteristics-over-time/
4. Memory bandwidth for CPUs and GPUs2 2https://www.karlrupp.net/2013/06/cpu-gpu-and-mic-hardware-characteristics-over-time/
5. VexCL — a vector expression template library for OpenCL/CUDA Fork m e on G itH ub Created for ease of C++ based GPGPU development: Convenient notation for vector expressions OpenCL/CUDA JIT code generation Easily combined with existing libraries/code Header-only Supported backends: OpenCL (Khronos C++ bindings) OpenCL (Boost.Compute) NVIDIA CUDA JIT-compiled OpenMP The source code is available under the MIT license: https://github.com/ddemidov/vexcl
6. Hello OpenCL Compute sum of two vectors in parallel: A and B are large vectors. Compute A = A + B. Overview of (any) OpenCL solution: Initialize OpenCL context Allocate memory Transfer input data Run computations Get the results
7. Hello OpenCL #include <iostream> #include <vector> #include <string> #include <stdexcept> #define __CL_ENABLE_EXCEPTIONS #include <CL/cl.hpp> int main() { std::vector<cl::Platform> platform; cl::Platform::get(&platform); if (platform.empty()) throw std::runtime_error("No OpenCL platforms"); cl::Context context; std::vector<cl::Device> device; for(auto p = platform.begin(); device.empty() && p != platform.end(); p++) { std::vector<cl::Device> dev; p->getDevices(CL_DEVICE_TYPE_GPU, &dev); for(auto d = dev.begin(); device.empty() && d != dev.end(); d++) { if (!d->getInfo<CL_DEVICE_AVAILABLE>()) continue; device.push_back(*d); try { context = cl::Context(device); } catch(...) { device.clear(); } } } if (device.empty()) throw std::runtime_error("No GPUs"); cl::CommandQueue queue(context, device[0]); const size_t n = 1024 * 1024; std::vector<double> a(n, 1.5), b(n, 2.7); cl::Buffer A(context, CL_MEM_READ_ONLY | CL_MEM_COPY_HOST_PTR, a.size() * sizeof(a[0]), a.data()); cl::Buffer B(context, CL_MEM_READ_WRITE | CL_MEM_COPY_HOST_PTR, b.size() * sizeof(b[0]), b.data()); std::string source = R"( kernel void add(ulong n, global const double *a, global double *b) { ulong i = get_global_id(0); if (i < n) b[i] += a[i]; } )"; cl::Program program(context, source); try { program.build(device); } catch (const cl::Error&) { std::cerr << "OpenCL compilation error" << std::endl << program.getBuildInfo<CL_PROGRAM_BUILD_LOG>(device[0]) << std::endl; throw std::runtime_error("OpenCL build error"); } cl::Kernel add(program, "add"); add.setArg(0, static_cast<cl_ulong>(n)); add.setArg(1, A); add.setArg(2, B); queue.enqueueNDRangeKernel(add, cl::NullRange, n, cl::NullRange); queue.enqueueReadBuffer(B, CL_TRUE, 0, b.size() * sizeof(b[0]), b.data()); std::cout << b[42] << std::endl; }
8. Hello OpenCL #include <iostream> #include <vector> #include <string> #include <stdexcept> #define __CL_ENABLE_EXCEPTIONS #include <CL/cl.hpp> int main() { std::vector<cl::Platform> platform; cl::Platform::get(&platform); if (platform.empty()) throw std::runtime_error("No OpenCL platforms"); cl::Context context; std::vector<cl::Device> device; for(auto p = platform.begin(); device.empty() && p != platform.end(); p++) { std::vector<cl::Device> dev; p->getDevices(CL_DEVICE_TYPE_GPU, &dev); for(auto d = dev.begin(); device.empty() && d != dev.end(); d++) { if (!d->getInfo<CL_DEVICE_AVAILABLE>()) continue; device.push_back(*d); try { context = cl::Context(device); } catch(...) { device.clear(); } } } if (device.empty()) throw std::runtime_error("No GPUs"); cl::CommandQueue queue(context, device[0]); const size_t n = 1024 * 1024; std::vector<double> a(n, 1.5), b(n, 2.7); cl::Buffer A(context, CL_MEM_READ_ONLY | CL_MEM_COPY_HOST_PTR, a.size() * sizeof(a[0]), a.data()); cl::Buffer B(context, CL_MEM_READ_WRITE | CL_MEM_COPY_HOST_PTR, b.size() * sizeof(b[0]), b.data()); std::string source = R"( kernel void add(ulong n, global const double *a, global double *b) { ulong i = get_global_id(0); if (i < n) b[i] += a[i]; } )"; cl::Program program(context, source); try { program.build(device); } catch (const cl::Error&) { std::cerr << "OpenCL compilation error" << std::endl << program.getBuildInfo<CL_PROGRAM_BUILD_LOG>(device[0]) << std::endl; throw std::runtime_error("OpenCL build error"); } cl::Kernel add(program, "add"); add.setArg(0, static_cast<cl_ulong>(n)); add.setArg(1, A); add.setArg(2, B); queue.enqueueNDRangeKernel(add, cl::NullRange, n, cl::NullRange); queue.enqueueReadBuffer(B, CL_TRUE, 0, b.size() * sizeof(b[0]), b.data()); std::cout << b[42] << std::endl; } 1. Query platforms 10 std::vector<cl::Platform> platform; 11 cl::Platform::get(&platform); 12 13 if (platform.empty()) 14 throw std::runtime_error("No OpenCL platforms");
9. Hello OpenCL #include <iostream> #include <vector> #include <string> #include <stdexcept> #define __CL_ENABLE_EXCEPTIONS #include <CL/cl.hpp> int main() { std::vector<cl::Platform> platform; cl::Platform::get(&platform); if (platform.empty()) throw std::runtime_error("No OpenCL platforms"); cl::Context context; std::vector<cl::Device> device; for(auto p = platform.begin(); device.empty() && p != platform.end(); p++) { std::vector<cl::Device> dev; p->getDevices(CL_DEVICE_TYPE_GPU, &dev); for(auto d = dev.begin(); device.empty() && d != dev.end(); d++) { if (!d->getInfo<CL_DEVICE_AVAILABLE>()) continue; device.push_back(*d); try { context = cl::Context(device); } catch(...) { device.clear(); } } } if (device.empty()) throw std::runtime_error("No GPUs"); cl::CommandQueue queue(context, device[0]); const size_t n = 1024 * 1024; std::vector<double> a(n, 1.5), b(n, 2.7); cl::Buffer A(context, CL_MEM_READ_ONLY | CL_MEM_COPY_HOST_PTR, a.size() * sizeof(a[0]), a.data()); cl::Buffer B(context, CL_MEM_READ_WRITE | CL_MEM_COPY_HOST_PTR, b.size() * sizeof(b[0]), b.data()); std::string source = R"( kernel void add(ulong n, global const double *a, global double *b) { ulong i = get_global_id(0); if (i < n) b[i] += a[i]; } )"; cl::Program program(context, source); try { program.build(device); } catch (const cl::Error&) { std::cerr << "OpenCL compilation error" << std::endl << program.getBuildInfo<CL_PROGRAM_BUILD_LOG>(device[0]) << std::endl; throw std::runtime_error("OpenCL build error"); } cl::Kernel add(program, "add"); add.setArg(0, static_cast<cl_ulong>(n)); add.setArg(1, A); add.setArg(2, B); queue.enqueueNDRangeKernel(add, cl::NullRange, n, cl::NullRange); queue.enqueueReadBuffer(B, CL_TRUE, 0, b.size() * sizeof(b[0]), b.data()); std::cout << b[42] << std::endl; } 2. Get the first available GPU 16 cl::Context context; 17 std::vector<cl::Device> device; 18 for(auto p = platform.begin(); device.empty() && p != platform.end(); p++) { 19 std::vector<cl::Device> dev; 20 p->getDevices(CL_DEVICE_TYPE_GPU, &dev); 21 for(auto d = dev.begin(); device.empty() && d != dev.end(); d++) { 22 if (!d->getInfo<CL_DEVICE_AVAILABLE>()) continue; 23 device.push_back(*d); 24 try { 25 context = cl::Context(device); 26 } catch(...) { 27 device.clear(); 28 } 29 } 30 } 31 if (device.empty()) throw std::runtime_error("No GPUs"); 32 33 cl::CommandQueue queue(context, device[0]);
10. Hello OpenCL #include <iostream> #include <vector> #include <string> #include <stdexcept> #define __CL_ENABLE_EXCEPTIONS #include <CL/cl.hpp> int main() { std::vector<cl::Platform> platform; cl::Platform::get(&platform); if (platform.empty()) throw std::runtime_error("No OpenCL platforms"); cl::Context context; std::vector<cl::Device> device; for(auto p = platform.begin(); device.empty() && p != platform.end(); p++) { std::vector<cl::Device> dev; p->getDevices(CL_DEVICE_TYPE_GPU, &dev); for(auto d = dev.begin(); device.empty() && d != dev.end(); d++) { if (!d->getInfo<CL_DEVICE_AVAILABLE>()) continue; device.push_back(*d); try { context = cl::Context(device); } catch(...) { device.clear(); } } } if (device.empty()) throw std::runtime_error("No GPUs"); cl::CommandQueue queue(context, device[0]); const size_t n = 1024 * 1024; std::vector<double> a(n, 1.5), b(n, 2.7); cl::Buffer A(context, CL_MEM_READ_ONLY | CL_MEM_COPY_HOST_PTR, a.size() * sizeof(a[0]), a.data()); cl::Buffer B(context, CL_MEM_READ_WRITE | CL_MEM_COPY_HOST_PTR, b.size() * sizeof(b[0]), b.data()); std::string source = R"( kernel void add(ulong n, global const double *a, global double *b) { ulong i = get_global_id(0); if (i < n) b[i] += a[i]; } )"; cl::Program program(context, source); try { program.build(device); } catch (const cl::Error&) { std::cerr << "OpenCL compilation error" << std::endl << program.getBuildInfo<CL_PROGRAM_BUILD_LOG>(device[0]) << std::endl; throw std::runtime_error("OpenCL build error"); } cl::Kernel add(program, "add"); add.setArg(0, static_cast<cl_ulong>(n)); add.setArg(1, A); add.setArg(2, B); queue.enqueueNDRangeKernel(add, cl::NullRange, n, cl::NullRange); queue.enqueueReadBuffer(B, CL_TRUE, 0, b.size() * sizeof(b[0]), b.data()); std::cout << b[42] << std::endl; } 3. Prepare and copy input data 35 const size_t n = 1024 * 1024; 36 std::vector<double> a(n, 1.5), b(n, 2.7); 37 38 cl::Buffer A(context, CL_MEM_READ_ONLY | CL_MEM_COPY_HOST_PTR, 39 a.size() * sizeof(a[0]), a.data()); 40 41 cl::Buffer B(context, CL_MEM_READ_WRITE | CL_MEM_COPY_HOST_PTR, 42 b.size() * sizeof(b[0]), b.data());
11. Hello OpenCL #include <iostream> #include <vector> #include <string> #include <stdexcept> #define __CL_ENABLE_EXCEPTIONS #include <CL/cl.hpp> int main() { std::vector<cl::Platform> platform; cl::Platform::get(&platform); if (platform.empty()) throw std::runtime_error("No OpenCL platforms"); cl::Context context; std::vector<cl::Device> device; for(auto p = platform.begin(); device.empty() && p != platform.end(); p++) { std::vector<cl::Device> dev; p->getDevices(CL_DEVICE_TYPE_GPU, &dev); for(auto d = dev.begin(); device.empty() && d != dev.end(); d++) { if (!d->getInfo<CL_DEVICE_AVAILABLE>()) continue; device.push_back(*d); try { context = cl::Context(device); } catch(...) { device.clear(); } } } if (device.empty()) throw std::runtime_error("No GPUs"); cl::CommandQueue queue(context, device[0]); const size_t n = 1024 * 1024; std::vector<double> a(n, 1.5), b(n, 2.7); cl::Buffer A(context, CL_MEM_READ_ONLY | CL_MEM_COPY_HOST_PTR, a.size() * sizeof(a[0]), a.data()); cl::Buffer B(context, CL_MEM_READ_WRITE | CL_MEM_COPY_HOST_PTR, b.size() * sizeof(b[0]), b.data()); std::string source = R"( kernel void add(ulong n, global const double *a, global double *b) { ulong i = get_global_id(0); if (i < n) b[i] += a[i]; } )"; cl::Program program(context, source); try { program.build(device); } catch (const cl::Error&) { std::cerr << "OpenCL compilation error" << std::endl << program.getBuildInfo<CL_PROGRAM_BUILD_LOG>(device[0]) << std::endl; throw std::runtime_error("OpenCL build error"); } cl::Kernel add(program, "add"); add.setArg(0, static_cast<cl_ulong>(n)); add.setArg(1, A); add.setArg(2, B); queue.enqueueNDRangeKernel(add, cl::NullRange, n, cl::NullRange); queue.enqueueReadBuffer(B, CL_TRUE, 0, b.size() * sizeof(b[0]), b.data()); std::cout << b[42] << std::endl; } 4. Write and compile the compute kernel 44 std::string source = R"( 45 kernel void add(ulong n, global const double *a, global double *b) { 46 ulong i = get_global_id(0); 47 if (i < n) b[i] += a[i]; 48 } 49 )"; 50 51 cl::Program program(context, source); 52 53 try { 54 program.build(device); 55 } catch (const cl::Error&) { 56 std::cerr 57 << "OpenCL compilation error" << std::endl 58 << program.getBuildInfo<CL_PROGRAM_BUILD_LOG>(device[0]) 59 << std::endl; 60 throw std::runtime_error("OpenCL build error"); 61 } 62 cl::Kernel add(program, "add");
12. Hello OpenCL #include <iostream> #include <vector> #include <string> #include <stdexcept> #define __CL_ENABLE_EXCEPTIONS #include <CL/cl.hpp> int main() { std::vector<cl::Platform> platform; cl::Platform::get(&platform); if (platform.empty()) throw std::runtime_error("No OpenCL platforms"); cl::Context context; std::vector<cl::Device> device; for(auto p = platform.begin(); device.empty() && p != platform.end(); p++) { std::vector<cl::Device> dev; p->getDevices(CL_DEVICE_TYPE_GPU, &dev); for(auto d = dev.begin(); device.empty() && d != dev.end(); d++) { if (!d->getInfo<CL_DEVICE_AVAILABLE>()) continue; device.push_back(*d); try { context = cl::Context(device); } catch(...) { device.clear(); } } } if (device.empty()) throw std::runtime_error("No GPUs"); cl::CommandQueue queue(context, device[0]); const size_t n = 1024 * 1024; std::vector<double> a(n, 1.5), b(n, 2.7); cl::Buffer A(context, CL_MEM_READ_ONLY | CL_MEM_COPY_HOST_PTR, a.size() * sizeof(a[0]), a.data()); cl::Buffer B(context, CL_MEM_READ_WRITE | CL_MEM_COPY_HOST_PTR, b.size() * sizeof(b[0]), b.data()); std::string source = R"( kernel void add(ulong n, global const double *a, global double *b) { ulong i = get_global_id(0); if (i < n) b[i] += a[i]; } )"; cl::Program program(context, source); try { program.build(device); } catch (const cl::Error&) { std::cerr << "OpenCL compilation error" << std::endl << program.getBuildInfo<CL_PROGRAM_BUILD_LOG>(device[0]) << std::endl; throw std::runtime_error("OpenCL build error"); } cl::Kernel add(program, "add"); add.setArg(0, static_cast<cl_ulong>(n)); add.setArg(1, A); add.setArg(2, B); queue.enqueueNDRangeKernel(add, cl::NullRange, n, cl::NullRange); queue.enqueueReadBuffer(B, CL_TRUE, 0, b.size() * sizeof(b[0]), b.data()); std::cout << b[42] << std::endl; } 5. Set kernel arguments and launch the computation 64 add.setArg(0, static_cast<cl_ulong>(n)); 65 add.setArg(1, A); 66 add.setArg(2, B); 67 68 queue.enqueueNDRangeKernel(add, cl::NullRange, n, cl::NullRange);
13. Hello OpenCL #include <iostream> #include <vector> #include <string> #include <stdexcept> #define __CL_ENABLE_EXCEPTIONS #include <CL/cl.hpp> int main() { std::vector<cl::Platform> platform; cl::Platform::get(&platform); if (platform.empty()) throw std::runtime_error("No OpenCL platforms"); cl::Context context; std::vector<cl::Device> device; for(auto p = platform.begin(); device.empty() && p != platform.end(); p++) { std::vector<cl::Device> dev; p->getDevices(CL_DEVICE_TYPE_GPU, &dev); for(auto d = dev.begin(); device.empty() && d != dev.end(); d++) { if (!d->getInfo<CL_DEVICE_AVAILABLE>()) continue; device.push_back(*d); try { context = cl::Context(device); } catch(...) { device.clear(); } } } if (device.empty()) throw std::runtime_error("No GPUs"); cl::CommandQueue queue(context, device[0]); const size_t n = 1024 * 1024; std::vector<double> a(n, 1.5), b(n, 2.7); cl::Buffer A(context, CL_MEM_READ_ONLY | CL_MEM_COPY_HOST_PTR, a.size() * sizeof(a[0]), a.data()); cl::Buffer B(context, CL_MEM_READ_WRITE | CL_MEM_COPY_HOST_PTR, b.size() * sizeof(b[0]), b.data()); std::string source = R"( kernel void add(ulong n, global const double *a, global double *b) { ulong i = get_global_id(0); if (i < n) b[i] += a[i]; } )"; cl::Program program(context, source); try { program.build(device); } catch (const cl::Error&) { std::cerr << "OpenCL compilation error" << std::endl << program.getBuildInfo<CL_PROGRAM_BUILD_LOG>(device[0]) << std::endl; throw std::runtime_error("OpenCL build error"); } cl::Kernel add(program, "add"); add.setArg(0, static_cast<cl_ulong>(n)); add.setArg(1, A); add.setArg(2, B); queue.enqueueNDRangeKernel(add, cl::NullRange, n, cl::NullRange); queue.enqueueReadBuffer(B, CL_TRUE, 0, b.size() * sizeof(b[0]), b.data()); std::cout << b[42] << std::endl; } 6. Get the results from the compute device 70 queue.enqueueReadBuffer(B, CL_TRUE, 0, b.size() * sizeof(b[0]), b.data()); 71 std::cout << b[42] << std::endl;
14. Hello VexCL hello.cpp 1 #include <iostream> 2 #include <vector> 3 #include <vexcl/vexcl.hpp> 4 5 int main() { 6 vex::Context ctx( vex::Filter::GPU ); 7 if (!ctx) throw std::runtime_error("No GPUs"); 8 9 size_t n = 1024 * 1024; 10 std::vector<double> a(n, 1.5), b(n, 2.7); 11 12 vex::vector<double> A(ctx, a); 13 vex::vector<double> B(ctx, b); 14 15 B += A; 16 17 vex::copy(B, b); 18 std::cout << b[42] << std::endl; 19 } CMakeLists.txt 1 cmake_minimum_required(VERSION 3.1) 2 project(hello) 3 4 find_package(VexCL) 5 6 add_executable(hello hello.cpp) 7 target_link_libraries(hello VexCL::OpenCL) Use VexCL::Compute, VexCL::CUDA, or VexCL::JIT for use with Boost.Compute, CUDA, or OpenMP backend
15. Interface
16. Initialization Multi-device and multi-platform computations are supported. Some operations are restricted to single-device contexts. VexCL context is initialized from combination of device filters. Initialize VexCL context on selected devices 1 vex::Context ctx( vex::Filter::Any );
17. Initialization Multi-device and multi-platform computations are supported. Some operations are restricted to single-device contexts. VexCL context is initialized from combination of device filters. Initialize VexCL context on selected devices 1 vex::Context ctx( vex::Filter::GPU );
18. Initialization Multi-device and multi-platform computations are supported. Some operations are restricted to single-device contexts. VexCL context is initialized from combination of device filters. Initialize VexCL context on selected devices 1 vex::Context ctx(vex::Filter::Name("Intel"));
19. Initialization Multi-device and multi-platform computations are supported. Some operations are restricted to single-device contexts. VexCL context is initialized from combination of device filters. Initialize VexCL context on selected devices 1 vex::Context ctx(vex::Filter::GPU && vex::Filter::Platform("AMD"));
20. Memory and work splitting 1 vex::Context ctx( vex::Filter::Count(1) ); 2 3 vex::vector<double> x(ctx, N); 4 vex::vector<double> y(ctx, N); 5 6 x = vex::element_index() * (1.0 / N); 7 y = sin(2 * x) + sqrt(1 - x * x); x y
21. Memory and work splitting 1 vex::Context ctx( vex::Filter::GPU ); 2 3 vex::vector<double> x(ctx, N); 4 vex::vector<double> y(ctx, N); 5 6 x = vex::element_index() * (1.0 / N); 7 y = sin(2 * x) + sqrt(1 - x * x); x y
22. Memory and work splitting 1 vex::Context ctx( vex::Filter::DoublePrecision ); 2 3 vex::vector<double> x(ctx, N); 4 vex::vector<double> y(ctx, N); 5 6 x = vex::element_index() * (1.0 / N); 7 y = sin(2 * x) + sqrt(1 - x * x); x y
23. Copies between host and device memory 1 vex::vector<double> d(ctx, n); 2 std::vector<double> h(n); 3 double a[100]; STL-like range copies 1 vex::copy(d.begin(), d.end(), h.begin()); 2 vex::copy(d.begin(), d.begin() + 100, a); Simple copies 1 vex::copy(d, h); 2 vex::copy(h, d); Map OpenCL buffer to host pointer 1 auto p = d.map(devnum); 2 std::sort(&p[0], &p[d.part_size(devnum)]); Access single element (slow) 1 double v = d[42]; 2 d[0] = 0;
24. Expressions are translated into compute kernels This expression: 1 x = 2 * y - sin(z); export VEXCL_SHOW_KERNELS=1 to see the generated code. . . . results in this kernel: 1 kernel void vexcl_vector_kernel( 2 ulong n, 3 global double * prm_1, 4 int prm_2, 5 global double * prm_3, 6 global double * prm_4 7 ) 8 { 9 for(size_t idx = get_global_id(0); idx < n; idx += get_global_size(0)) { 10 prm_1[idx] = ( ( prm_2 * prm_3[idx] ) - sin( prm_4[idx] ) ); 11 } 12 } − ∗ sin 2 y z
25. What vector expressions are supported? All vectors in an expression have to be compatible: Have same size Located on same devices What may be used: Vectors, scalars, constants Arithmetic, logical operators Built-in functions User-defined functions Random number generators Slicing and permutations Reduce to a scalar (sum, min, max) Reduce across chosen dimensions Stencil operations Sparse matrix – vector products Fast Fourier Transform Sort, scan, reduce by key
26. Example: Monte Carlo π Compute approximate value of π: area of circle area of square = πr2 (2r)2 = π 4 , π = 4 area of circle area of square ≈ 4 count(points in circle) count(all points)      1 vex::Random<cl_double2> rnd; // Generates 2D points in [0, 1] × [0, 1] 2 vex::Reductor<size_t, vex::SUM> sum(ctx); 3 4 double pi = 4.0 * sum( length( rnd(vex::element_index(0, n), seed) ) < 1 ) / n;
27. Monte Carlo π: the generated kernel #if defined(cl_khr_fp64) #pragma OPENCL EXTENSION cl_khr_fp64: enable #elif defined(cl_amd_fp64) #pragma OPENCL EXTENSION cl_amd_fp64: enable #endif void philox_uint_4_10 ( uint * ctr, uint * key ) { uint m[4]; m[0] = mul_hi(0xD2511F53, ctr[0]); m[1] = 0xD2511F53 * ctr[0]; m[2] = mul_hi(0xCD9E8D57, ctr[2]); m[3] = 0xCD9E8D57 * ctr[2]; ctr[0] = m[2] ˆ ctr[1] ˆ key[0]; ctr[1] = m[3]; ctr[2] = m[0] ˆ ctr[3] ˆ key[1]; ctr[3] = m[1]; key[0] += 0x9E3779B9; key[1] += 0xBB67AE85; m[0] = mul_hi(0xD2511F53, ctr[0]); m[1] = 0xD2511F53 * ctr[0]; m[2] = mul_hi(0xCD9E8D57, ctr[2]); m[3] = 0xCD9E8D57 * ctr[2]; ctr[0] = m[2] ˆ ctr[1] ˆ key[0]; ctr[1] = m[3]; ctr[2] = m[0] ˆ ctr[3] ˆ key[1]; ctr[3] = m[1]; key[0] += 0x9E3779B9; key[1] += 0xBB67AE85; m[0] = mul_hi(0xD2511F53, ctr[0]); m[1] = 0xD2511F53 * ctr[0]; m[2] = mul_hi(0xCD9E8D57, ctr[2]); m[3] = 0xCD9E8D57 * ctr[2]; ctr[0] = m[2] ˆ ctr[1] ˆ key[0]; ctr[1] = m[3]; ctr[2] = m[0] ˆ ctr[3] ˆ key[1]; ctr[3] = m[1]; key[0] += 0x9E3779B9; key[1] += 0xBB67AE85; m[0] = mul_hi(0xD2511F53, ctr[0]); m[1] = 0xD2511F53 * ctr[0]; m[2] = mul_hi(0xCD9E8D57, ctr[2]); m[3] = 0xCD9E8D57 * ctr[2]; ctr[0] = m[2] ˆ ctr[1] ˆ key[0]; ctr[1] = m[3]; ctr[2] = m[0] ˆ ctr[3] ˆ key[1]; ctr[3] = m[1]; key[0] += 0x9E3779B9; key[1] += 0xBB67AE85; m[0] = mul_hi(0xD2511F53, ctr[0]); m[1] = 0xD2511F53 * ctr[0]; m[2] = mul_hi(0xCD9E8D57, ctr[2]); m[3] = 0xCD9E8D57 * ctr[2]; ctr[0] = m[2] ˆ ctr[1] ˆ key[0]; ctr[1] = m[3]; ctr[2] = m[0] ˆ ctr[3] ˆ key[1]; ctr[3] = m[1]; key[0] += 0x9E3779B9; key[1] += 0xBB67AE85; m[0] = mul_hi(0xD2511F53, ctr[0]); m[1] = 0xD2511F53 * ctr[0]; m[2] = mul_hi(0xCD9E8D57, ctr[2]); m[3] = 0xCD9E8D57 * ctr[2]; ctr[0] = m[2] ˆ ctr[1] ˆ key[0]; ctr[1] = m[3]; ctr[2] = m[0] ˆ ctr[3] ˆ key[1]; ctr[3] = m[1]; key[0] += 0x9E3779B9; key[1] += 0xBB67AE85; m[0] = mul_hi(0xD2511F53, ctr[0]); m[1] = 0xD2511F53 * ctr[0]; m[2] = mul_hi(0xCD9E8D57, ctr[2]); m[3] = 0xCD9E8D57 * ctr[2]; ctr[0] = m[2] ˆ ctr[1] ˆ key[0]; ctr[1] = m[3]; ctr[2] = m[0] ˆ ctr[3] ˆ key[1]; ctr[3] = m[1]; key[0] += 0x9E3779B9; key[1] += 0xBB67AE85; m[0] = mul_hi(0xD2511F53, ctr[0]); m[1] = 0xD2511F53 * ctr[0]; m[2] = mul_hi(0xCD9E8D57, ctr[2]); m[3] = 0xCD9E8D57 * ctr[2]; ctr[0] = m[2] ˆ ctr[1] ˆ key[0]; ctr[1] = m[3]; ctr[2] = m[0] ˆ ctr[3] ˆ key[1]; ctr[3] = m[1]; key[0] += 0x9E3779B9; key[1] += 0xBB67AE85; m[0] = mul_hi(0xD2511F53, ctr[0]); m[1] = 0xD2511F53 * ctr[0]; m[2] = mul_hi(0xCD9E8D57, ctr[2]); m[3] = 0xCD9E8D57 * ctr[2]; ctr[0] = m[2] ˆ ctr[1] ˆ key[0]; ctr[1] = m[3]; ctr[2] = m[0] ˆ ctr[3] ˆ key[1]; ctr[3] = m[1]; key[0] += 0x9E3779B9; key[1] += 0xBB67AE85; m[0] = mul_hi(0xD2511F53, ctr[0]); m[1] = 0xD2511F53 * ctr[0]; m[2] = mul_hi(0xCD9E8D57, ctr[2]); m[3] = 0xCD9E8D57 * ctr[2]; ctr[0] = m[2] ˆ ctr[1] ˆ key[0]; ctr[1] = m[3]; ctr[2] = m[0] ˆ ctr[3] ˆ key[1]; ctr[3] = m[1]; } double2 random_double2_philox ( ulong prm1, ulong prm2 ) { union { uint ctr[4]; ulong res_i[2]; double res_f[2]; double2 res; } ctr; uint key[2]; ctr.ctr[0] = prm1; ctr.ctr[1] = prm2; ctr.ctr[2] = prm1; ctr.ctr[3] = prm2; key[0] = 0x12345678; key[1] = 0x12345678; philox_uint_4_10(ctr.ctr, key); ctr.res_f[0] = ctr.res_i[0] / 18446744073709551615.0; ctr.res_f[1] = ctr.res_i[1] / 18446744073709551615.0; return ctr.res; } ulong SUM_ulong ( ulong prm1, ulong prm2 ) { return prm1 + prm2; } kernel void vexcl_reductor_kernel ( ulong n, ulong prm_1, ulong prm_2, double prm_3, global ulong * g_odata, local ulong * smem ) { ulong mySum = (ulong)0; for(ulong idx = get_global_id(0); idx < n; idx += get_global_size(0)) { mySum = SUM_ulong(mySum, ( length( random_double2_philox( (prm_1 + idx), prm_2 ) ) < prm_3 )); } local ulong * sdata = smem; size_t tid = get_local_id(0); size_t block_size = get_local_size(0); sdata[tid] = mySum; barrier(CLK_LOCAL_MEM_FENCE); if (block_size >= 1024) { if (tid < 512) { sdata[tid] = mySum = SUM_ulong(mySum, sdata[tid + 512]); } barrier(CLK_LOCAL_MEM_FENCE); } if (block_size >= 512) { if (tid < 256) { sdata[tid] = mySum = SUM_ulong(mySum, sdata[tid + 256]); } barrier(CLK_LOCAL_MEM_FENCE); } if (block_size >= 256) { if (tid < 128) { sdata[tid] = mySum = SUM_ulong(mySum, sdata[tid + 128]); } barrier(CLK_LOCAL_MEM_FENCE); } if (block_size >= 128) { if (tid < 64) { sdata[tid] = mySum = SUM_ulong(mySum, sdata[tid + 64]); } barrier(CLK_LOCAL_MEM_FENCE); } if (tid < 32) { volatile local ulong * smem = sdata; if (block_size >= 64) { smem[tid] = mySum = SUM_ulong(mySum, smem[tid + 32]); } if (block_size >= 32) { smem[tid] = mySum = SUM_ulong(mySum, smem[tid + 16]); } if (block_size >= 16) { smem[tid] = mySum = SUM_ulong(mySum, smem[tid + 8]); } if (block_size >= 8) { smem[tid] = mySum = SUM_ulong(mySum, smem[tid + 4]); } if (block_size >= 4) { smem[tid] = mySum = SUM_ulong(mySum, smem[tid + 2]); } if (block_size >= 2) { smem[tid] = mySum = SUM_ulong(mySum, smem[tid + 1]); } } if (tid == 0) g_odata[get_group_id(0)] = sdata[0]; }
28. Solving ODEs on GPUs
29. Solving ODEs on GPUs Lorenz attractor system ˙ x = −σ (x − y) , ˙ y = Rx − y − xz, ˙ z = −bz + xy. 20 0 20 20 0 20 40 20 40 60 80 Lorenz attractor trajectory Parameter study for the Lorenz attractor system: Solve large number of Lorenz systems, each for a different value of R. Let’s use Boost.odeint together with VexCL for that. [1] K. Ahnert, D. Demidov, and M. Mulansky. Solving ordinary differential equations on GPUs. In Numerical Computations with GPUs (pp. 125-157). Springer, 2014. doi:10.1007/978-3-319-06548-9 7
30. Using Boost.odeint Generic ODE: dx dt = ˙ x = f (x, t), x(0) = x0. Using Boost.odeint: Define state type (what is x?) Choose integration method Provide system function (define f (x, t)) Integrate over time
31. Implementation #include <iostream> #include <vector> #include <vexcl/vexcl.hpp> #include <boost/numeric/odeint.hpp> #include <boost/numeric/odeint/external/vexcl/vexcl.hpp> namespace odeint = boost::numeric::odeint; typedef vex::multivector<double, 3> state_type; typedef odeint::runge_kutta4_classic< state_type, double, state_type, double, odeint::vector_space_algebra, odeint::default_operations > Stepper; struct lorenz_system { const vex::vector<double> &R; double sigma, b; void operator()(const state_type &x, state_type &dxdt, double t) const { dxdt = std::make_tuple( sigma * (x(1) - x(0)), R * x(0) - x(1) - x(0) * x(2), x(0) * x(1) - b * x(2)); } }; int main(int argc, char *argv[]) { const size_t n = (argc > 1) ? std::stoi(argv[1]) : 32; const double tmax = 1.0, dt = 0.01; const double Rmin = 0.1, Rmax = 50.0, dR = (Rmax - Rmin) / (n - 1); vex::Context ctx(vex::Filter::Env && vex::Filter::DoublePrecision); state_type X(ctx, n); vex::vector<double> R(ctx, n); X = 10.0; R = Rmin + dR * vex::element_index(); lorenz_system sys{R, 10.0, 8.0/3}; odeint::integrate_const(Stepper(), sys, X, 0.0, tmax, dt); std::cout << "x = " << X << std::endl; }
32. Implementation #include <iostream> #include <vector> #include <vexcl/vexcl.hpp> #include <boost/numeric/odeint.hpp> #include <boost/numeric/odeint/external/vexcl/vexcl.hpp> namespace odeint = boost::numeric::odeint; typedef vex::multivector<double, 3> state_type; typedef odeint::runge_kutta4_classic< state_type, double, state_type, double, odeint::vector_space_algebra, odeint::default_operations > Stepper; struct lorenz_system { const vex::vector<double> &R; double sigma, b; void operator()(const state_type &x, state_type &dxdt, double t) const { dxdt = std::make_tuple( sigma * (x(1) - x(0)), R * x(0) - x(1) - x(0) * x(2), x(0) * x(1) - b * x(2)); } }; int main(int argc, char *argv[]) { const size_t n = (argc > 1) ? std::stoi(argv[1]) : 32; const double tmax = 1.0, dt = 0.01; const double Rmin = 0.1, Rmax = 50.0, dR = (Rmax - Rmin) / (n - 1); vex::Context ctx(vex::Filter::Env && vex::Filter::DoublePrecision); state_type X(ctx, n); vex::vector<double> R(ctx, n); X = 10.0; R = Rmin + dR * vex::element_index(); lorenz_system sys{R, 10.0, 8.0/3}; odeint::integrate_const(Stepper(), sys, X, 0.0, tmax, dt); std::cout << "x = " << X << std::endl; } 1. State type and stepper type 9 typedef vex::multivector<double, 3> state_type; 10 11 typedef odeint::runge_kutta4_classic< 12 state_type, double, state_type, double, 13 odeint::vector_space_algebra, odeint::default_operations 14 > Stepper;
33. Implementation #include <iostream> #include <vector> #include <vexcl/vexcl.hpp> #include <boost/numeric/odeint.hpp> #include <boost/numeric/odeint/external/vexcl/vexcl.hpp> namespace odeint = boost::numeric::odeint; typedef vex::multivector<double, 3> state_type; typedef odeint::runge_kutta4_classic< state_type, double, state_type, double, odeint::vector_space_algebra, odeint::default_operations > Stepper; struct lorenz_system { const vex::vector<double> &R; double sigma, b; void operator()(const state_type &x, state_type &dxdt, double t) const { dxdt = std::make_tuple( sigma * (x(1) - x(0)), R * x(0) - x(1) - x(0) * x(2), x(0) * x(1) - b * x(2)); } }; int main(int argc, char *argv[]) { const size_t n = (argc > 1) ? std::stoi(argv[1]) : 32; const double tmax = 1.0, dt = 0.01; const double Rmin = 0.1, Rmax = 50.0, dR = (Rmax - Rmin) / (n - 1); vex::Context ctx(vex::Filter::Env && vex::Filter::DoublePrecision); state_type X(ctx, n); vex::vector<double> R(ctx, n); X = 10.0; R = Rmin + dR * vex::element_index(); lorenz_system sys{R, 10.0, 8.0/3}; odeint::integrate_const(Stepper(), sys, X, 0.0, tmax, dt); std::cout << "x = " << X << std::endl; } 2. System function 10 struct lorenz_system { 11 const vex::vector<double> &R; 12 double sigma, b; 13 14 void operator()(const state_type &x, state_type &dxdt, double t) const { 15 dxdt = std::make_tuple( 16 sigma * (x(1) - x(0)), 17 R * x(0) - x(1) - x(0) * x(2), 18 x(0) * x(1) - b * x(2)); 19 } 20 };
34. Implementation #include <iostream> #include <vector> #include <vexcl/vexcl.hpp> #include <boost/numeric/odeint.hpp> #include <boost/numeric/odeint/external/vexcl/vexcl.hpp> namespace odeint = boost::numeric::odeint; typedef vex::multivector<double, 3> state_type; typedef odeint::runge_kutta4_classic< state_type, double, state_type, double, odeint::vector_space_algebra, odeint::default_operations > Stepper; struct lorenz_system { const vex::vector<double> &R; double sigma, b; void operator()(const state_type &x, state_type &dxdt, double t) const { dxdt = std::make_tuple( sigma * (x(1) - x(0)), R * x(0) - x(1) - x(0) * x(2), x(0) * x(1) - b * x(2)); } }; int main(int argc, char *argv[]) { const size_t n = (argc > 1) ? std::stoi(argv[1]) : 32; const double tmax = 1.0, dt = 0.01; const double Rmin = 0.1, Rmax = 50.0, dR = (Rmax - Rmin) / (n - 1); vex::Context ctx(vex::Filter::Env && vex::Filter::DoublePrecision); state_type X(ctx, n); vex::vector<double> R(ctx, n); X = 10.0; R = Rmin + dR * vex::element_index(); lorenz_system sys{R, 10.0, 8.0/3}; odeint::integrate_const(Stepper(), sys, X, 0.0, tmax, dt); std::cout << "x = " << X << std::endl; } 3. Integrate 27 int main(int argc, char *argv[]) { 28 const size_t n = (argc > 1) ? std::stoi(argv[1]) : 32; 29 const double tmax = 1.0, dt = 0.01; 30 const double Rmin = 0.1, Rmax = 50.0, dR = (Rmax - Rmin) / (n - 1); 31 32 vex::Context ctx(vex::Filter::Env && vex::Filter::DoublePrecision); 33 34 state_type X(ctx, n); 35 vex::vector<double> R(ctx, n); 36 37 X = 10.0; 38 R = Rmin + dR * vex::element_index(); 39 40 lorenz_system sys{R, 10.0, 8.0/3}; 41 odeint::integrate_const(Stepper(), sys, X, 0.0, tmax, dt); 42 43 std::cout << "x = " << X << std::endl; 44 }
35. Performance NVIDIA Tesla K40c, Intel Core i7 920 103 104 105 106 N 10 1 100 101 102 T(sec) OpenMP VexCL 103 104 105 106 N 100 101 T(OpenMP) / T
36. Performance NVIDIA Tesla K40c, Intel Core i7 920 103 104 105 106 N 10 1 100 101 102 T(sec) OpenMP VexCL 103 104 105 106 N 100 101 T(OpenMP) / T Problems: Runge-Kutta method uses 4 temporary vectors. Single Runge-Kutta step is translated into several kernels.
37. What if we did this manually? Create monolithic kernel for a single step of the Runge-Kutta method. Launch the kernel in a loop. This would be 10x faster! At the expense of odeint’s generality. Monolithic OpenCL kernel for RK4 1 double3 lorenz_system(double r, double sigma, double b, double3 s) { 2 return (double3)( sigma * (s.y - s.x), 3 r * s.x - s.y - s.x * s.z, 4 s.x * s.y - b * s.z); 5 } 6 kernel void lorenz_ensemble( 7 ulong n, double dt, double sigma, double b, 8 const global double *R, 9 global double *X, 10 global double *Y, 11 global double *Z 12 ) 13 { 14 for(size_t i = get_global_id(0); i < n; i += get_global_size(0)) { 15 double r = R[i]; 16 double3 s = (double3)(X[i], Y[i], Z[i]); 17 double3 k1, k2, k3, k4; 18 19 k1 = dt * lorenz_system(r, sigma, b, s); 20 k2 = dt * lorenz_system(r, sigma, b, s + 0.5 * k1); 21 k3 = dt * lorenz_system(r, sigma, b, s + 0.5 * k2); 22 k4 = dt * lorenz_system(r, sigma, b, s + k3); 23 24 s += (k1 + 2 * k2 + 2 * k3 + k4) / 6; 25 26 X[i] = s.x; Y[i] = s.y; Z[i] = s.z; 27 } 28 }
38. VexCL symbolic types VexCL provides vex::symbolic<T> class template. Its instance dumps to an std::ostream any arithmetic operations applied to it: 1 vex::symbolic<double> x = 6; 2 vex::symbolic<double> y = 7; 3 x = sin(x * y); double var1 = 6; double var2 = 7; var1 = sin( ( var1 * var2 ) );
39. VexCL symbolic types VexCL provides vex::symbolic<T> class template. Its instance dumps to an std::ostream any arithmetic operations applied to it: 1 vex::symbolic<double> x = 6; 2 vex::symbolic<double> y = 7; 3 x = sin(x * y); double var1 = 6; double var2 = 7; var1 = sin( ( var1 * var2 ) ); 1 template <class T> 2 T squared_radius(const T &x, const T &y) { 3 return x * x + y * y; 4 } 5 template <class T> 6 T radius(const T &x, const T &y) { 7 return sqrt(squared_radius(x, y)); 8 } 9 vex::symbolic<double> a = 3, b = 4; 10 vex::symbolic<double> c = radius(a, b); double var1 = 3; double var2 = 4; double var3 = ( ( var1 * var1 ) + ( var2 * var2 ) ); double var4 = sqrt( var3 );
40. Generate monolithic kernel using Boost.odeint algorithm Overview (see [1] for more details): Use vex::symbolic<T> or boost::array<vex::symbolic<T>, N> as state type. Provide generic system functor. Record single step of a Boost.odeint stepper. Generate and use monolithic kernel. [1] K. Ahnert, D. Demidov, and M. Mulansky. Solving ordinary differential equations on GPUs. In Numerical Computations with GPUs (pp. 125-157). Springer, 2014. doi:10.1007/978-3-319-06548-9 7
41. Generate monolithic kernel using Boost.odeint algorithm Overview (see [1] for more details): Use vex::symbolic<T> or boost::array<vex::symbolic<T>, N> as state type. Provide generic system functor. Record single step of a Boost.odeint stepper. Generate and use monolithic kernel. Restrictions: Algorithms have to be embarrassingly parallel. Only linear flow is allowed (no conditionals or data-dependent loops). [1] K. Ahnert, D. Demidov, and M. Mulansky. Solving ordinary differential equations on GPUs. In Numerical Computations with GPUs (pp. 125-157). Springer, 2014. doi:10.1007/978-3-319-06548-9 7
42. Performance of the generated kernel 103 104 105 106 N 10 2 10 1 100 101 102 T(sec) OpenMP VexCL VexCL (symb) 103 104 105 106 N 100 101 102 T(OpenMP) / T
43. Comparing backends performance 103 104 105 106 N 10 2 10 1 100 101 T(sec) Intel Core i7 920 @ 2.67GHz OpenCL Boost.Compute OpenMP (JIT) 103 104 105 106 N 10 2 10 1 100 T(sec) NVIDIA Tesla K40c OpenCL Boost.Compute CUDA
44. Summary VexCL allows to write compact and readable code. It’s great for fast prototyping of scientific GPGPU applications. The performance is often on-par with manually written kernels. Using custom kernels or third-party functionality is still possible.
45. Summary VexCL allows to write compact and readable code. It’s great for fast prototyping of scientific GPGPU applications. The performance is often on-par with manually written kernels. Using custom kernels or third-party functionality is still possible. It stresses the compiler greatly. Compilation takes a lot of RAM and a lot of time. But, it’s easy to combine C++ with Python: http://pybind11.readthedocs.io https://xkcd.com/303/
46. Creating python bindings for C++ with pybind11 #include <iostream> #include <vector> #include <vexcl/vexcl.hpp> #include <boost/numeric/odeint.hpp> #include <boost/numeric/odeint/external/vexcl/vexcl.hpp> #include <pybind11/pybind11.h> #include <pybind11/numpy.h> namespace odeint = boost::numeric::odeint; namespace py = pybind11; typedef vex::multivector<double, 3> state_type; typedef odeint::runge_kutta4_classic< state_type, double, state_type, double, odeint::vector_space_algebra, odeint::default_operations > Stepper; vex::Context& ctx(std::string name = "") { static vex::Context c(vex::Filter::Env && vex::Filter::Name(name)); return c; } struct lorenz_system { int n; double sigma, b; vex::vector<double> R; state_type X; lorenz_system(double sigma, double b, py::array_t<double> R) : n(R.size()), sigma(sigma), b(b), R(ctx(), n, R.data()), X(ctx(), n) {} void operator()(const state_type &x, state_type &dxdt, double t) const { dxdt = std::make_tuple( sigma * (x(1) - x(0)), R * x(0) - x(1) - x(0) * x(2), x(0) * x(1) - b * x(2)); } py::array_t<double> advance(py::array_t<double> x_in, int steps, double dt) { for(int i=0, b=0, e=n; i<3; ++i, b+=n, e+=n) vex::copy(x_in.data()+b, x_in.data()+e, X(i).begin()); odeint::integrate_n_steps(Stepper(), std::ref(*this), X, 0.0, dt, steps); py::array_t<double> x_out(std::array<size_t,2>{x_in.shape(0), x_in.shape(1)}); for(int i=0, b=0; i<3; ++i, b+=n) vex::copy(X(i).begin(), X(i).end(), x_out.mutable_data()+b); return x_out; } }; PYBIND11_PLUGIN(pylorenz) { py::module m("pylorenz"); m.def("context", [](std::string name) { std::ostringstream s; s << ctx(name); py::print(s.str()); }, py::arg("name") = std::string("")); py::class_<lorenz_system>(m, "Stepper") .def(py::init<double, double, py::array_t<double>>()) .def("advance", &lorenz_system::advance) ; return m.ptr(); }
47. Creating python bindings for C++ with pybind11 #include <iostream> #include <vector> #include <vexcl/vexcl.hpp> #include <boost/numeric/odeint.hpp> #include <boost/numeric/odeint/external/vexcl/vexcl.hpp> #include <pybind11/pybind11.h> #include <pybind11/numpy.h> namespace odeint = boost::numeric::odeint; namespace py = pybind11; typedef vex::multivector<double, 3> state_type; typedef odeint::runge_kutta4_classic< state_type, double, state_type, double, odeint::vector_space_algebra, odeint::default_operations > Stepper; vex::Context& ctx(std::string name = "") { static vex::Context c(vex::Filter::Env && vex::Filter::Name(name)); return c; } struct lorenz_system { int n; double sigma, b; vex::vector<double> R; state_type X; lorenz_system(double sigma, double b, py::array_t<double> R) : n(R.size()), sigma(sigma), b(b), R(ctx(), n, R.data()), X(ctx(), n) {} void operator()(const state_type &x, state_type &dxdt, double t) const { dxdt = std::make_tuple( sigma * (x(1) - x(0)), R * x(0) - x(1) - x(0) * x(2), x(0) * x(1) - b * x(2)); } py::array_t<double> advance(py::array_t<double> x_in, int steps, double dt) { for(int i=0, b=0, e=n; i<3; ++i, b+=n, e+=n) vex::copy(x_in.data()+b, x_in.data()+e, X(i).begin()); odeint::integrate_n_steps(Stepper(), std::ref(*this), X, 0.0, dt, steps); py::array_t<double> x_out(std::array<size_t,2>{x_in.shape(0), x_in.shape(1)}); for(int i=0, b=0; i<3; ++i, b+=n) vex::copy(X(i).begin(), X(i).end(), x_out.mutable_data()+b); return x_out; } }; PYBIND11_PLUGIN(pylorenz) { py::module m("pylorenz"); m.def("context", [](std::string name) { std::ostringstream s; s << ctx(name); py::print(s.str()); }, py::arg("name") = std::string("")); py::class_<lorenz_system>(m, "Stepper") .def(py::init<double, double, py::array_t<double>>()) .def("advance", &lorenz_system::advance) ; return m.ptr(); } 1. State type and stepper type 12 typedef vex::multivector<double, 3> state_type; 13 14 typedef odeint::runge_kutta4_classic< 15 state_type, double, state_type, double, 16 odeint::vector_space_algebra, odeint::default_operations 17 > Stepper;
48. Creating python bindings for C++ with pybind11 #include <iostream> #include <vector> #include <vexcl/vexcl.hpp> #include <boost/numeric/odeint.hpp> #include <boost/numeric/odeint/external/vexcl/vexcl.hpp> #include <pybind11/pybind11.h> #include <pybind11/numpy.h> namespace odeint = boost::numeric::odeint; namespace py = pybind11; typedef vex::multivector<double, 3> state_type; typedef odeint::runge_kutta4_classic< state_type, double, state_type, double, odeint::vector_space_algebra, odeint::default_operations > Stepper; vex::Context& ctx(std::string name = "") { static vex::Context c(vex::Filter::Env && vex::Filter::Name(name)); return c; } struct lorenz_system { int n; double sigma, b; vex::vector<double> R; state_type X; lorenz_system(double sigma, double b, py::array_t<double> R) : n(R.size()), sigma(sigma), b(b), R(ctx(), n, R.data()), X(ctx(), n) {} void operator()(const state_type &x, state_type &dxdt, double t) const { dxdt = std::make_tuple( sigma * (x(1) - x(0)), R * x(0) - x(1) - x(0) * x(2), x(0) * x(1) - b * x(2)); } py::array_t<double> advance(py::array_t<double> x_in, int steps, double dt) { for(int i=0, b=0, e=n; i<3; ++i, b+=n, e+=n) vex::copy(x_in.data()+b, x_in.data()+e, X(i).begin()); odeint::integrate_n_steps(Stepper(), std::ref(*this), X, 0.0, dt, steps); py::array_t<double> x_out(std::array<size_t,2>{x_in.shape(0), x_in.shape(1)}); for(int i=0, b=0; i<3; ++i, b+=n) vex::copy(X(i).begin(), X(i).end(), x_out.mutable_data()+b); return x_out; } }; PYBIND11_PLUGIN(pylorenz) { py::module m("pylorenz"); m.def("context", [](std::string name) { std::ostringstream s; s << ctx(name); py::print(s.str()); }, py::arg("name") = std::string("")); py::class_<lorenz_system>(m, "Stepper") .def(py::init<double, double, py::array_t<double>>()) .def("advance", &lorenz_system::advance) ; return m.ptr(); } 2. Context initialization 19 vex::Context& ctx(std::string name = "") { 20 static vex::Context c(vex::Filter::Env && vex::Filter::Name(name)); 21 return c; 22 }
49. Creating python bindings for C++ with pybind11 #include <iostream> #include <vector> #include <vexcl/vexcl.hpp> #include <boost/numeric/odeint.hpp> #include <boost/numeric/odeint/external/vexcl/vexcl.hpp> #include <pybind11/pybind11.h> #include <pybind11/numpy.h> namespace odeint = boost::numeric::odeint; namespace py = pybind11; typedef vex::multivector<double, 3> state_type; typedef odeint::runge_kutta4_classic< state_type, double, state_type, double, odeint::vector_space_algebra, odeint::default_operations > Stepper; vex::Context& ctx(std::string name = "") { static vex::Context c(vex::Filter::Env && vex::Filter::Name(name)); return c; } struct lorenz_system { int n; double sigma, b; vex::vector<double> R; state_type X; lorenz_system(double sigma, double b, py::array_t<double> R) : n(R.size()), sigma(sigma), b(b), R(ctx(), n, R.data()), X(ctx(), n) {} void operator()(const state_type &x, state_type &dxdt, double t) const { dxdt = std::make_tuple( sigma * (x(1) - x(0)), R * x(0) - x(1) - x(0) * x(2), x(0) * x(1) - b * x(2)); } py::array_t<double> advance(py::array_t<double> x_in, int steps, double dt) { for(int i=0, b=0, e=n; i<3; ++i, b+=n, e+=n) vex::copy(x_in.data()+b, x_in.data()+e, X(i).begin()); odeint::integrate_n_steps(Stepper(), std::ref(*this), X, 0.0, dt, steps); py::array_t<double> x_out(std::array<size_t,2>{x_in.shape(0), x_in.shape(1)}); for(int i=0, b=0; i<3; ++i, b+=n) vex::copy(X(i).begin(), X(i).end(), x_out.mutable_data()+b); return x_out; } }; PYBIND11_PLUGIN(pylorenz) { py::module m("pylorenz"); m.def("context", [](std::string name) { std::ostringstream s; s << ctx(name); py::print(s.str()); }, py::arg("name") = std::string("")); py::class_<lorenz_system>(m, "Stepper") .def(py::init<double, double, py::array_t<double>>()) .def("advance", &lorenz_system::advance) ; return m.ptr(); } 3. System function 24 struct lorenz_system { 25 int n; 26 double sigma, b; 27 vex::vector<double> R; 28 state_type X; 29 30 lorenz_system(double sigma, double b, py::array_t<double> R) 31 : n(R.size()), sigma(sigma), b(b), R(ctx(), n, R.data()), X(ctx(), n) {} 32 33 void operator()(const state_type &x, state_type &dxdt, double t) const { 34 dxdt = std::make_tuple( 35 sigma * (x(1) - x(0)), 36 R * x(0) - x(1) - x(0) * x(2), 37 x(0) * x(1) - b * x(2)); 38 } 39 40 py::array_t<double> advance(py::array_t<double> x_in, int steps, double dt) { 41 for(int i=0, b=0, e=n; i<3; ++i, b+=n, e+=n) 42 vex::copy(x_in.data()+b, x_in.data()+e, X(i).begin()); 43 44 odeint::integrate_n_steps(Stepper(), std::ref(*this), X, 0.0, dt, steps); 45 46 py::array_t<double> x_out(std::array<size_t,2>{x_in.shape(0), x_in.shape(1)}); 47 for(int i=0, b=0; i<3; ++i, b+=n) 48 vex::copy(X(i).begin(), X(i).end(), x_out.mutable_data()+b); 49 50 return x_out; 51 } 52 };
50. Creating python bindings for C++ with pybind11 #include <iostream> #include <vector> #include <vexcl/vexcl.hpp> #include <boost/numeric/odeint.hpp> #include <boost/numeric/odeint/external/vexcl/vexcl.hpp> #include <pybind11/pybind11.h> #include <pybind11/numpy.h> namespace odeint = boost::numeric::odeint; namespace py = pybind11; typedef vex::multivector<double, 3> state_type; typedef odeint::runge_kutta4_classic< state_type, double, state_type, double, odeint::vector_space_algebra, odeint::default_operations > Stepper; vex::Context& ctx(std::string name = "") { static vex::Context c(vex::Filter::Env && vex::Filter::Name(name)); return c; } struct lorenz_system { int n; double sigma, b; vex::vector<double> R; state_type X; lorenz_system(double sigma, double b, py::array_t<double> R) : n(R.size()), sigma(sigma), b(b), R(ctx(), n, R.data()), X(ctx(), n) {} void operator()(const state_type &x, state_type &dxdt, double t) const { dxdt = std::make_tuple( sigma * (x(1) - x(0)), R * x(0) - x(1) - x(0) * x(2), x(0) * x(1) - b * x(2)); } py::array_t<double> advance(py::array_t<double> x_in, int steps, double dt) { for(int i=0, b=0, e=n; i<3; ++i, b+=n, e+=n) vex::copy(x_in.data()+b, x_in.data()+e, X(i).begin()); odeint::integrate_n_steps(Stepper(), std::ref(*this), X, 0.0, dt, steps); py::array_t<double> x_out(std::array<size_t,2>{x_in.shape(0), x_in.shape(1)}); for(int i=0, b=0; i<3; ++i, b+=n) vex::copy(X(i).begin(), X(i).end(), x_out.mutable_data()+b); return x_out; } }; PYBIND11_PLUGIN(pylorenz) { py::module m("pylorenz"); m.def("context", [](std::string name) { std::ostringstream s; s << ctx(name); py::print(s.str()); }, py::arg("name") = std::string("")); py::class_<lorenz_system>(m, "Stepper") .def(py::init<double, double, py::array_t<double>>()) .def("advance", &lorenz_system::advance) ; return m.ptr(); } 4. Python bindings 54 PYBIND11_PLUGIN(pylorenz) { 55 py::module m("pylorenz"); 56 57 m.def("context", [](std::string name) { 58 std::ostringstream s; s << ctx(name); py::print(s.str()); 59 }, py::arg("name") = std::string("")); 60 61 py::class_<lorenz_system>(m, "Stepper") 62 .def(py::init<double, double, py::array_t<double>>()) 63 .def("advance", &lorenz_system::advance) 64 ; 65 66 return m.ptr(); 67 }
51. Calling C++ code from Python 1 import pylorenz as lorenz 2 3 n = 32 # Number of parameters 4 m = 500 # Length of trajectory 5 6 # Parameters 7 R = linspace(0.1, 10, n) 8 sigma = 10.0 9 b = 8/3 10 11 # Initial solution 12 S = empty((m, 3, n)) 13 S[0,:,:] = 10.0 14 15 # Integration 16 ode = lorenz.Stepper(sigma, b, R) 17 for i in range(1,m): 18 S[i] = ode.advance(S[i-1], 1, 0.01)
52. Projects using VexCL AMGCL — an efficient, flexible, and extensible Algebraic Multigrid implementation: https://github.com/ddemidov/amgcl Boost.odeint — numerical solution of Ordinary Differential Equations: https://github.com/boostorg/odeint Antioch — A New Templated Implementation Of Chemistry for Hydrodynamics (The University of Texas at Austin): https://github.com/libantioch/antioch FDBB — Fluid Dynamics Building Blocks (TU Delft): https://gitlab.com/mmoelle1/FDBB
53. Source code: https://github.com/ddemidov/vexcl Documentation: http://vexcl.readthedocs.io Slides: https://speakerdeck.com/ddemidov Example codes: https://github.com/ddemidov/vexcl-talks