def to_tex3d(data):
"""
Source: https://wiki.tiker.net/PyCUDA/Examples/Demo3DSurface
"""
d, h, w = data.shape
descr = cuda.ArrayDescriptor3D()
descr.width = w
descr.height = h
descr.depth = d
descr.format = cuda.dtype_to_array_format(data.dtype)
descr.num_channels = 1
descr.flags = 0
if isinstance(data, gpuarray.GPUArray):
data = data.get()
device_array = cuda.Array(descr)
copy = cuda.Memcpy3D()
copy.set_src_host(data)
copy.set_dst_array(device_array)
copy.width_in_bytes = copy.src_pitch = data.strides[1]
copy.src_height = copy.height = h
copy.depth = d
copy()
return device_array
def numpy3d_to_array(np_array, allow_surface_bind=False, layered=True):
d, h, w = np_array.shape
descr = cuda.ArrayDescriptor3D()
descr.width = w
descr.height = h
descr.depth = d
descr.format = cuda.dtype_to_array_format(np_array.dtype)
descr.num_channels = 1
descr.flags = 0
if allow_surface_bind:
descr.flags = cuda.array3d_flags.SURFACE_LDST
if layered:
descr.flags = cuda.array3d_flags.ARRAY3D_LAYERED
device_array = cuda.Array(descr)
copy = cuda.Memcpy3D()
copy.set_src_host(np_array)
copy.set_dst_array(device_array)
copy.width_in_bytes = copy.src_pitch = np_array.strides[1]
copy.src_height = copy.height = h
copy.depth = d
copy()
return device_array
def create_3d_texture(a, module, variable, point_sampling=False):
a = numpy.asfortranarray(a)
w, h, d = a.shape
descr = cuda.ArrayDescriptor3D()
descr.width = w
descr.height = h
descr.depth = d
descr.format = cuda.dtype_to_array_format(a.dtype)
descr.num_channels = 1
descr.flags = 0
ary = cuda.Array(descr)
copy = cuda.Memcpy3D()
copy.set_src_host(a)
copy.set_dst_array(ary)
copy.width_in_bytes = copy.src_pitch = a.strides[1]
copy.src_height = copy.height = h
copy.depth = d
copy()
out_texref = module.get_texref(variable)
out_texref.set_array(ary)
if point_sampling:
out_texref.set_filter_mode(cuda.filter_mode.POINT)
else:
out_texref.set_filter_mode(cuda.filter_mode.LINEAR)
return out_texref
def numpy3d_to_array(np_array, allow_surface_bind=True):
import pycuda.autoinit
d, h, w = np_array.shape
descr = drv.ArrayDescriptor3D()
descr.width = w
descr.height = h
descr.depth = d
descr.format = drv.dtype_to_array_format(np_array.dtype)
descr.num_channels = 1
descr.flags = 0
if allow_surface_bind:
descr.flags = drv.array3d_flags.SURFACE_LDST
device_array = drv.Array(descr)
copy = drv.Memcpy3D()
copy.set_src_host(np_array)
copy.set_dst_array(device_array)
copy.width_in_bytes = copy.src_pitch = np_array.strides[1]
copy.src_height = copy.height = h
copy.depth = d
copy()
return device_array
def numpy3d_to_array(np_array):
'''Copy a 3D (d,h,w) numpy array into a 3D pycuda array that can be used
to set a texture. (For some reason, gpuarrays can't be used to do that
directly). A transpose happens implicitly; the CUDA array has dim (w,h,d).'''
import pycuda.autoinit
d, h, w = np_array.shape
descr = driver.ArrayDescriptor3D()
descr.width = w
descr.height = h
descr.depth = d
if np_array.dtype == np.float64:
descr.format = driver.array_format.SIGNED_INT32
descr.num_channels = 2
else:
descr.format = driver.dtype_to_array_format(np_array.dtype)
descr.num_channels = 1
descr.flags = 0
device_array = driver.Array(descr)
copy = driver.Memcpy3D()
copy.set_src_host(np_array)
copy.set_dst_array(device_array)
copy.width_in_bytes = copy.src_pitch = np_array.strides[1]
copy.src_height = copy.height = h
copy.depth = d
copy()
return device_array
def copyTexture(self, data, pixelSize=None, extent=None, isocenter=None):
# Convert data to float32 array in Contiguous ordering.
self.arrIn = np.array(data, dtype=np.float32, order='C')
d, h, w = self.arrIn.shape
descr = cuda.ArrayDescriptor3D()
descr.width = w
descr.height = h
descr.depth = d
descr.format = cuda.dtype_to_array_format(self.arrIn.dtype)
descr.num_channels = 1
# descr.flags = 0
self.gpuTexture = cuda.Array(descr)
# Copy array data across. This puts a 3D array in linear memory on the GPU.
copy = cuda.Memcpy3D()
copy.set_src_host(self.arrIn)
copy.set_dst_array(self.gpuTexture)
copy.src_pitch = self.arrIn.strides[1]
copy.width_in_bytes = self.arrIn.strides[1]
copy.height = h
copy.depth = d
copy.src_height = h
copy()
self.pixelSize = pixelSize
self.isocenter = isocenter
# Extent[l,r,b,t,f,b]
self.extent = extent
# Trigger for setting bottom left corner as 0,0,0.
self.zeroExtent = False
def gpuArray3DtocudaArray(gpuArray, allowSurfaceBind=False, precision='float'):
#import pycuda.autoinit
d, h, w = gpuArray.shape
descr3D = cuda.ArrayDescriptor3D()
descr3D.width = w
descr3D.height = h
descr3D.depth = d
if precision == 'float':
descr3D.format = cuda.dtype_to_array_format(gpuArray.dtype)
descr3D.num_channels = 1
elif precision == 'double':
descr3D.format = cuda.array_format.SIGNED_INT32
descr3D.num_channels = 2
else:
print("ERROR: CUDA_ARRAY incompatible precision")
sys.exit()
descr3D.flags = 0
if allowSurfaceBind:
descr3D.flags = cuda.array3d_flags.SURFACE_LDST
cudaArray = cuda.Array(descr3D)
copy3D = cuda.Memcpy3D()
copy3D.set_src_device(gpuArray.ptr)
copy3D.set_dst_array(cudaArray)
copy3D.width_in_bytes = copy3D.src_pitch = gpuArray.strides[1]
copy3D.src_height = copy3D.height = h
copy3D.depth = d
copy3D()
return cudaArray, copy3D
def numpy3d_to_array(np_array, allow_surface_bind=True):
"""Converts 3D numpy array to 3D device array.
"""
# numpy3d_to_array
# taken from pycuda mailing list (striped for C ordering only)
d, h, w = np_array.shape
descr = cuda.ArrayDescriptor3D()
descr.width = w
descr.height = h
descr.depth = d
descr.format = cuda.dtype_to_array_format(np_array.dtype)
descr.num_channels = 1
descr.flags = 0
if allow_surface_bind:
descr.flags = cuda.array3d_flags.SURFACE_LDST
device_array = cuda.Array(descr)
copy = cuda.Memcpy3D()
copy.set_src_host(np_array)
copy.set_dst_array(device_array)
copy.width_in_bytes = copy.src_pitch = np_array.strides[1]
copy.src_height = copy.height = h
copy.depth = d
copy()
return device_array
def __init__(self):
self.d_params = cuda.mem_alloc(
self.ntemporal_samples * DevSrc.max_params * 4)
self.palette_surf_dsc = util.argset(cuda.ArrayDescriptor3D(),
height=self.palette_height, width=self.palette_width, depth=0,
format=cuda.array_format.SIGNED_INT32,
num_channels=2, flags=cuda.array3d_flags.SURFACE_LDST)
self.d_pal_array = cuda.Array(self.palette_surf_dsc)
def test_3d_texture(self):
# adapted from code by Nicolas Pinto
w = 2
h = 4
d = 8
shape = (w, h, d)
a = numpy.asarray(numpy.random.randn(*shape),
dtype=numpy.float32,
order="F")
descr = drv.ArrayDescriptor3D()
descr.width = w
descr.height = h
descr.depth = d
descr.format = drv.dtype_to_array_format(a.dtype)
descr.num_channels = 1
descr.flags = 0
ary = drv.Array(descr)
copy = drv.Memcpy3D()
copy.set_src_host(a)
copy.set_dst_array(ary)
copy.width_in_bytes = copy.src_pitch = a.strides[1]
copy.src_height = copy.height = h
copy.depth = d
copy()
mod = SourceModule("""
texture<float, 3, cudaReadModeElementType> mtx_tex;
__global__ void copy_texture(float *dest)
{
int x = threadIdx.x;
int y = threadIdx.y;
int z = threadIdx.z;
int dx = blockDim.x;
int dy = blockDim.y;
int i = (z*dy + y)*dx + x;
dest[i] = tex3D(mtx_tex, x, y, z);
//dest[i] = x;
}
""")
copy_texture = mod.get_function("copy_texture")
mtx_tex = mod.get_texref("mtx_tex")
mtx_tex.set_array(ary)
dest = numpy.zeros(shape, dtype=numpy.float32, order="F")
copy_texture(drv.Out(dest), block=shape, texrefs=[mtx_tex])
assert la.norm(dest - a) == 0
def malloc_gpu_arrays(nx, ny, nz, cex, cey, cez):
print 'rank= %d, (%d, %d, %d)' % (rank, nx, ny, nz),
total_bytes = nx * ny * nz * 4 * 9
if total_bytes / (1024**3) == 0:
print '%d MB' % (total_bytes / (1024**2))
else:
print '%1.2f GB' % (float(total_bytes) / (1024**3))
if nz % Dx != 0:
print "Error: nz is not multiple of %d" % (Dx)
sys.exit()
if (nx * ny) % Dy != 0:
print "Error: nx*ny is not multiple of %d" % (Dy)
sys.exit()
f = np.zeros((nx, ny, nz), 'f')
ex_gpu = cuda.to_device(f)
ey_gpu = cuda.to_device(f)
ez_gpu = cuda.to_device(f)
hx_gpu = cuda.to_device(f)
hy_gpu = cuda.to_device(f)
hz_gpu = cuda.to_device(f)
descr = cuda.ArrayDescriptor3D()
descr.width = nz
descr.height = ny
descr.depth = nx
descr.format = cuda.dtype_to_array_format(f.dtype)
descr.num_channels = 1
descr.flags = 0
tcex_gpu = cuda.Array(descr)
tcey_gpu = cuda.Array(descr)
tcez_gpu = cuda.Array(descr)
mcopy = cuda.Memcpy3D()
mcopy.width_in_bytes = mcopy.src_pitch = f.strides[1]
mcopy.src_height = mcopy.height = ny
mcopy.depth = nx
mcopy.set_src_host(cex)
mcopy.set_dst_array(tcex_gpu)
mcopy()
mcopy.set_src_host(cey)
mcopy.set_dst_array(tcey_gpu)
mcopy()
mcopy.set_src_host(cez)
mcopy.set_dst_array(tcez_gpu)
mcopy()
eh_fields = [ex_gpu, ey_gpu, ez_gpu, hx_gpu, hy_gpu, hz_gpu]
tex_fields = [tcex_gpu, tcey_gpu, tcez_gpu]
return eh_fields, tex_fields
def texCubeToGPU(texCube):
descr = cuda.ArrayDescriptor3D()
descr.width = texCube.shape[2]
descr.height = texCube.shape[1]
descr.depth = 6
descr.format = cuda.dtype_to_array_format(texCube.dtype)
descr.num_channels = 4
descr.flags = cuda.array3d_flags.CUBEMAP
texCubeArray = cuda.Array(descr)
copy = cuda.Memcpy3D()
copy.set_src_host(texCube)
copy.set_dst_array(texCubeArray)
copy.width_in_bytes = copy.src_pitch = texCube.strides[1] #d*h*w*c
copy.src_height = copy.height = texCube.shape[1]
copy.depth = 6
copy()
return texCubeArray
def np3DtoCudaArray(npArray, allowSurfaceBind=False):
#import pycuda.autoinit
d, h, w = npArray.shape
descr3D = cuda.ArrayDescriptor3D()
descr3D.width = w
descr3D.height = h
descr3D.depth = d
descr3D.format = cuda.dtype_to_array_format(npArray.dtype)
descr3D.num_channels = 1
descr3D.flags = 0
if allowSurfaceBind:
descr3D.flags = cuda.array3d_flags.SURFACE_LDST
cudaArray = cuda.Array(descr3D)
copy3D = cuda.Memcpy3D()
copy3D.set_src_host(npArray)
copy3D.set_dst_array(cudaArray)
copy3D.width_in_bytes = copy3D.src_pitch = npArray.strides[1]
copy3D.src_height = copy3D.height = h
copy3D.depth = d
copy3D()
return cudaArray, copy3D
def gpu3D(src):
"""
"""
w, h, d = src.shape
descr = cuda.ArrayDescriptor3D()
descr.width = w
descr.height = h
descr.depth = d
descr.format = cuda.dtype_to_array_format(src.dtype)
descr.num_channels = 1
descr.flags = 0
dst = cuda.Array(descr)
copy = cuda.Memcpy3D()
copy.set_src_host(src)
copy.set_dst_array(dst)
copy.width_in_bytes = copy.src_pitch = src.strides[1]
copy.src_height = copy.height = h
copy.depth = d
copy()
return dst
def _prepare_F_texture(self):
descr = drv.ArrayDescriptor3D()
descr.width = self.side
descr.height = self.side
descr.depth = self.side
descr.format = drv.dtype_to_array_format(self.F_gpu.dtype)
descr.num_channels = 1
descr.flags = 0
F_array = drv.Array(descr)
copy = drv.Memcpy3D()
copy.set_src_device(self.F_gpu.gpudata)
copy.set_dst_array(F_array)
copy.width_in_bytes = copy.src_pitch = self.F_gpu.strides[1]
copy.src_height = copy.height = self.side
copy.depth = self.side
self.F_gpu_to_array_copy = copy
self.F_gpu_to_array_copy()
self.F_texture.set_array(F_array)
def alloc_coeff_arrays(s):
f = np.zeros((s.nx, s.ny, s.nz), 'f')
s.cex = np.ones_like(f) * 0.5
s.cex[:, -1, :] = 0
s.cex[:, :, -1] = 0
s.cey = np.ones_like(f) * 0.5
s.cey[:, :, -1] = 0
s.cey[-1, :, :] = 0
s.cez = np.ones_like(f) * 0.5
s.cez[-1, :, :] = 0
s.cez[:, -1, :] = 0
descr = cuda.ArrayDescriptor3D()
descr.width = s.nz
descr.height = s.ny
descr.depth = s.nx
descr.format = cuda.dtype_to_array_format(f.dtype)
descr.num_channels = 1
descr.flags = 0
s.tcex_gpu = cuda.Array(descr)
s.tcey_gpu = cuda.Array(descr)
s.tcez_gpu = cuda.Array(descr)
mcpy = cuda.Memcpy3D()
mcpy.width_in_bytes = mcpy.src_pitch = f.strides[1]
mcpy.src_height = mcpy.height = s.ny
mcpy.depth = s.nx
mcpy.set_src_host(s.cex)
mcpy.set_dst_array(s.tcex_gpu)
mcpy()
mcpy.set_src_host(s.cey)
mcpy.set_dst_array(s.tcey_gpu)
mcpy()
mcpy.set_src_host(s.cez)
mcpy.set_dst_array(s.tcez_gpu)
mcpy()
print 'mem %d MB' % (total_bytes / (1024**2))
else:
print 'mem %1.2f GB' % (float(total_bytes) / (1024**3))
# memory allocate
f = np.zeros((nx, ny, nz), 'f', order='F')
ex_gpu = cuda.to_device(f)
ey_gpu = cuda.to_device(f)
ez_gpu = cuda.to_device(f)
hx_gpu = cuda.to_device(f)
hy_gpu = cuda.to_device(f)
hz_gpu = cuda.to_device(f)
# memory allocate with cuda array
descr = cuda.ArrayDescriptor3D()
descr.width = nx
descr.height = ny
descr.depth = nz
descr.format = cuda.dtype_to_array_format(f.dtype)
descr.num_channels = 1
descr.flags = 0
cex_gpu = cuda.Array(descr)
cey_gpu = cuda.Array(descr)
cez_gpu = cuda.Array(descr)
chx_gpu = cuda.Array(descr)
chy_gpu = cuda.Array(descr)
chz_gpu = cuda.Array(descr)
mcopy = cuda.Memcpy3D()
import pycuda.driver as drv
import pycuda.gpuarray as gpuarray
import pycuda.autoinit
from pycuda.compiler import SourceModule
import numpy as np
w = 2
h = 3
d = 4
shape = (d, h, w)
a = np.arange(24).reshape(*shape, order='C').astype('float32')
print(a.shape, a.strides)
print(a)
descr = drv.ArrayDescriptor3D()
descr.width = w
descr.height = h
descr.depth = d
descr.format = drv.dtype_to_array_format(a.dtype)
descr.num_channels = 1
descr.flags = 0
ary = drv.Array(descr)
copy = drv.Memcpy3D()
copy.set_src_host(a)
copy.set_dst_array(ary)
copy.width_in_bytes = copy.src_pitch = a.strides[1]
copy.src_height = copy.height = h
copy.depth = d
def np3DtoCudaArray(npArray, prec, order = "C", allowSurfaceBind=False):
''' Some parameters like stride are explained in PyCUDA: driver.py test_driver.py gpuarray.py'''
# For 1D-2D Cuda Arrays the descriptor is the same just puttin LAYERED flags
# if order != "C": raise LogicError("Just implemented for C order")
dimension = len(npArray.shape)
case = order in ["C","F"]
if not case:
raise LogicError("order must be either F or C")
# if dimension == 1:
# w = npArray.shape[0]
# h, d = 0,0
if dimension == 2:
if order == "C": stride = 0
if order == "F": stride = -1
h, w = npArray.shape
d = 1
if allowSurfaceBind:
descrArr = cuda.ArrayDescriptor3D()
descrArr.width = w
descrArr.height = h
descrArr.depth = d
else:
descrArr = cuda.ArrayDescriptor()
descrArr.width = w
descrArr.height = h
# descrArr.depth = d
elif dimension == 3:
if order == "C": stride = 1
if order == "F": stride = 1
d, h, w = npArray.shape
descrArr = cuda.ArrayDescriptor3D()
descrArr.width = w
descrArr.height = h
descrArr.depth = d
else:
raise LogicError("CUDArray dimesnsion 2 and 3 supported at the moment ... ")
if prec == 'float':
descrArr.format = cuda.dtype_to_array_format(npArray.dtype)
descrArr.num_channels = 1
elif prec == 'cfloat': # Hack for complex 64 = (float 32, float 32) == (re,im)
descrArr.format = cuda.array_format.SIGNED_INT32 # Reading data as int2 (hi=re,lo=im) structure
descrArr.num_channels = 2
elif prec == 'double': # Hack for doubles
descrArr.format = cuda.array_format.SIGNED_INT32 # Reading data as int2 (hi,lo) structure
descrArr.num_channels = 2
elif prec == 'cdouble': # Hack for doubles
descrArr.format = cuda.array_format.SIGNED_INT32 # Reading data as int4 (re=(hi,lo),im=(hi,lo)) structure
descrArr.num_channels = 4
else:
descrArr.format = cuda.dtype_to_array_format(npArray.dtype)
descrArr.num_channels = 1
if allowSurfaceBind:
if dimension==2: descrArr.flags |= cuda.array3d_flags.ARRAY3D_LAYERED
descrArr.flags |= cuda.array3d_flags.SURFACE_LDST
cudaArray = cuda.Array(descrArr)
if allowSurfaceBind or dimension==3 :
copy3D = cuda.Memcpy3D()
copy3D.set_src_host(npArray)
copy3D.set_dst_array(cudaArray)
copy3D.width_in_bytes = copy3D.src_pitch = npArray.strides[stride]
# if dimension==3: copy3D.width_in_bytes = copy3D.src_pitch = npArray.strides[1] #Jut C order support
# if dimension==2: copy3D.width_in_bytes = copy3D.src_pitch = npArray.strides[0] #Jut C order support
copy3D.src_height = copy3D.height = h
copy3D.depth = d
copy3D()
return cudaArray, copy3D
else:
# if dimension == 3:
# copy3D = cuda.Memcpy3D()
# copy3D.set_src_host(npArray)
# copy3D.set_dst_array(cudaArray)
# copy3D.width_in_bytes = copy3D.src_pitch = npArray.strides[stride]
# # if dimension==3: copy3D.width_in_bytes = copy3D.src_pitch = npArray.strides[1] #Jut C order support
# # if dimension==2: copy3D.width_in_bytes = copy3D.src_pitch = npArray.strides[0] #Jut C order support
# copy3D.src_height = copy3D.height = h
# copy3D.depth = d
# copy3D()
# return cudaArray, copy3D
# if dimension == 2:
cudaArray = cuda.Array(descrArr)
copy2D = cuda.Memcpy2D()
copy2D.set_src_host(npArray)
copy2D.set_dst_array(cudaArray)
copy2D.width_in_bytes = copy2D.src_pitch = npArray.strides[stride]
# copy2D.width_in_bytes = copy2D.src_pitch = npArray.strides[0] #Jut C order support
copy2D.src_height = copy2D.height = h
copy2D(aligned=True)
return cudaArray, copy2D