On Wed, 25 Apr 2012 12:17:33 -0400, Andrea Borsic <[email protected]> wrote: > Hi Andreas, > > I'd like to ask you a question (but I don't plan to bother you in the > future with PyOpnCL questions), I hope you don't mind. > > I am at a stage where I am trying to figure out whether I can use > PyOpenCL for my work, and wanted to ask you one information regarding > copying only parts of a buffer from host to device. > > In most of the problems in medical imaging I am dealing with I need to > copy data from a 3D array to the GPU in a slice by slice fashion. Whole > 3D volumes do not fit on the GPU, but fortunately many algorithms can > work in "sliding slice" way, where only a certain thickness of the > volume is copied to the GPU, and as the algorithm proceeds a new slice > is added and one is discarded from the back of the stack. The bottom > line is that I need to copy only one 2D slice at a time from host to > device, from a 3D array. > > I currently use, in C, clEnqueueWriteBuffer pointing to the base of the > 3D buffer, specifying the current slice offset and numbers of bytes to copy. > > I am looking to do the same with PyOpenCL, I did various searches on the > internet, but I am not quite sure that I understand how to specify an > offset and num_bytes in a memory transfer operation. > > From the documentation of pyopencl.enqueue_copy and it seems that for > host <-> Buffer copies the supported parameter is "device_offset", but I > would need actually to specify a host_offset, to address the single > slice, and a byte_count, to read only 1 slice. These parameters seem to > be available only for Buffer <-> Buffer transfers (which I assume is a > GPU <-> GPU transfer ?) > > What's the correct way of copying only a subset of a host memory buffer > to device and vice-versa (writing back from device to host to a > particular range within a buffer ?)
(cc'ing pyopencl list) I assume your data is sitting in a numpy array on the host. Then all you need to do is enqueue_copy(dev_buf, host[1000:2000]), i.e. pass the desired slice of the numpy array to enqueue_copy, instead of the whole array. Obviously, this will only work if the numpy array resulting from the slice access is contiguous in host memory. Hope this helps! Andreas
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