Hi Andreas,
Thanks very much for your suggestion. Unfortunately I still did not
manage to get this working.
For example this small test:
------------------------------------------
import pyopencl as cl
import numpy as np
ctx = cl.create_some_context()
queue = cl.CommandQueue(ctx)
mf = cl.mem_flags
# 3D sorce array 10x10x200
source_buff_host=np.zeros((10,10,200),dtype=np.float32)
# 2D "slice" dev array 10x10x1
dest_buff_dev = cl.Buffer(ctx, mf.READ_ONLY,
source_buff_host.shape[0]*source_buff_host.shape[1]*source_buff_host.itemsize)
# copy one 2D slice to the dev buffer
cl.enqueue_copy(queue, dest_buff_dev, source_buff_host[:,:,1])
------------------------------------------
Results in the following error:
File "/Users/andrea_borsic/Dropbox/ImageAnalisisAndVisualization/mCT/VES
PyOpenCL/SliceCopyTest.py", line 15, in <module>
cl.enqueue_copy(queue, dest_buff_dev, source_buff_host[:,:,1])
File
"/Library/Python/2.7/site-packages/pyopencl-2011.2-py2.7-macosx-10.7-intel.egg/pyopencl/__init__.py",
line 755, in enqueue_copy
return _cl._enqueue_write_buffer(queue, dest, src, **kwargs)
TypeError: expected a single-segment buffer object
Any suggestion is really appreciated !
Best Regards,
Andrea
On 4/25/12 12:56 PM, Andreas Kloeckner wrote:
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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