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GPU issues when creating supervoxels #106
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Hi Niccolo, Sorry to hear about the issues. Do you always get the same error even if you change the supervoxel parameters? Also it would be useful to know what code your googling suggested needs changing to fix it and was the requirements.txt file you found the one from this issue #105 ? Best Wishes, Olly |
Hi Olly, thank you for the quick reply! create_supervoxels
I haven't played with the spacing parameter, as I don't believe I will need it. I have tried to change compactness to 15 with both SP shape (5,5,5) and (20,20,20), the behaviour was the same as above (only one crash, on the gaussian filtered data with the larger size). Regarding the googling, what I meant was that I just googled for "QObject::~QObject: Timers cannot be stopped from another thread" (without quotes) and found some threads both on Qt Forum and stackoverflow (nothing specifically related to SuRVoS, though). The proposed solutions all seemed to require debugging and modifying of the code, while I was hoping that it was just a dependency issue which I could fix without a lot of trouble. Apologies for the misunderstanding! Yes, the requirements.txt that I used was the one from issue #105. I didn't have PyQt, which I believe was causing the issues with the GUI buttons. All the best, |
Hi Niccolò, You're welcome. Thanks for the reply. Yes unfortunately there are some issues with supervoxel calculation in terms of the data size limit (which will depend on your graphics card memory size) and some combinations of parameters that cause issues. We are working to fix them for SuRVoS2 which we hope to release in the New Year. Unfortunately we're not making many changes to this version of SuRVoS anymore but if we resolve some of the issues you found I'll put a bug fix in. Best Wishes, Olly |
Hi Olly, thank you for the reply. It seems odd for it to be a hardware limit, as a 350 x 350 x 350 volume with 16-bit depth should be only 82 MB in size. My GPU is a bit old, but it shouldn't be that bad (it's supposed to have 4GB of memory). Is the supervoxel calculation that demanding on the GPU? Best, |
Hi Niccolò, It's not quite as simple as just the data size, since there seems to be a limit on the number of supervoxels. You might be able to process larger data if you use larger supervoxels. Also the GPU based supervoxel algorithm is inefficient in some ways - multiple searches are made in parallel for each pixel but this is still faster than using a CPU. Best Wishes, Olly |
Hi,
I have installed SuRVoS from conda channel (using Anaconda on Windows), following all the steps of the Installation guide. The environment uses Python 3.6, and I have checked all the dependencies (I was initially experiencing crashes when clicking some buttons of the GUI, but that seems to have been fixed by updating some packages according to a more recent requirements.txt that I found among the closed issues).
Now all the different filters seem to work just fine, however when I try to compute supervoxels the GUI crashes and I receive this error message on the Anaconda prompt:
create_supervoxels
[GPU] Selected CUDA device: 0
[GPU] Device 0: "Quadro K4200" with compute capability 3.0, 1024 threads pb.
[CUDA ERROR] Memcpy back: unspecified launch failure
QObject::~QObject: Timers cannot be stopped from another thread
Any ideas on what might be the issue? I have tried googling but what I found would require me to change the code, which I am not feeling comfortable enough in trying (it also seems odd that I would be the first to report such an issue, if that was the case).
All the best,
Niccolò
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