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Is there GPU/CUDA support for eddy? #94
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Hi Vishwesh, I have not yet invested time into attempting to get CUDA working within Docker for this tool. Singularity is much more amenable to running on high-performance computing services, and I was able to get the CUDA version of FSL's If there's demand for getting CUDA working from within Docker, I can have it as a listed issue; but I'm unlikely to be able to implement a solution myself in the near future as I happen to not have easy access to a Linux system with functioning CUDA at the present moment. Cheers |
Hi Rob, thanks for making this great app! Any tips on getting eddy_cuda working on Singularity? Is there a specific version of cuda I need to match the eddy that's in the container? In the past (but not on this particular computer), I've had success running singularity run with the --nv flag to get eddy_cuda working on a different BIDS app. On this computer I've gotten eddy_cuda working on a different BIDS app through docker. I also was able to make the nvidia/cuda singularity image output nvidia-smi, meaning my singuliarty/cuda compatibility should be working. And here's the error I get (assuming the system in this case means the container): Would be grateful for any advice! Brian |
Hi Brian, For me personally, getting CUDA working through Singularity only required a fairly brief exchange with the sysadmins of the relevant HPC. It involved setting envvar If you want to see the particular complaint generated by If there are other tools that are able to provide CUDA support in Singularity in a way that requires less hoops from the user's perspective, I'd be interested in adopting such solutions; but it's not something I can afford to spend a large amount of time investigating. Hope that's enough to set you on a path to a working solution |
Thanks for the reply, Rob. A colleague and I have been trying to get this working for a few days without success. Do you still have access to the exact command you used? We are running it on a machine with only CUDA 9.1, so versioning shouldn't be an issue, despite getting the same error message as this thread. We've tried using If you still have the exact command you used that would be a helpful piece of information. Cheers, |
With my own use I'm actually executing a different container, but
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Good lookin' out, @Lestropie! We got it to work. Here is the command we used, in case it's useful to anyone who sees this. We are running on GCP running Rhel 7 with only cuda 9.1 installed:
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Hey folks, I am on a mission to do the same on my end :-), we have a HPC cluster with GPU and talking to the sysadmin he also raised the concern that the newer cluster with A100 won't support cuda9_1 but would require cuda_11. Has anyone come around that issue? Seems a bit disastrous as it would suggest that one would need a RTX 10xx generation GPU? |
This would depend entirely on FSL compiling the |
Hi Also there is NOW an eddy_cuda10.2 so that looks promising. |
The Docker file does not seem to contain any kind of CUDA installation. Is there any kind of future plan to extend this app with GPU support?
mrtrix3_connectome.py: [WARNING] CUDA version of FSL "eddy" present on system, but does not execute successfully; OpenMP version will instead be used
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