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How do I enable checkpointing or resume execution for the stitch_layout step? #188
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Hi @liu-wq
This is very odd. For reference, whole mouse brain stitching should take in the order of half an hour to an hour maybe on our workstations.
So first I would try to understand why it is slow before trying to run only parts.(a rat brain is bigger but not that much bigger than a mouse).
the biggest pipeline (vasculature, multichannel, whole mouse brain) may take up to a day- Can you confirm the process is running in parallel (resources monitoring
- Can you confirm that you converted tiles to .npy
- Can you check which step is slow if any in particular (from the logs)
- Can you test your IO throughput ?
Hi,
Because I run ClearMap on the HPC. There is have time limit for the task. I want to stitch the whole brain of rats, and 20 threads ran for 7 days, still have not finished. The re-run seems to be starting from the beginning, and I would like to ask how to skip the parts that have already been done.
Thanks,
Weiqiang