GenevieveBuckley

Scan, chunks processed: 100%|█████████████████████| 6/6 [00:00<00:00,  6.69it/s]
Traceback (most recent call last):
  File "/home/supervisor/miniforge3/envs/napari-bootstrapper/lib/python3.10/site-packages/superqt/utils/_qthreading.py", line 613, in reraise
    raise e
  File "/home/supervisor/miniforge3/envs/napari-bootstrapper/lib/python3.10/site-packages/superqt/utils/_qthreading.py", line 175, in run
    result = self.work()
  File "/home/supervisor/miniforge3/envs/napari-bootstrapper/lib/python3.10/site-packages/superqt/utils/_qthreading.py", line 354, in work
    return self._func(*self._args, **self._kwargs)
  File "/home/supervisor/miniforge3/envs/napari-bootstrapper/lib/python3.10/site-packages/napari_bootstrapper/_widget.py", line 331, in _run_prediction
    out_lsds = prepare_ds(

GenevieveBuckley

micro-sam speed tests

8th September 2023. Results from Constantin's development/benchmarks.py script.

Summary: something about AMG is really killing the performance for MPS backends.

• We'll need to do some line profiling on that part of the code to get more information.
• I am suspicious that the fallback to CPU might somehow involve a lot of transferring large tensors back and forth between the cpu and mps, and perhaps that is a large part of why it is so much slower than the cpu only computation.

  Running benchmark_amg ...
  

[W MPSFallback.mm:11] Warning: The operator 'torchvision::nms' is not currently supported on the MPS backend and will fall back to run on the CPU. This may have performance implications. (function operator())

GenevieveBuckley

pre-commit-hooks.nix: updating /workspace/copier repo
pre-commit installed at .git/hooks/pre-commit
pre-commit installed at .git/hooks/commit-msg
direnv: No virtual environment exists. Executing `poetry install` to create one.
Creating virtualenv copier-tqPO6HKK-py3.10 in /workspace/.pyenv_mirror/poetry/virtualenvs
Installing dependencies from lock file

Package operations: 70 installs, 1 update, 0 removals

  • Installing six (1.16.0)

GenevieveBuckley

GenevieveBuckley

GenevieveBuckley

Windows: open the miniforge terminal prompt

conda info --envs
# prints a list of the virtual environments you have
conda create --name myenv
# create a new virtual environment

conda activate myenv
# activate a virtual environment

GenevieveBuckley

GenevieveBuckley

GenevieveBuckley

GenevieveBuckley

(napari) genevieve@genevieve-G5-5500:~$ pip install napari-pymeshlab
Collecting napari-pymeshlab
  Using cached napari_pymeshlab-0.0.5-py3-none-any.whl (27 kB)
Requirement already satisfied: npe2 in ./anaconda3/envs/napari/lib/python3.10/site-packages (from napari-pymeshlab) (0.6.2)
Requirement already satisfied: numpy in ./anaconda3/envs/napari/lib/python3.10/site-packages (from napari-pymeshlab) (1.24.2)
Collecting pymeshlab
  Downloading pymeshlab-2022.2.post2-cp310-cp310-manylinux1_x86_64.whl (56.9 MB)
     ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 56.9/56.9 MB 2.4 MB/s eta 0:00:00
Requirement already satisfied: rich in ./anaconda3/envs/napari/lib/python3.10/site-packages (from npe2->napari-pymeshlab) (13.3.1)
Requirement already satisfied: psygnal>=0.3.0 in ./anaconda3/envs/napari/lib/python3.10/site-packages (from npe2->napari-pymeshlab) (0.7.2)