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MannLabs / scPortrait

https://mannlabs.github.io/scPortrait/
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Segmentation Error when using cellpose 3.1.0 on MacOS MPS backend #106

Open sophiamaedler opened 1 week ago

sophiamaedler commented 1 week ago

When trying to segment on macOS with the MPS backend with cellpose version 3.1.0 I encounter the following error: 

Traceback (most recent call last):
  File "/Users/orat/opt/anaconda3/lib/python3.9/site-packages/cellpose/gui/gui.py", line 1001, in calibrate_size
    diams, _ = self.model.sz.eval(self.stack[self.currentZ].copy(),
  File "/Users/orat/opt/anaconda3/lib/python3.9/site-packages/cellpose/models.py", line 776, in eval
    masks = self.cp.eval(
  File "/Users/orat/opt/anaconda3/lib/python3.9/site-packages/cellpose/models.py", line 534, in eval
    masks = self._compute_masks(x.shape, dP, cellprob, flow_threshold=flow_threshold,
  File "/Users/orat/opt/anaconda3/lib/python3.9/site-packages/cellpose/models.py", line 620, in _compute_masks
    outputs = dynamics.resize_and_compute_masks(
  File "/Users/orat/opt/anaconda3/lib/python3.9/site-packages/cellpose/dynamics.py", line 839, in resize_and_compute_masks
    mask = compute_masks(dP, cellprob, niter=niter,
  File "/Users/orat/opt/anaconda3/lib/python3.9/site-packages/cellpose/dynamics.py", line 906, in compute_masks
    mask = get_masks_torch(p_final, inds, dP.shape[1:], 
  File "/Users/orat/opt/anaconda3/lib/python3.9/site-packages/cellpose/dynamics.py", line 757, in get_masks_torch
    coo = torch.sparse_coo_tensor(pt, torch.ones(pt.shape[1], device=pt.device, dtype=torch.int)

NET ERROR: Could not run 'aten::_sparse_coo_tensor_with_dims_and_tensors' with arguments from the 'SparseMPS' backend. This could be because the operator doesn't exist for this backend, or was omitted during the selective/custom build process (if using custom build). If you are a Facebook employee using PyTorch on mobile, please visit https://fburl.com/ptmfixes for possible resolutions. 'aten::_sparse_coo_tensor_with_dims_and_tensors' is only available for these backends: [MPS, Meta, SparseCPU, SparseMeta, BackendSelect, Python, FuncTorchDynamicLayerBackMode, Functionalize, Named, Conjugate, Negative, ZeroTensor, ADInplaceOrView, AutogradOther, AutogradCPU, AutogradCUDA, AutogradHIP, AutogradXLA, AutogradMPS, AutogradIPU, AutogradXPU, AutogradHPU, AutogradVE, AutogradLazy, AutogradMTIA, AutogradPrivateUse1, AutogradPrivateUse2, AutogradPrivateUse3, AutogradMeta, AutogradNestedTensor, Tracer, AutocastCPU, AutocastXPU, AutocastMPS, AutocastCUDA, FuncTorchBatched, BatchedNestedTensor, FuncTorchVmapMode, Batched, VmapMode, FuncTorchGradWrapper, PythonTLSSnapshot, FuncTorchDynamicLayerFrontMode, PreDispatch, PythonDispatcher].

MPS: registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/mps/MPSFallback.mm:75 [backend fallback]
Meta: registered at /Users/runner/work/pytorch/pytorch/pytorch/build/aten/src/ATen/RegisterMeta.cpp:26996 [kernel]
SparseCPU: registered at /Users/runner/work/pytorch/pytorch/pytorch/build/aten/src/ATen/RegisterSparseCPU.cpp:1406 [kernel]
SparseMeta: registered at /Users/runner/work/pytorch/pytorch/pytorch/build/aten/src/ATen/RegisterSparseMeta.cpp:290 [kernel]
BackendSelect: registered at /Users/runner/work/pytorch/pytorch/pytorch/build/aten/src/ATen/RegisterBackendSelect.cpp:792 [kernel]
Python: registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/core/PythonFallbackKernel.cpp:153 [backend fallback]
FuncTorchDynamicLayerBackMode: registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/functorch/DynamicLayer.cpp:497 [backend fallback]
Functionalize: registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/FunctionalizeFallbackKernel.cpp:349 [backend fallback]
Named: registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/core/NamedRegistrations.cpp:7 [backend fallback]
Conjugate: registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/ConjugateFallback.cpp:17 [backend fallback]
Negative: registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/native/NegateFallback.cpp:18 [backend fallback]
ZeroTensor: registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/ZeroTensorFallback.cpp:86 [backend fallback]
ADInplaceOrView: fallthrough registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/core/VariableFallbackKernel.cpp:96 [backend fallback]
AutogradOther: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
AutogradCPU: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
AutogradCUDA: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
AutogradHIP: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
AutogradXLA: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
AutogradMPS: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
AutogradIPU: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
AutogradXPU: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
AutogradHPU: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
AutogradVE: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
AutogradLazy: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
AutogradMTIA: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
AutogradPrivateUse1: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
AutogradPrivateUse2: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
AutogradPrivateUse3: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
AutogradMeta: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
AutogradNestedTensor: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/VariableType_2.cpp:19981 [autograd kernel]
Tracer: registered at /Users/runner/work/pytorch/pytorch/pytorch/torch/csrc/autograd/generated/TraceType_2.cpp:17715 [kernel]
AutocastCPU: fallthrough registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/autocast_mode.cpp:321 [backend fallback]
AutocastXPU: fallthrough registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/autocast_mode.cpp:463 [backend fallback]
AutocastMPS: fallthrough registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/autocast_mode.cpp:209 [backend fallback]
AutocastCUDA: fallthrough registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/autocast_mode.cpp:165 [backend fallback]
FuncTorchBatched: registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/functorch/LegacyBatchingRegistrations.cpp:731 [backend fallback]
BatchedNestedTensor: registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/functorch/LegacyBatchingRegistrations.cpp:758 [backend fallback]
FuncTorchVmapMode: fallthrough registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/functorch/VmapModeRegistrations.cpp:27 [backend fallback]
Batched: registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/LegacyBatchingRegistrations.cpp:1075 [backend fallback]
VmapMode: fallthrough registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/VmapModeRegistrations.cpp:33 [backend fallback]
FuncTorchGradWrapper: registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/functorch/TensorWrapper.cpp:207 [backend fallback]
PythonTLSSnapshot: registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/core/PythonFallbackKernel.cpp:161 [backend fallback]
FuncTorchDynamicLayerFrontMode: registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/functorch/DynamicLayer.cpp:493 [backend fallback]
PreDispatch: registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/core/PythonFallbackKernel.cpp:165 [backend fallback]
PythonDispatcher: registered at /Users/runner/work/pytorch/pytorch/pytorch/aten/src/ATen/core/PythonFallbackKernel.cpp:157 [backend fallback]

This issue is known: https://github.com/MouseLand/cellpose/issues/1034

Should we limit the cellpose version to < 3.1.0 until this issue has been addressed @nik-as @namsaraeva?

namsaraeva commented 1 week ago

@sophiamaedler I would limit the cellpose version for now, yes.

sophiamaedler commented 2 days ago

keeping open until issue has been addressed in cellpose and the version restriction can be lifted