torchgeo v0.2.1 #3

regro-cf-autotick-bot · 2022-03-20T20:19:12Z

It is very likely that the current package version for this feedstock is out of date.

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Dependencies have been updated if changed: see upstream
Tests have passed
Updated license if changed and license_file is packaged

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Pending Dependency Version Updates

Here is a list of all the pending dependency version updates for this repo. Please double check all dependencies before merging.

Name	Upstream Version	Current Version
torchvision	0.12.0

Dependency Analysis

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Packages found in the meta.yaml but not found by source code inspection:

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_{This PR was created by the regro-cf-autotick-bot. The regro-cf-autotick-bot is a service to automatically track the dependency graph, migrate packages, and propose package version updates for conda-forge. Feel free to drop us a line if there are any issues! This PR was generated by https://github.com/regro/autotick-bot/actions/runs/2012852621, please use this URL for debugging.}

…nda-forge-pinning 2022.03.20.19.31.27

conda-forge-linter · 2022-03-20T20:19:16Z

Hi! This is the friendly automated conda-forge-linting service.

I just wanted to let you know that I linted all conda-recipes in your PR (recipe) and found it was in an excellent condition.

adamjstewart · 2022-03-21T00:35:19Z

Unclear why the tests are failing. It seems to hit a segfault during the middle of our import tests, which usually suggests that one of the dependencies can't find it's shared object libraries correctly. The import tests pass with Spack so it's not a bug in TorchGeo.

I'm also unsure who to reach out to for help on this or how to debug this. It's one of our required deps, I think imported in our datamodules, which is unfortunately most of the deps. Maybe we could try to install our deps with conda and see if we can reproduce the issue locally?

calebrob6 · 2022-03-21T01:03:12Z

tests passed before updating versions, right?

adamjstewart · 2022-03-21T01:29:35Z

Yes, the tests passed when we did the 0.2.0 release.

adamjstewart · 2022-03-21T01:36:34Z

I can reproduce locally, debugging now.

adamjstewart · 2022-03-21T01:38:13Z

$ python -X faulthandler
Python 3.9.10 | packaged by conda-forge | (main, Feb  1 2022, 21:24:37) 
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import torchgeo.datamodules
Fatal Python error: Segmentation fault

Current thread 0x00007fcc14455740 (most recent call first):
  File "/anaconda/envs/adam/lib/python3.9/ctypes/__init__.py", line 374 in __init__
  File "/anaconda/envs/adam/lib/python3.9/site-packages/torch/_ops.py", line 220 in load_library
  File "/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/extension.py", line 85 in _load_library
  File "/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/io/image.py", line 9 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 850 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/io/__init__.py", line 20 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 850 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/datasets/video_utils.py", line 8 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 850 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/datasets/kinetics.py", line 15 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 850 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/datasets/__init__.py", line 23 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 850 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1058 in _handle_fromlist
  File "/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/__init__.py", line 7 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 850 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "<frozen importlib._bootstrap>", line 1030 in _gcd_import
  File "/anaconda/envs/adam/lib/python3.9/importlib/__init__.py", line 127 in import_module
  File "/anaconda/envs/adam/lib/python3.9/site-packages/torchmetrics/utilities/imports.py", line 57 in _module_available
  File "/anaconda/envs/adam/lib/python3.9/site-packages/torchmetrics/utilities/imports.py", line 75 in _compare_version
  File "/anaconda/envs/adam/lib/python3.9/site-packages/torchmetrics/utilities/imports.py", line 111 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 850 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "/anaconda/envs/adam/lib/python3.9/site-packages/torchmetrics/functional/audio/pit.py", line 24 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 850 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "/anaconda/envs/adam/lib/python3.9/site-packages/torchmetrics/functional/audio/__init__.py", line 14 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 850 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 972 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "/anaconda/envs/adam/lib/python3.9/site-packages/torchmetrics/functional/__init__.py", line 14 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 850 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap>", line 1058 in _handle_fromlist
  File "/anaconda/envs/adam/lib/python3.9/site-packages/torchmetrics/__init__.py", line 14 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 850 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "/anaconda/envs/adam/lib/python3.9/site-packages/pytorch_lightning/utilities/types.py", line 25 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 850 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "/anaconda/envs/adam/lib/python3.9/site-packages/pytorch_lightning/callbacks/base.py", line 26 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 850 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "/anaconda/envs/adam/lib/python3.9/site-packages/pytorch_lightning/callbacks/__init__.py", line 14 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  File "<frozen importlib._bootstrap_external>", line 850 in exec_module
  File "<frozen importlib._bootstrap>", line 680 in _load_unlocked
  File "<frozen importlib._bootstrap>", line 986 in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 1007 in _find_and_load
  File "/anaconda/envs/adam/lib/python3.9/site-packages/pytorch_lightning/__init__.py", line 20 in <module>
  File "<frozen importlib._bootstrap>", line 228 in _call_with_frames_removed
  ...
Segmentation fault (core dumped)

adamjstewart · 2022-03-21T01:41:13Z

Okay, so it's trying to load /anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so, but that library has a ton of missing symbols:

$ ldd -r /anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so
	linux-vdso.so.1 (0x00007ffdb7926000)
	libpng16.so.16 => /anaconda/envs/adam/lib/python3.9/site-packages/torchvision/../../../libpng16.so.16 (0x00007f96a2422000)
	libjpeg.so.9 => /anaconda/envs/adam/lib/python3.9/site-packages/torchvision/../../../libjpeg.so.9 (0x00007f96a23e3000)
	libc10.so => not found
	libtorch_cpu.so => not found
	libstdc++.so.6 => /anaconda/envs/adam/lib/python3.9/site-packages/torchvision/../../../libstdc++.so.6 (0x00007f96a20a7000)
	libgcc_s.so.1 => /anaconda/envs/adam/lib/python3.9/site-packages/torchvision/../../../libgcc_s.so.1 (0x00007f96a23ad000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f96a1cb6000)
	libz.so.1 => /anaconda/envs/adam/lib/python3.9/site-packages/torchvision/../../.././libz.so.1 (0x00007f96a2393000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f96a1918000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f96a2252000)
undefined symbol: _ZN3c1019UndefinedTensorImpl10_singletonE	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c106detail12infer_schema20make_function_schemaENS_8ArrayRefINS1_11ArgumentDefEEES4_	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c1017RegisterOperatorsD1Ev	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZNK3c106IValue23reportToTensorTypeErrorEv	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN5torch3jit17parseSchemaOrNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c106detail14torchCheckFailEPKcS2_jS2_	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c105ErrorC2ENS_14SourceLocationENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c1021AutogradMetaInterfaceD2Ev	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c1010TensorImpl17set_autograd_metaESt10unique_ptrINS_21AutogradMetaInterfaceESt14default_deleteIS2_EE	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c106detail14torchCheckFailEPKcS2_jRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c1010TensorType3getEv	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZNK2at10TensorBase21__dispatch_contiguousEN3c1012MemoryFormatE	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c1017RegisterOperatorsC1EOS0_	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZTVN5torch8autograd12AutogradMetaE	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c106detail23torchInternalAssertFailEPKcS2_jS2_S2_	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c1010StringType3getEv	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZNK3c1010TensorImpl36is_contiguous_nondefault_policy_implENS_12MemoryFormatE	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN2at4_ops7permute4callERKNS_6TensorEN3c108ArrayRefIlEE	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN2at4_ops19empty_memory_format4callEN3c108ArrayRefIlEENS2_8optionalINS2_10ScalarTypeEEENS5_INS2_6LayoutEEENS5_INS2_6DeviceEEENS5_IbEENS5_INS2_12MemoryFormatEEE	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c1013DeviceObjType3getEv	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c107IntType3getEv	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN2at4_ops9from_file4callEN3c1017basic_string_viewIcEENS2_8optionalIbEENS5_IlEENS5_INS2_10ScalarTypeEEENS5_INS2_6LayoutEEENS5_INS2_6DeviceEEES6_	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN6caffe28TypeMeta26error_unsupported_typemetaES0_	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c1017RegisterOperatorsC1Ev	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c104impl23ExcludeDispatchKeyGuardC1ENS_14DispatchKeySetE	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c1017RegisterOperators25checkSchemaAndRegisterOp_EONS0_7OptionsE	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c106detail23torchInternalAssertFailEPKcS2_jS2_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZNK2at10TensorBase8data_ptrIhEEPT_v	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN3c104impl23ExcludeDispatchKeyGuardD1Ev	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)
undefined symbol: _ZN2at11TensorMaker11make_tensorEv	(/anaconda/envs/adam/lib/python3.9/site-packages/torchvision/image.so)

adamjstewart · 2022-03-21T01:46:45Z

I believe the issue is that conda installs PyTorch 1.11.0 (the latest release) but installs torchvision 0.11.0 (the previous release) and torchvision requires exact matching versions of PyTorch to use. So we can either pin PyTorch to the previous version, or ignore the issue and wait for conda-forge/torchvision-feedstock#45 to be completed. My personal preference would be to simply merge this as is and assume that torchvision's feedstock will figure things out. If any users have an issue, they can always workaround this by pinning the PyTorch version.

adamjstewart · 2022-03-21T01:57:48Z

Opened an issue here for follow-up: conda-forge/torchvision-feedstock#47

ngam · 2022-05-26T21:45:14Z

@adamjstewart did you merge this even tho it was not passing CI?

adamjstewart · 2022-05-26T21:51:20Z

Yes. There were no issues with this feedstock, only issues with the torchvision feedstock which were eventually fixed, see conda-forge/torchvision-feedstock#47.

ngam · 2022-05-26T21:56:52Z

Yes. There were no issues with this feedstock, only issues with the torchvision feedstock which were eventually fixed, see conda-forge/torchvision-feedstock#47.

Yes, but this is not how this works :) The CI here should pass and this should've waited until the torchvision issue was fixed. As a result, the 0.2.1 version was never uploaded to anaconda.org.

You could merge #5 to upload stuff

adamjstewart · 2022-05-26T21:57:41Z

Gotcha, thanks for the explanation!

regro-cf-autotick-bot added 2 commits March 20, 2022 20:18

updated v0.2.1

0ada69f

MNT: Re-rendered with conda-build 3.21.8, conda-smithy 3.18.0, and co…

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…nda-forge-pinning 2022.03.20.19.31.27

regro-cf-autotick-bot requested review from adamjstewart and calebrob6 as code owners March 20, 2022 20:19

Update dependencies

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torchgeo v0.2.1 #3

torchgeo v0.2.1 #3

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adamjstewart commented May 26, 2022

torchgeo v0.2.1 #3

torchgeo v0.2.1 #3

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regro-cf-autotick-bot commented Mar 20, 2022

Pending Dependency Version Updates

Dependency Analysis

Packages found in the meta.yaml but not found by source code inspection:

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