Core Compatibility Report: shivering-raccoon/v0
| ✔️ |
bioimageio format validation |
| status |
passed |
| source |
https://hypha.aicell.io/bioimage-io/artifacts/shivering-raccoon/files/rdf.yaml?version=v0 |
| id |
10.5281/zenodo.6406803/6406804 |
| format version |
model 0.4.10 |
| bioimageio.spec |
0.5.6.0 |
|
Location |
Details |
| ✔️ |
|
Successfully created `ModelDescr` instance. |
| ✔️ |
|
bioimageio.spec format validation model 0.4.10 |
| ⚠ |
weights.pytorch_state_dict.dependencies |
Custom dependencies (conda:environment.yaml) specified. Avoid this whenever possible to allow execution in a wider range of software environments. |
| ⚠ |
weights.pytorch_state_dict.pytorch_version |
missing. Please specify the PyTorch version these PyTorch state dict weights were created with. |
| ⚠ |
weights.torchscript.pytorch_version |
missing. Please specify the PyTorch version these Torchscript weights were created with. |
| ❌ |
weights.pytorch_state_dict |
Reproduce test outputs from test inputs (pytorch_state_dict) |
| ❌ |
weights.pytorch_state_dict |
/usr/share/miniconda/envs/96189b829af48e5ff48931e2aad6d1ff4eafea247b62c8a70dc5ba4e3f69fc2b/lib/python3.10/site-packages/torch/lib/libtorch_cpu.so: undefined symbol: iJIT_NotifyEvent |
|
|
See Traceback 1. |
|
weights.pytorch_state_dict |
recommended conda environment (Reproduce test outputs from test inputs (pytorch_state_dict)) |
|
|
%YAML 1.2
---
name: torch-em-deploy
channels:
- pytorch
- conda-forge
- nodefaults
dependencies:
- conda-forge::bioimageio.core
- pip
- pytorch>=1.6,<2.0
|
|
weights.pytorch_state_dict |
conda compare (Reproduce test outputs from test inputs (pytorch_state_dict)) |
|
|
Success. All the packages in the specification file are present in the environment with matching
version and build string. |
| ✔️ |
weights.torchscript |
Reproduce test outputs from test inputs (torchscript) |
|
weights.torchscript |
recommended conda environment (Reproduce test outputs from test inputs (torchscript)) |
|
|
%YAML 1.2
---
channels:
- pytorch
- conda-forge
- nodefaults
dependencies:
- conda-forge::bioimageio.core
- mkl ==2024.0.0
- numpy <2
- pip
- pytorch==1.10.1
- setuptools <70.0.0
- torchaudio==0.10.1
- torchvision==0.11.2
|
|
weights.torchscript |
conda compare (Reproduce test outputs from test inputs (torchscript)) |
|
|
See Conda Environment Comparison 1. |
Traceback 1
╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮
│ /usr/share/miniconda/envs/96189b829af48e5ff48931e2aad6d1ff4eafea247b62c8a70dc5ba4e3f69fc2b/lib/p │
│ │
│ 774 │ │ test_input = get_test_input_sample(model) │
│ 775 │ │ expected = get_test_output_sample(model) │
│ 776 │ │ │
│ ❱ 777 │ │ with create_prediction_pipeline( │
│ 778 │ │ │ bioimageio_model=model, devices=devices, weight_format=weight_format │
│ 779 │ │ ) as prediction_pipeline: │
│ 780 │ │ │ results = prediction_pipeline.predict_sample_without_blocking(test_input) │
│ │
│ /usr/share/miniconda/envs/96189b829af48e5ff48931e2aad6d1ff4eafea247b62c8a70dc5ba4e3f69fc2b/lib/p │
│ │
│ 368 │ │ │ f"deprecated create_prediction_pipeline kwargs: {set(deprecated_kwargs)}" │
│ 369 │ │ ) │
│ 370 │ │
│ ❱ 371 │ model_adapter = model_adapter or create_model_adapter( │
│ 372 │ │ model_description=bioimageio_model, │
│ 373 │ │ devices=devices, │
│ 374 │ │ weight_format_priority_order=weights_format and (weights_format,), │
│ │
│ /usr/share/miniconda/envs/96189b829af48e5ff48931e2aad6d1ff4eafea247b62c8a70dc5ba4e3f69fc2b/lib/p │
│ │
│ 166 │ │ assert errors │
│ 167 │ │ if len(weight_format_priority_order) == 1: │
│ 168 │ │ │ assert len(errors) == 1 │
│ ❱ 169 │ │ │ raise errors[0] │
│ 170 │ │ │
│ 171 │ │ else: │
│ 172 │ │ │ msg = ( │
│ │
│ /usr/share/miniconda/envs/96189b829af48e5ff48931e2aad6d1ff4eafea247b62c8a70dc5ba4e3f69fc2b/lib/p │
│ │
│ 107 │ │ │ if wf == "pytorch_state_dict": │
│ 108 │ │ │ │ assert weights.pytorch_state_dict is not None │
│ 109 │ │ │ │ try: │
│ ❱ 110 │ │ │ │ │ from .pytorch_backend import PytorchModelAdapter │
│ 111 │ │ │ │ │ │
│ 112 │ │ │ │ │ return PytorchModelAdapter( │
│ 113 │ │ │ │ │ │ model_description=model_description, devices=devices │
│ │
│ /usr/share/miniconda/envs/96189b829af48e5ff48931e2aad6d1ff4eafea247b62c8a70dc5ba4e3f69fc2b/lib/p │
│ │
│ 5 from pathlib import Path │
│ 6 from typing import Any, List, Literal, Optional, Sequence, Union │
│ 7 │
│ ❱ 8 import torch │
│ 9 from loguru import logger │
│ 10 from numpy.typing import NDArray │
│ 11 from torch import nn │
│ │
│ /usr/share/miniconda/envs/96189b829af48e5ff48931e2aad6d1ff4eafea247b62c8a70dc5ba4e3f69fc2b/lib/p │
│ │
│ 215 │ # See Note [Global dependencies] │
│ 216 │ if USE_GLOBAL_DEPS: │
│ 217 │ │ _load_global_deps() │
│ ❱ 218 │ from torch._C import * # noqa: F403 │
│ 219 │
│ 220 # Appease the type checker; ordinarily this binding is inserted by the │
│ 221 # torch._C module initialization code in C │
╰──────────────────────────────────────────────────────────────────────────────────────────────────╯
ImportError: /usr/share/miniconda/envs/96189b829af48e5ff48931e2aad6d1ff4eafea247b62c8a70dc5ba4e3f69fc2b/lib/python3.10/site-packages/torch/lib/libtorch_cpu.so: undefined symbol: iJIT_NotifyEvent
Conda Environment Comparison 1
usage: conda [-h] [-v] [--no-plugins] [-V] COMMAND ... conda is a tool for managing and
deploying applications, environments and packages. options: -h, --help Show this
help message and exit. -v, --verbose Can be used multiple times. Once for detailed
output, twice for INFO logging, thrice for DEBUG logging, four
times for TRACE logging. --no-plugins Disable all plugins that are not built into
conda. -V, --version Show the conda version number and exit. commands: The
following built-in and plugins subcommands are available. COMMAND activate
Activate a conda environment. clean Remove unused packages and caches.
commands List all available conda subcommands (including those
from plugins). Generally only used by tab-completion. compare Compare packages
between conda environments. config Modify configuration values in .condarc.
content-trust Signing and verification tools for Conda create Create a
new conda environment from a list of specified packages. deactivate
Deactivate the current active conda environment. doctor Display a health report
for your environment. env Create and manage conda environments. export
Export a given environment info Display information about current conda
install. init Initialize conda for shell interaction. install
Install a list of packages into a specified conda environment. list
List installed packages in a conda environment. notices Retrieve latest channel
notifications. package Create low-level conda packages. (EXPERIMENTAL)
remove (uninstall) Remove a list of packages from a specified conda
environment. rename Rename an existing environment. repoquery
Advanced search for repodata. run Run an executable in a conda environment.
search Search for packages and display associated information
using the MatchSpec format. token Set repository access token and configure
default_channels tos A subcommand for viewing, accepting, rejecting, and
otherwise interacting with a channel's Terms of Service (ToS). This
plugin periodically checks for updated Terms of Service for the
active/selected channels. Channels with a Terms of Service will need
to be accepted or rejected prior to use. Conda will only allow package
installation from channels without a Terms of Service or with an
accepted Terms of Service. Attempting to use a channel with a rejected
Terms of Service will result in an error. update (upgrade) Update conda packages to the
latest compatible version.