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Graph Neural Network Library for PyTorch
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Many tests failed in test_graphmask_explainer.py #9675

Open beew opened 1 week ago

beew commented 1 week ago

🐛 Describe the bug

After installing pyg (with pip) I ran the tests and got a lot of errors, all from the module

test/explain/algorithmtest_graphic_explainer.py

running pytest

============================================================================================= short test summary info =============================================================================================
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-node-model-MaskType.object-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-node-model-MaskType.object-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-node-model-MaskType.common_attributes-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-node-model-MaskType.common_attributes-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-node-model-MaskType.attributes-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-node-model-MaskType.attributes-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-node-phenomenon-MaskType.object-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-node-phenomenon-MaskType.object-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-node-phenomenon-MaskType.common_attributes-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-node-phenomenon-MaskType.common_attributes-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-node-phenomenon-MaskType.attributes-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-node-phenomenon-MaskType.attributes-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-edge-model-MaskType.object-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-edge-model-MaskType.object-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-edge-model-MaskType.common_attributes-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-edge-model-MaskType.common_attributes-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-edge-model-MaskType.attributes-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-edge-model-MaskType.attributes-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-edge-phenomenon-MaskType.object-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-edge-phenomenon-MaskType.object-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-edge-phenomenon-MaskType.common_attributes-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-edge-phenomenon-MaskType.common_attributes-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-edge-phenomenon-MaskType.attributes-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-edge-phenomenon-MaskType.attributes-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-graph-model-MaskType.object-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-graph-model-MaskType.object-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-graph-model-MaskType.common_attributes-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-graph-model-MaskType.common_attributes-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-graph-model-MaskType.attributes-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-graph-model-MaskType.attributes-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-graph-phenomenon-MaskType.object-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-graph-phenomenon-MaskType.object-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-graph-phenomenon-MaskType.common_attributes-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-graph-phenomenon-MaskType.common_attributes-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-graph-phenomenon-MaskType.attributes-MaskType.object] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
FAILED test/explain/algorithm/test_graphmask_explainer.py::test_graph_mask_explainer_binary_classification[None-probs-graph-phenomenon-MaskType.attributes-None] - IndexError: Dimension out of range (expected to be in range of [-2, 1], but got 2)
....

FAILED test/nn/test_model_hub.py::test_save_pretrained_with_push_to_hub - AssertionError: expected call not found.

A more detailed log for some of the tests are attached

fail.log

Versions

.
PyTorch version: 2.4.1+cpu
Is debug build: False
CUDA used to build PyTorch: None
ROCM used to build PyTorch: N/A

OS: Ubuntu 22.04.5 LTS (x86_64)
GCC version: (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
Clang version: 14.0.0-1ubuntu1.1
CMake version: version 3.26.0
Libc version: glibc-2.35

Python version: 3.10.9 (main, Mar 31 2023, 07:34:00) [GCC 11.3.0] (64-bit runtime)
Python platform: Linux-6.8.0-45-generic-x86_64-with-glibc2.35
Is CUDA available: False
CUDA runtime version: No CUDA
CUDA_MODULE_LOADING set to: N/A
GPU models and configuration: No CUDA
Nvidia driver version: No CUDA
cuDNN version: No CUDA
HIP runtime version: N/A
MIOpen runtime version: N/A
Is XNNPACK available: True

CPU:
Architecture:                         x86_64
CPU op-mode(s):                       32-bit, 64-bit
Address sizes:                        39 bits physical, 48 bits virtual
Byte Order:                           Little Endian
CPU(s):                               8
On-line CPU(s) list:                  0-7
Vendor ID:                            GenuineIntel
Model name:                           Intel(R) Core(TM) i5-10210U CPU @ 1.60GHz
CPU family:                           6
Model:                                142
Thread(s) per core:                   2
Core(s) per socket:                   4
Socket(s):                            1
Stepping:                             12
CPU max MHz:                          4200.0000
CPU min MHz:                          400.0000
BogoMIPS:                             4199.88
Flags:                                fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb ssbd ibrs ibpb stibp ibrs_enhanced tpr_shadow flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid mpx rdseed adx smap clflushopt intel_pt xsaveopt xsavec xgetbv1 xsaves dtherm ida arat pln pts hwp hwp_notify hwp_act_window hwp_epp vnmi md_clear flush_l1d arch_capabilities
Virtualization:                       VT-x
L1d cache:                            128 KiB (4 instances)
L1i cache:                            128 KiB (4 instances)
L2 cache:                             1 MiB (4 instances)
L3 cache:                             6 MiB (1 instance)
NUMA node(s):                         1
NUMA node0 CPU(s):                    0-7
Vulnerability Gather data sampling:   Mitigation; Microcode
Vulnerability Itlb multihit:          KVM: Mitigation: VMX disabled
Vulnerability L1tf:                   Not affected
Vulnerability Mds:                    Not affected
Vulnerability Meltdown:               Not affected
Vulnerability Mmio stale data:        Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Reg file data sampling: Not affected
Vulnerability Retbleed:               Mitigation; Enhanced IBRS
Vulnerability Spec rstack overflow:   Not affected
Vulnerability Spec store bypass:      Mitigation; Speculative Store Bypass disabled via prctl
Vulnerability Spectre v1:             Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2:             Mitigation; Enhanced / Automatic IBRS; IBPB conditional; RSB filling; PBRSB-eIBRS SW sequence; BHI SW loop, KVM SW loop
Vulnerability Srbds:                  Mitigation; Microcode
Vulnerability Tsx async abort:        Not affected

Versions of relevant libraries:
[pip3] clip-anytorch==2.6.0
[pip3] denoising-diffusion-pytorch==2.0.17
[pip3] ema-pytorch==0.6.2
[pip3] flake8==7.1.1
[pip3] flake8-docstrings==1.7.0
[pip3] gpytorch==1.10
[pip3] intel_extension_for_pytorch==2.4.0
[pip3] mypy==1.2.0
[pip3] mypy-extensions==1.0.0
[pip3] numpy==1.23.5
[pip3] numpydoc==1.5.0
[pip3] numpyro==0.12.1
[pip3] paramfittorchdemo==0.0.1
[pip3] pytorch-fid==0.3.0
[pip3] pytorch-lightning==2.4.0
[pip3] torch==2.4.1+cpu
[pip3] torch_cluster==1.6.3+pt24cpu
[pip3] torch-geometric==2.6.0
[pip3] torch_scatter==2.1.2+pt24cpu
[pip3] torch_sparse==0.6.18+pt24cpu
[pip3] torch_spline_conv==1.2.2+pt24cpu
[pip3] torch-tb-profiler==0.4.3
[pip3] torch-tda==0.0.1
[pip3] torch-topological==0.1.7
[pip3] torchaudio==2.4.1+cpu
[pip3] torchdata==0.8.0
[pip3] torchdiffeq==0.2.4
[pip3] torchensemble==0.2.0
[pip3] torchmetrics==1.4.2
[pip3] torchsde==0.2.6
[pip3] torchtext==0.18.0
[pip3] torchvision==0.19.1+cpu
[pip3] triton==2.0.0
[conda] Could not collect

In addition, I have 

pyg-lib  0.4.0+pt24cpu
akihironitta commented 7 hours ago

Would you mind sharing the output of pip list as well?

All test cases succeed in my env:

$ pip list
Package                  Version     Editable project location
------------------------ ----------- ----------------------------------------------------
aiohappyeyeballs         2.4.0
aiohttp                  3.10.5
aiosignal                1.3.1
async-timeout            4.0.3
attrs                    24.2.0
autoflake                2.3.1
certifi                  2024.7.4
charset-normalizer       3.3.2
exceptiongroup           1.2.2
filelock                 3.13.1
flake8                   7.1.1
frozenlist               1.4.1
fsspec                   2024.2.0
idna                     3.7
iniconfig                2.0.0
Jinja2                   3.1.3
joblib                   1.4.2
littleutils              0.2.4
MarkupSafe               2.1.5
mccabe                   0.7.0
mpmath                   1.3.0
multidict                6.0.5
networkx                 3.2.1
numpy                    2.1.0
nvidia-cublas-cu12       12.1.3.1
nvidia-cuda-cupti-cu12   12.1.105
nvidia-cuda-nvrtc-cu12   12.1.105
nvidia-cuda-runtime-cu12 12.1.105
nvidia-cudnn-cu12        9.1.0.70
nvidia-cufft-cu12        11.0.2.54
nvidia-curand-cu12       10.3.2.106
nvidia-cusolver-cu12     11.4.5.107
nvidia-cusparse-cu12     12.1.0.106
nvidia-nccl-cu12         2.20.5
nvidia-nvjitlink-cu12    12.1.105
nvidia-nvtx-cu12         12.1.105
ogb                      1.3.6
outdated                 0.2.2
packaging                24.1
pandas                   2.2.3
pip                      24.0
pluggy                   1.5.0
psutil                   6.0.0
pycodestyle              2.12.1
pyflakes                 3.2.0
pyparsing                3.1.2
pytest                   8.3.3
python-dateutil          2.9.0.post0
pytz                     2024.2
requests                 2.32.3
scikit-learn             1.5.2
scipy                    1.14.1
setuptools               69.5.1
six                      1.16.0
sympy                    1.12
threadpoolctl            3.5.0
tomli                    2.0.2
torch                    2.4.0+cu121
torch-geometric          2.6.0       /home/aki/work/github.com/pyg-team/pytorch_geometric
tqdm                     4.66.5
triton                   3.0.0
typing_extensions        4.9.0
tzdata                   2024.2
urllib3                  2.2.2
wheel                    0.43.0
yarl                     1.9.4
beew commented 7 hours ago

@akihironitta

Here it is 

--------------------------------- ----------------- --------------------------------------------------
2to3                              1.0
absl-py                           1.4.0
accelerate                        0.19.0
accessible-pygments               0.0.4
aesara                            2.8.12
aiofiles                          22.1.0
aiohappyeyeballs                  2.4.0
aiohttp                           3.10.5
aiolimiter                        1.0.0
aiosignal                         1.3.1
aiosqlite                         0.18.0
alabaster                         0.7.13
alembic                           1.10.4
aniso8601                         9.0.1
annoy                             1.17.1
ansi2html                         1.8.0
anyascii                          0.3.1
anyio                             3.6.2
appdirs                           1.4.4
apptools                          5.2.0
APScheduler                       3.10.0
argon2-cffi                       21.3.0
argon2-cffi-bindings              21.2.0
array-record                      0.2.0
arrow                             1.2.3
arviz                             0.19.0
astor                             0.8.1
astroid                           3.1.0
asttokens                         2.2.1
astunparse                        1.6.3
async-timeout                     4.0.2
asyncssh                          2.17.0
atomicwrites                      1.4.1
attrdict                          2.0.1
attrs                             22.2.0
audioread                         3.0.0
autobahn                          23.1.2
autoflake                         2.1.1
autograd                          1.5
autograd-gamma                    0.5.0
autopep8                          2.0.4
Babel                             2.11.0
backcall                          0.2.0
backends                          1.5.3
backoff                           2.2.1
bambi                             0.10.0
bangla                            0.0.2
bats-tda                          0.2.0
bctpy                             0.6.0
beartype                          0.13.1
beautifulsoup4                    4.11.2
beniget                           0.3.0
betterproto                       2.0.0b5
binaryornot                       0.4.4
black                             24.1.1
blackjax                          0.9.6
bleach                            6.0.0
blis                              0.7.9
blockdiag                         3.0.0
bnnumerizer                       0.0.2
bnunicodenormalizer               0.1.1
bokeh                             2.4.3
boltons                           23.0.0
breathe                           4.35.0
cachetools                        5.3.0
captum                            0.6.0
catalogue                         2.0.8
catboost                          1.1.1
category-encoders                 2.6.0
cattrs                            22.2.0
celluloid                         0.2.0
certifi                           2022.12.7
cffi                              1.15.1
cfgv                              3.3.1
cgen                              2020.1
chardet                           5.1.0
charset-normalizer                3.0.1
chex                              0.1.6
citeproc-py                       0.6.0
clean-fid                         0.1.35
click                             8.1.3
clikit                            0.6.2
clip-anytorch                     2.6.0
cloudpickle                       2.2.1
clr                               1.0.3
cmaes                             0.9.1
cmake                             3.26.0
cmdstanpy                         1.2.0
cmocean                           3.0.3
codecov                           2.1.12
colorama                          0.4.6
colorcet                          3.0.1
coloredlogs                       15.0.1
colorlog                          6.7.0
comm                              0.2.0
commonmark                        0.9.1
confection                        0.0.4
configobj                         5.0.8
cons                              0.4.5
contourpy                         1.0.7
convertdate                       2.4.0
cookiecutter                      2.1.1
coqpit                            0.0.17
corner                            2.2.2
coverage                          7.1.0
crashtest                         0.3.1
cryptography                      39.0.1
cycler                            0.11.0
cymem                             2.0.7
Cython                            0.29.28
daal                              2024.7.0
daal4py                           2024.7.0
daft                              0.1.2
dash                              2.8.1
dash-core-components              2.0.0
dash-html-components              2.0.0
dash-table                        5.0.0
dask                              2023.3.1
dask-glm                          0.2.0
dask-ml                           2023.3.24
datasets                          2.12.0
dateparser                        1.1.7
dateutils                         0.6.12
de-core-news-sm                   3.5.0
debugpy                           1.6.6
decorator                         5.1.1
defusedxml                        0.7.1
denoising-diffusion-pytorch       2.0.17
Deprecated                        1.2.13
dgl                               1.1
dglgo                             0.0.2
diff-match-patch                  20200713
diffrax                           0.4.1
dill                              0.3.6
dionysus                          2.0.9
distlib                           0.3.6
distributed                       2023.3.1
distro                            1.9.0
dm-tree                           0.1.8
dnspython                         2.3.0
docker-pycreds                    0.4.0
docopt                            0.6.2
docplex                           2.28.240
docstring_parser                  0.16
docstring-to-markdown             0.11
docutils                          0.18.1
dotmap                            1.3.30
duckdb                            1.0.0
duecredit                         0.9.2
eagerpy                           0.30.0
einops                            0.6.1
ema-pytorch                       0.6.2
email-validator                   2.0.0.post1
emcee                             3.1.4
engineering-notation              0.8.0
entrypoints                       0.4
envisage                          6.1.1
ephem                             4.1.4
equinox                           0.10.11
etils                             1.2.0
etuples                           0.3.8
exceptiongroup                    1.1.0
execnb                            0.1.6
execnet                           1.9.0
executing                         1.2.0
ExifRead                          3.0.0
expecttest                        0.2.1
fastcore                          1.7.9
fastdtw                           0.3.4
fastjsonschema                    2.16.2
fastprogress                      1.0.3
fastrlock                         0.8.1
fbpca                             1.0
fdm                               0.4.1
ffmpeg-python                     0.2.0
filelock                          3.16.1
flake8                            7.1.1
flake8-docstrings                 1.7.0
Flake8-pyproject                  1.2.3
flaky                             3.7.0
Flask                             2.2.3
Flask-Cors                        3.0.10
flask-restx                       1.1.0
Flask-WTF                         1.1.1
flatbuffers                       23.1.21
fonttools                         4.38.0
formulae                          0.3.4
formulaic                         0.5.2
fpdf2                             2.7.4
fqdn                              1.5.1
frozenlist                        1.3.3
fsspec                            2024.9.0
ftfy                              6.1.1
funcparserlib                     1.0.1
furo                              2022.12.7
furo-sphinx-search                0.2.0
future                            0.18.3
g2pkk                             0.1.2
gast                              0.4.0
gdown                             5.2.0
gensim                            4.3.1
geomstats                         2.5.0
gevent                            22.10.2
ghapi                             1.0.6
giotto-deep                       0.0.4
giotto-ph                         0.2.4
giotto-tda                        0.6.2
gitdb                             4.0.10
GitPython                         3.1.31
gmsh                              4.11.1
google-api-core                   2.11.0
google-auth                       2.16.0
google-auth-oauthlib              0.4.6
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akihironitta commented 7 hours ago

Had a quick look, but not sure which one is causing those test failures. Any chance you could investigate the cause, e.g., by removing irrelvant packages from the env? If you'd just like to contribute to PyG, I'd suggest creating a new env with only necessary packages.