Closed puririshi98 closed 1 year ago
lydiawunan
commented
1 year ago Thanks for the contribution! I tested the code on my macbook as well as a server with A100s and noticed the error: AttributeError: 'GlobalStorage' object has no attribute 'n_id'
I am wondering whether there is any dependency related to PyG version.
puririshi98
commented
1 year ago hmm yes it seems there is a version conflict, can you pip list so i can see your versions? i am using the pyg 23.07 container from NVIDIA that I develop: https://developer.nvidia.com/pyg-container-early-access
If i can isolate what the version difference is i can create a conditional that uses ur old code if their versions are before a certain number otherwise use the newer code
heres the pip list in that container:
root@riship-dt:/workspace# pip list
Package Version
------------------------- --------------------
absl-py 1.4.0
aiohttp 3.8.4
aiosignal 1.3.1
alembic 1.11.1
apex 0.1
argon2-cffi 21.3.0
argon2-cffi-bindings 21.2.0
asttokens 2.2.1
astunparse 1.6.3
async-timeout 4.0.2
attrs 23.1.0
audioread 3.0.0
backcall 0.2.0
beautifulsoup4 4.12.2
black 23.3.0
bleach 6.0.0
blinker 1.4
blis 0.7.9
Brotli 1.0.9
cachetools 5.3.1
catalogue 2.0.8
certifi 2023.5.7
cffi 1.15.1
charset-normalizer 3.1.0
click 8.1.3
cloudpickle 2.2.1
cmaes 0.9.1
cmake 3.26.4
colorlog 6.7.0
comm 0.1.3
confection 0.1.0
contourpy 1.1.0
coverage 7.2.7
cryptography 3.4.8
cubinlinker 0.3.0+2.g155b525
cuda-python 12.1.0rc5+1.g8659927
cudf 23.6.0
cugraph 23.6.0
cugraph-dgl 23.6.0
cugraph-service-client 23.6.0
cugraph-service-server 23.6.0
cuml 23.6.0
cupy-cuda12x 12.1.0
cycler 0.11.0
cymem 2.0.7
Cython 0.29.36
dask 2023.3.2
dask-cuda 23.6.0
dask-cudf 23.6.0
dbus-python 1.2.18
debugpy 1.6.7
decorator 5.1.1
defusedxml 0.7.1
distributed 2023.3.2.1
distro 1.7.0
distro-info 1.1build1
DLLogger 1.0.0
dm-tree 0.1.8
einops 0.6.1
exceptiongroup 1.1.2
execnet 1.9.0
executing 1.2.0
expecttest 0.1.3
fastjsonschema 2.17.1
fastrlock 0.8.1
filelock 3.12.2
flake8 6.0.0
flash-attn 1.0.7
fonttools 4.40.0
frozenlist 1.3.3
fsspec 2023.6.0
gast 0.5.4
gevent 22.10.2
geventhttpclient 2.0.2
google-auth 2.21.0
google-auth-oauthlib 0.4.6
gp 0.1
graphsurgeon 0.4.6
greenlet 2.0.2
grpcio 1.56.0
httplib2 0.20.2
hypothesis 5.35.1
idna 3.4
importlib-metadata 6.7.0
iniconfig 2.0.0
intel-openmp 2021.4.0
ipykernel 6.24.0
ipython 8.14.0
ipython-genutils 0.2.0
isort 5.12.0
jedi 0.18.2
jeepney 0.7.1
Jinja2 3.1.2
joblib 1.3.0
json5 0.9.14
jsonschema 4.18.0
jsonschema-specifications 2023.6.1
jupyter_client 8.3.0
jupyter_core 5.3.1
jupyter-tensorboard 0.2.0
jupyterlab 2.3.2
jupyterlab-pygments 0.2.2
jupyterlab-server 1.2.0
jupytext 1.14.7
keyring 23.5.0
kiwisolver 1.4.4
langcodes 3.3.0
launchpadlib 1.10.16
lazr.restfulclient 0.14.4
lazr.uri 1.0.6
librosa 0.9.2
lightning-utilities 0.9.0
littleutils 0.2.2
llvmlite 0.40.1
locket 1.0.0
Mako 1.2.4
Markdown 3.4.3
markdown-it-py 3.0.0
MarkupSafe 2.1.3
matplotlib 3.7.2
matplotlib-inline 0.1.6
mccabe 0.7.0
mdit-py-plugins 0.4.0
mdurl 0.1.2
mistune 3.0.1
mkl 2021.1.1
mkl-devel 2021.1.1
mkl-include 2021.1.1
mock 5.0.2
more-itertools 8.10.0
mpmath 1.3.0
msgpack 1.0.5
multidict 6.0.4
murmurhash 1.0.9
mypy-extensions 1.0.0
nbclient 0.8.0
nbconvert 7.6.0
nbformat 5.9.0
nest-asyncio 1.5.6
networkx 2.6.3
ninja 1.11.1
notebook 6.4.10
numba 0.57.1+1.gf851d279c
numpy 1.22.2
nvidia-dali-cuda120 1.27.0
nvidia-pyindex 1.0.9
nvtx 0.2.5
oauthlib 3.2.2
ogb 1.3.6
onnx 1.14.0
opencv 4.7.0
optuna 3.2.0
outdated 0.2.2
packaging 23.1
pandas 1.5.2
pandocfilters 1.5.0
parso 0.8.3
partd 1.4.0
pathspec 0.11.1
pathy 0.10.2
pexpect 4.8.0
pickleshare 0.7.5
Pillow 9.2.0
pip 23.1.2
platformdirs 3.8.0
pluggy 1.2.0
ply 3.11
polygraphy 0.47.1
pooch 1.7.0
preshed 3.0.8
prettytable 3.8.0
prometheus-client 0.17.0
prompt-toolkit 3.0.39
protobuf 3.20.3
psutil 5.9.4
ptxcompiler 0.8.1+1.gb323413
ptyprocess 0.7.0
pure-eval 0.2.2
pyarrow 11.0.0
pyasn1 0.5.0
pyasn1-modules 0.3.0
pybind11 2.10.4
pycocotools 2.0+nv0.7.3
pycodestyle 2.10.0
pycparser 2.21
pydantic 1.10.11
pyflakes 3.0.1
pyg-lib 0.2.0
Pygments 2.15.1
PyGObject 3.42.1
PyJWT 2.3.0
pylibcugraph 23.6.0
pylibcugraphops 23.6.0
pylibraft 23.6.0
pynvml 11.4.1
pyparsing 3.0.9
pytest 7.4.0
pytest-cov 4.1.0
pytest-flakefinder 1.1.0
pytest-rerunfailures 12.0
pytest-shard 0.1.2
pytest-xdist 3.3.1
python-apt 2.4.0+ubuntu1
python-dateutil 2.8.2
python-hostlist 1.23.0
python-rapidjson 1.10
pytorch-quantization 2.1.2
pytz 2023.3
PyYAML 6.0
pyzmq 25.1.0
raft-dask 23.6.0
referencing 0.29.1
regex 2023.6.3
requests 2.31.0
requests-oauthlib 1.3.1
resampy 0.4.2
rmm 23.6.0
rpds-py 0.8.8
rsa 4.9
scikit-learn 1.2.0
scipy 1.11.0
SecretStorage 3.3.1
Send2Trash 1.8.2
setuptools 68.0.0
six 1.16.0
smart-open 6.3.0
sortedcontainers 2.4.0
soundfile 0.12.1
soupsieve 2.4.1
spacy 3.5.4
spacy-legacy 3.0.12
spacy-loggers 1.0.4
sphinx-glpi-theme 0.3
SQLAlchemy 2.0.18
srsly 2.4.6
stack-data 0.6.2
sympy 1.12
tabulate 0.9.0
tbb 2021.9.0
tblib 2.0.0
tensorboard 2.9.0
tensorboard-data-server 0.6.1
tensorboard-plugin-wit 1.8.1
tensorrt 8.6.1
terminado 0.17.1
thinc 8.1.10
threadpoolctl 3.1.0
thriftpy2 0.4.16
tinycss2 1.2.1
toml 0.10.2
tomli 2.0.1
toolz 0.12.0
torch 2.1.0a0+b5021ba
torch_geometric 2.4.0
torch-tensorrt 1.5.0.dev0
torchdata 0.7.0a0
torchmetrics 1.0.0
torchtext 0.16.0a0
torchvision 0.16.0a0
tornado 6.3.2
tqdm 4.65.0
traitlets 5.9.0
transformer-engine 0.10.0+96ed6fc
treelite 3.2.0
treelite-runtime 3.2.0
triton 2.1.0
tritonclient 2.35.0
typer 0.9.0
types-dataclasses 0.6.6
typing_extensions 4.7.0
ucx-py 0.32.0
uff 0.6.9
unattended-upgrades 0.1
urllib3 1.26.16
wadllib 1.3.6
wasabi 1.1.2
wcwidth 0.2.6
webencodings 0.5.1
Werkzeug 2.3.6
wget 3.2
wheel 0.40.0
xdoctest 1.0.2
xgboost 1.7.5
yarl 1.9.2
zict 3.0.0
zipp 3.15.0
zope.event 5.0
zope.interface 6.0
Please find the list as follows.
conda list
# packages in environment at /home/nanwu/anaconda3/envs/pytorch:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
blas 1.0 mkl
brotlipy 0.7.0 py39h27cfd23_1003
bzip2 1.0.8 h7b6447c_0
ca-certificates 2022.07.19 h06a4308_0
certifi 2022.6.15 py39h06a4308_0
cffi 1.15.1 py39h74dc2b5_0
charset-normalizer 2.0.4 pyhd3eb1b0_0
cryptography 37.0.1 py39h9ce1e76_0
cudatoolkit 11.3.1 h2bc3f7f_2
cycler 0.11.0 pypi_0 pypi
ffmpeg 4.3 hf484d3e_0 pytorch
fonttools 4.37.1 pypi_0 pypi
freetype 2.11.0 h70c0345_0
giflib 5.2.1 h7b6447c_0
gmp 6.2.1 h295c915_3
gnutls 3.6.15 he1e5248_0
idna 3.3 pyhd3eb1b0_0
intel-openmp 2021.4.0 h06a4308_3561
jinja2 3.1.2 pypi_0 pypi
joblib 1.1.0 pypi_0 pypi
jpeg 9e h7f8727e_0
kiwisolver 1.4.4 pypi_0 pypi
lame 3.100 h7b6447c_0
lcms2 2.12 h3be6417_0
ld_impl_linux-64 2.38 h1181459_1
lerc 3.0 h295c915_0
libdeflate 1.8 h7f8727e_5
libffi 3.3 he6710b0_2
libgcc-ng 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libiconv 1.16 h7f8727e_2
libidn2 2.3.2 h7f8727e_0
libpng 1.6.37 hbc83047_0
libstdcxx-ng 11.2.0 h1234567_1
libtasn1 4.16.0 h27cfd23_0
libtiff 4.4.0 hecacb30_0
libunistring 0.9.10 h27cfd23_0
libwebp 1.2.2 h55f646e_0
libwebp-base 1.2.2 h7f8727e_0
lz4-c 1.9.3 h295c915_1
markupsafe 2.1.1 pypi_0 pypi
matplotlib 3.5.3 pypi_0 pypi
mkl 2021.4.0 h06a4308_640
mkl-service 2.4.0 py39h7f8727e_0
mkl_fft 1.3.1 py39hd3c417c_0
mkl_random 1.2.2 py39h51133e4_0
mlxtend 0.20.0 pypi_0 pypi
ncurses 6.3 h5eee18b_3
nettle 3.7.3 hbbd107a_1
networkx 2.8.6 pypi_0 pypi
numpy 1.23.1 py39h6c91a56_0
numpy-base 1.23.1 py39ha15fc14_0
nvidia-ml-py3 7.352.0 pypi_0 pypi
openh264 2.1.1 h4ff587b_0
openssl 1.1.1q h7f8727e_0
packaging 21.3 pypi_0 pypi
pandas 1.4.4 pypi_0 pypi
pillow 9.2.0 py39hace64e9_1
pip 22.1.2 py39h06a4308_0
pycparser 2.21 pyhd3eb1b0_0
pyg-lib 0.2.0+pt112cu113 pypi_0 pypi
pyopenssl 22.0.0 pyhd3eb1b0_0
pyparsing 3.0.9 pypi_0 pypi
pysocks 1.7.1 py39h06a4308_0
python 3.9.13 haa1d7c7_1
python-dateutil 2.8.2 pypi_0 pypi
pytorch 1.12.1 py3.9_cuda11.3_cudnn8.3.2_0 pytorch
pytorch-mutex 1.0 cuda pytorch
pytz 2022.2.1 pypi_0 pypi
readline 8.1.2 h7f8727e_1
requests 2.28.1 py39h06a4308_0
scikit-learn 1.1.2 pypi_0 pypi
scipy 1.9.1 pypi_0 pypi
setuptools 63.4.1 py39h06a4308_0
six 1.16.0 pyhd3eb1b0_1
sqlite 3.39.2 h5082296_0
threadpoolctl 3.1.0 pypi_0 pypi
tk 8.6.12 h1ccaba5_0
torch-geometric 2.1.0.post1 pypi_0 pypi
torch-scatter 2.0.9 pypi_0 pypi
torch-sparse 0.6.15 pypi_0 pypi
torchaudio 0.12.1 py39_cu113 pytorch
torchvision 0.13.1 py39_cu113 pytorch
tqdm 4.64.1 pypi_0 pypi
typing_extensions 4.3.0 py39h06a4308_0
tzdata 2022a hda174b7_0
urllib3 1.26.11 py39h06a4308_0
wheel 0.37.1 pyhd3eb1b0_0
xz 5.2.5 h7f8727e_1
zlib 1.2.12 h7f8727e_2
zstd 1.5.2 ha4553b6_0@lydiawunan hopefully my recent change should allow your older environment to work. if you'd like to try the new code you can use https://developer.nvidia.com/pyg-container-early-access to get the latest nvidia container in early access
puririshi98
commented
1 year ago @lydiawunan anything else needed for merging?
lydiawunan
commented
1 year ago Thanks for the follow-up! Just merged the code and updated the readme accordingly.
on my 2 x a5000 desktop training gets 1.4x speedup inference gets 1.75x speedup