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Environment issues and some name inconsistency #2
Description
Dear authors,
Hi, when I install the environment by running 'conda env create -f env.yml', I got stuck in the 'solving environment' step of conda.
Could you check this step? I think something might be wrong here ~.
Also, there are some errors when I run the training code. Some places you name it cdvae but you use crystalvae to refer it in the pipeline.
Activity
txie-93 commentedon Jan 26, 2022
Thanks for reaching out @YKQ98
For the first question, it seems the step 'solving environment' is taking a very long time. But I was able to successfully install the conda packages after waiting several hours. I don't know why it takes so long to solve the environment though..
For the crystvae, these are some leftovers from the refactoring and sorry about that. They should be resolved in #1. Let me know if you have more errors after pulling the latest commits.
YKQ98 commentedon Jan 26, 2022
Thank you for the feedback!
Actually I manually installed all the packages needed and the code works fine.
sgbaird commentedon Jun 4, 2022
Seems like a good use-case for
mamba. @YKQ98 what did you run for installing the packages manually? Did you keep some of the requirements as concrete or convert them to abstract (unpinned) dependencies? I take it you probably used a two-step installation, one withcondaand a second command withpip. Is that the case?matminer>=0.7.3 instead of =0.7.3
sgbaird commentedon Jun 11, 2022
A more useful error message produced by
mamba:sgbaird commentedon Jun 12, 2022
My attempt at a manual install:
Also tried Lightning-AI/pytorch-lightning#7110 (comment):
Same error.
Tried installing with:
Failed via mamba, possibly due to issue with mamba and WSL (it wasn't working before with using `mamba` instead of `conda` above)
(cdvae) sgbaird@Dell-G7:~/GitHub/sparks-baird/cdvae$ mamba install -c conda-forge pytorch-lightning=1.5.10- python 3.9.*
- pytorch-lightning=1.5.10
- ca-certificates
- certifi
- openssl
- fsspec 2022.5.0 pyhd8ed1ab_0 conda-forge/noarch 98kB
- pydeprecate 0.3.2 pyhd8ed1ab_0 conda-forge/noarch 13kB
- torchmetrics 0.9.1 pyhd8ed1ab_0 conda-forge/noarch 200kB
- ca-certificates 2022.4.26 h06a4308_0 pkgs/main
- ca-certificates 2022.5.18.1 ha878542_0 conda-forge/linux-64 Cached
- pytorch-lightning 0.8.5 py_0 conda-forge
- pytorch-lightning 1.5.10 pyhd8ed1ab_0 conda-forge/noarch 308kB
- setuptools 61.2.0 py39h06a4308_0 pkgs/main
- setuptools 59.5.0 py39hf3d152e_0 conda-forge/linux-64 1MB
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█████████████████████████████████████████████████████████████
Looking for: ['pytorch-lightning=1.5.10']
pkgs/r/linux-64 No change
pkgs/r/noarch No change
pkgs/main/noarch No change
pkgs/main/linux-64 No change
conda-forge/noarch @ 1.5MB/s 5.8s
conda-forge/linux-64 @ 2.4MB/s 11.7s
Pinned packages:
Transaction
Prefix: /home/sgbaird/miniconda3/envs/cdvae
Updating specs:
Package Version Build Channel Size
─────────────────────────────────────────────────────────────────────────────────────
Install:
─────────────────────────────────────────────────────────────────────────────────────
Upgrade:
─────────────────────────────────────────────────────────────────────────────────────
Downgrade:
─────────────────────────────────────────────────────────────────────────────────────
Summary:
Install: 3 packages
Upgrade: 2 packages
Downgrade: 1 packages
Total download: 2MB
─────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n] Y
>>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<
$ /home/sgbaird/miniconda3/condabin/mamba install -c conda-forge pytorch-lightning=1.5.10environment variables:
CIO_TEST=
CONDA_DEFAULT_ENV=cdvae
CONDA_EXE=/home/sgbaird/miniconda3/bin/conda
CONDA_MKL_INTERFACE_LAYER_BACKUP=
CONDA_PREFIX=/home/sgbaird/miniconda3/envs/cdvae
CONDA_PREFIX_1=/home/sgbaird/miniconda3
CONDA_PROMPT_MODIFIER=(cdvae)
CONDA_PYTHON_EXE=/home/sgbaird/miniconda3/bin/python
CONDA_ROOT=/home/sgbaird/miniconda3
CONDA_SHLVL=2
CURL_CA_BUNDLE=
PATH=/home/sgbaird/.vscode-
server/bin/4af164ea3a06f701fe3e89a2bcbb421d2026b68f/bin/remote-cli:/ho
me/sgbaird/.local/bin:/home/sgbaird/miniconda3/envs/cdvae/bin:/home/sg
baird/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/us
r/bin:/sbin:/bin:/usr/games:/usr/local/games:/usr/lib/wsl/lib:/mnt/c/P
ython310/Scripts:/mnt/c/Python310:/mnt/c/Program Files/NVIDIA GPU
Computing Toolkit/CUDA/v11.2/bin:/mnt/c/Program Files/NVIDIA GPU
Computing Toolkit/CUDA/v11.2/libnvvp:/mnt/c/Windows/system32:/mnt/c/Wi
ndows:/mnt/c/Windows/System32/Wbem:/mnt/c/Windows/System32/WindowsPowe
rShell/v1.0:/mnt/c/Windows/System32/OpenSSH:/mnt/c/Program
Files/MATLAB/R2021a/runtime/win64:/mnt/c/Program
Files/MATLAB/R2021a/bin:/mnt/c/Program
Files/Git/cmd:/mnt/c/ProgramData/chocolatey/bin:/mnt/c/Program
Files/PuTTY:/mnt/c/Program Files (x86)/NVIDIA
Corporation/PhysX/Common:/mnt/c/Program Files/NVIDIA
Corporation/NVIDIA NvDLISR:/mnt/c/Program Files/NVIDIA
Corporation/Nsight Compute 2020.3.1:/mnt/c/WINDOWS/system32:/mnt/c/WIN
DOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPower
Shell/v1.0:/mnt/c/WINDOWS/System32/OpenSSH:/mnt/c/Program
Files/P403n1x87/Austin:/mnt/c/Program Files/dotnet:/mnt/c/Program
Files/Wolfram Research/WolframScript:/mnt/c/Program Files/nodejs:/mnt/
c/Ruby31-x64/bin:/mnt/c/Users/sterg/AppData/Local/Programs/Python/Pyth
on38/Scripts:/mnt/c/Users/sterg/AppData/Local/Programs/Python/Python38
:/mnt/c/Windows/system32:/mnt/c/Windows:/mnt/c/Windows/System32/Wbem:/
mnt/c/Windows/System32/WindowsPowerShell/v1.0:/mnt/c/Windows/System32/
OpenSSH:/mnt/c/Program Files/Wolfram
Research/WolframScript:/mnt/c/Program
Files/MATLAB/R2021a/runtime/win64:/mnt/c/Program
Files/MATLAB/R2021a/bin:/mnt/c/Program Files/Git/cmd:/mnt/c/Users/ster
g/AppData/Local/Microsoft/WindowsApps:/mnt/c/Users/sterg/AppData/Local
/atom/bin:/mnt/c/Users/sterg/AppData/Local/GitHubDesktop/bin:/mnt/c/Fu
llProf_Suite:/mnt/c/texlive/2021/bin/win32:/mnt/c/Users/sterg/AppData/
Local/Pandoc:/mnt/c/Users/sterg/AppData/Local/Programs/Microsoft VS
Code/bin:/mnt/c/Program Files/Graphviz/bin:/mnt/c/Users/sterg/AppData/
Local/Microsoft/WindowsApps:/mnt/c/Users/sterg/AppData/Local/Packages/
PythonSoftwareFoundation.Python.3.9_qbz5n2kfra8p0/LocalCache/local-pac
kages/Python39/Scripts:/mnt/c/Users/sterg/AppData/Roaming/Python/Scrip
ts:/mnt/c/Users/sterg/Miniconda3:/mnt/c/Users/sterg/Miniconda3/scripts
:/mnt/c/Users/sterg/Miniconda3/Library/bin:/mnt/c/Users/sterg/AppData/
Roaming/npm:/snap/bin
REQUESTS_CA_BUNDLE=
SSL_CERT_FILE=
populated config files :
conda version : 4.13.0
conda-build version : not installed
python version : 3.9.5.final.0
virtual packages : __linux=5.10.16.3=0
__glibc=2.31=0
__unix=0=0
__archspec=1=x86_64
base environment : /home/sgbaird/miniconda3 (writable)
conda av data dir : /home/sgbaird/miniconda3/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/conda-forge/linux-64
https://conda.anaconda.org/conda-forge/noarch
https://repo.anaconda.com/pkgs/main/linux-64
https://repo.anaconda.com/pkgs/main/noarch
https://repo.anaconda.com/pkgs/r/linux-64
https://repo.anaconda.com/pkgs/r/noarch
package cache : /home/sgbaird/miniconda3/pkgs
/home/sgbaird/.conda/pkgs
envs directories : /home/sgbaird/miniconda3/envs
/home/sgbaird/.conda/envs
platform : linux-64
user-agent : conda/4.13.0 requests/2.27.1 CPython/3.9.5 Linux/5.10.16.3-microsoft-standard-WSL2 ubuntu/20.04.2 glibc/2.31
UID:GID : 1000:1000
netrc file : None
offline mode : False
An unexpected error has occurred. Conda has prepared the above report.
Trying:
and it took maybe a few minutes to solve. It seems to be loading the CIF files now. (~30 min to load ~30k CIF files from string representation, so saving the pymatgen
Structureobjects directly would probably save some time, maybe not much compared to the time it takes to train though).sgbaird commentedon Jun 12, 2022
So, first making sure that I'm actually in the WSL storage, the following seems to work:
I'm running this in debugging mode with VS Code.
My
.envfile:and just in case, also set it in a custom launch file:
{ // Use IntelliSense to learn about possible attributes. // Hover to view descriptions of existing attributes. // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387 "version": "0.2.0", "configurations": [ { "name": "CDVAE MP-20", "type": "python", "request": "launch", "program": "${file}", "console": "integratedTerminal", "justMyCode": false, "args": [ "data=mp_20", "expname=mp_20" ], "env": { "PROJECT_ROOT": "/home/sgbaird/cdvae", "HYDRA_JOBS": "/home/sgbaird/hydra", "WABDB_DIR": "/home/sgbaird/wabdb" } } ] }sgbaird commentedon Jun 12, 2022
Still ran into an error eventually:
Seems related: https://discuss.pytorch.org/t/leaf-variable-was-used-in-an-inplace-operation/308
Not sure if there are notifications on the closed issue: @YKQ98 @txie-93
@YKQ98 might be worth opening back up, otherwise I can open a fresh issue, too.