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CABLE-LSM / benchcab

Tool for evaluation of CABLE land surface model
https://benchcab.readthedocs.io/en/latest/
Apache License 2.0
2 stars 3 forks source link

pip install no longer works... #187

Open bschroeter opened 11 months ago

bschroeter commented 11 months ago

Just tried to install on Gadi for local development with pip install -e . in the root directory and get the following error:

(benchcab-dev) pip install -e .
Traceback (most recent call last):
  File "/g/data/v14/REDACTED/apps/miniconda3/envs/benchcab-dev/bin/pip", line 6, in <module>
    from pip._internal.cli.main import main
  File "/g/data/v14/REDACTED/apps/miniconda3/envs/benchcab-dev/lib/python3.9/site-packages/pip/_internal/cli/main.py", line 10, in <module>
    from pip._internal.cli.autocompletion import autocomplete
  File "/g/data/v14/REDACTED/apps/miniconda3/envs/benchcab-dev/lib/python3.9/site-packages/pip/_internal/cli/autocompletion.py", line 10, in <module>
    from pip._internal.cli.main_parser import create_main_parser
  File "/g/data/v14/REDACTED/apps/miniconda3/envs/benchcab-dev/lib/python3.9/site-packages/pip/_internal/cli/main_parser.py", line 9, in <module>
    from pip._internal.build_env import get_runnable_pip
  File "/g/data/v14/REDACTED/apps/miniconda3/envs/benchcab-dev/lib/python3.9/site-packages/pip/_internal/build_env.py", line 19, in <module>
    from pip._internal.cli.spinners import open_spinner
  File "/g/data/v14/REDACTED/apps/miniconda3/envs/benchcab-dev/lib/python3.9/site-packages/pip/_internal/cli/spinners.py", line 9, in <module>
    from pip._internal.utils.logging import get_indentation
  File "/g/data/v14/REDACTED/apps/miniconda3/envs/benchcab-dev/lib/python3.9/site-packages/pip/_internal/utils/logging.py", line 29, in <module>
    from pip._internal.utils.misc import ensure_dir
  File "/g/data/v14/REDACTED/apps/miniconda3/envs/benchcab-dev/lib/python3.9/site-packages/pip/_internal/utils/misc.py", line 43, in <module>
    from pip._internal.exceptions import CommandError, ExternallyManagedEnvironment
  File "/g/data/v14/REDACTED/apps/miniconda3/envs/benchcab-dev/lib/python3.9/site-packages/pip/_internal/exceptions.py", line 18, in <module>
    from pip._vendor.requests.models import Request, Response
  File "/g/data/v14/REDACTED/apps/miniconda3/envs/benchcab-dev/lib/python3.9/site-packages/pip/_vendor/requests/__init__.py", line 43, in <module>
    from pip._vendor import urllib3
  File "/g/data/v14/REDACTED/apps/miniconda3/envs/benchcab-dev/lib/python3.9/site-packages/pip/_vendor/urllib3/__init__.py", line 13, in <module>
    from .connectionpool import HTTPConnectionPool, HTTPSConnectionPool, connection_from_url
  File "/g/data/v14/REDACTED/apps/miniconda3/envs/benchcab-dev/lib/python3.9/site-packages/pip/_vendor/urllib3/connectionpool.py", line 12, in <module>
    from .connection import (
  File "/g/data/v14/REDACTED/apps/miniconda3/envs/benchcab-dev/lib/python3.9/site-packages/pip/_vendor/urllib3/connection.py", line 15, in <module>
    from .util.proxy import create_proxy_ssl_context
  File "/g/data/v14/REDACTED/apps/miniconda3/envs/benchcab-dev/lib/python3.9/site-packages/pip/_vendor/urllib3/util/__init__.py", line 8, in <module>
    from .ssl_ import (
  File "/g/data/v14/REDACTED/apps/miniconda3/envs/benchcab-dev/lib/python3.9/site-packages/pip/_vendor/urllib3/util/ssl_.py", line 17, in <module>
    from .url import BRACELESS_IPV6_ADDRZ_RE, IPV4_RE
ValueError: source code string cannot contain null bytes

Does a pip install no longer work? Is there a preferred method to install on Gadi?

SeanBryan51 commented 11 months ago

I was able to pip install successfully with module load conda && conda activate benchcab-dev && pip install --user .. Although from looking at your output, it looks like the location of your benchcab-dev environment is different to mine: when I run which python while the environment is activated, the which command outputs /scratch/tm70/sb8430/conda/envs/benchcab-dev/bin/python. It could be worth trying to setup the environment again - to create a custom conda environment I follow the instructions here.

bschroeter commented 11 months ago

Yes, you are correct. I do use a custom conda installation. However, I have never had any issues with it before. I'll see what I can do. Thanks for your help

bschroeter commented 11 months ago

I still had issues with this when installing from "base nothing" - I will put together a reproducible example of the failures and update this issue.