Problem upgrading to 3.2.3

1

I was just trying to upgrade from 3.2.2 to 3.2.3. Thought it would be quick and easy but I ran into an error.

(as root) systemctl stop indico-celery.service
su - indico
source ~/.venv/bin/activate
export PATH=“$PATH:/usr/pgsql-13/bin”
pip install -U indico

things went fine then the error popped up:
.
.
.
Attempting uninstall: urllib3
Found existing installation: urllib3 1.26.12
Uninstalling urllib3-1.26.12:
Successfully uninstalled urllib3-1.26.12
Attempting uninstall: typing-extensions
Found existing installation: typing_extensions 4.4.0
Uninstalling typing_extensions-4.4.0:
Successfully uninstalled typing_extensions-4.4.0
Attempting uninstall: traitlets
Found existing installation: traitlets 5.5.0
Uninstalling traitlets-5.5.0:
Successfully uninstalled traitlets-5.5.0
Attempting uninstall: simplejson
Found existing installation: simplejson 3.17.6
Uninstalling simplejson-3.17.6:
Successfully uninstalled simplejson-3.17.6
ERROR: Could not install packages due to an OSError: [Errno 16] Device or resource busy: ‘.nfs000000005c193e62000003ba’

Should I just retry “pip install -U indico” or do something else? Thank you.

2

something is wrong with your NFS mount. but yes, simply retry

3

Retried and still getting that error:

  Attempting uninstall: prompt-toolkit
    Found existing installation: prompt-toolkit 3.0.32
    Uninstalling prompt-toolkit-3.0.32:
      Successfully uninstalled prompt-toolkit-3.0.32
  Attempting uninstall: pillow
    Found existing installation: Pillow 9.3.0
    Uninstalling Pillow-9.3.0:
      Successfully uninstalled Pillow-9.3.0
ERROR: Could not install packages due to an OSError: [Errno 16] Device or resource busy: '.nfs000000005c192fd30000047f'

The database and /opt/indico are on the NFS mount so I tried stopping more services before running the commands a third time.

systemctl stop httpd.service indico-celery.service indico-uwsgi.service
systemctl stop postgresql-13.service

This time there were a lot of Warnings but it looks like everything got installed.

Requirement already satisfied: setuptools in ./.venv/lib/python3.9/site-packages (from limits==3.2.0->indico) (67.0.0)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
Installing collected packages: packaging, ordered-set, mypy-extensions, mdurl, markupsafe, lxml, jedi, importlib-metadata, hiredis, greenlet, dnspython, bleach, attrs, asttokens, werkzeug, stack-data, sqlalchemy, marshmallow, markdown-it-py, mako, limits, jsonschema, cryptography, rich, marshmallow-dataclass, ipython, flask, authlib, alembic, flask-wtf, flask-limiter, flask-caching, flask-migrate, indico
  Attempting uninstall: packaging
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: packaging 21.3
    Uninstalling packaging-21.3:
      Successfully uninstalled packaging-21.3
  Attempting uninstall: mypy-extensions
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: mypy-extensions 0.4.3
    Uninstalling mypy-extensions-0.4.3:
      Successfully uninstalled mypy-extensions-0.4.3
  Attempting uninstall: markupsafe
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: MarkupSafe 2.1.1
    Uninstalling MarkupSafe-2.1.1:
      Successfully uninstalled MarkupSafe-2.1.1
  Attempting uninstall: lxml
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: lxml 4.9.1
    Uninstalling lxml-4.9.1:
      Successfully uninstalled lxml-4.9.1
  Attempting uninstall: jedi
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: jedi 0.18.1
    Uninstalling jedi-0.18.1:
      Successfully uninstalled jedi-0.18.1
  Attempting uninstall: importlib-metadata
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: importlib-metadata 5.0.0
    Uninstalling importlib-metadata-5.0.0:
      Successfully uninstalled importlib-metadata-5.0.0
  Attempting uninstall: hiredis
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: hiredis 2.0.0
    Uninstalling hiredis-2.0.0:
      Successfully uninstalled hiredis-2.0.0
  Attempting uninstall: greenlet
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: greenlet 2.0.1
    Uninstalling greenlet-2.0.1:
      Successfully uninstalled greenlet-2.0.1
  Attempting uninstall: dnspython
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: dnspython 2.2.1
    Uninstalling dnspython-2.2.1:
      Successfully uninstalled dnspython-2.2.1
  Attempting uninstall: bleach
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: bleach 5.0.1
    Uninstalling bleach-5.0.1:
      Successfully uninstalled bleach-5.0.1
  Attempting uninstall: attrs
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: attrs 22.1.0
    Uninstalling attrs-22.1.0:
      Successfully uninstalled attrs-22.1.0
  Attempting uninstall: asttokens
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: asttokens 2.1.0
    Uninstalling asttokens-2.1.0:
      Successfully uninstalled asttokens-2.1.0
  Attempting uninstall: werkzeug
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: Werkzeug 2.2.2
    Uninstalling Werkzeug-2.2.2:
      Successfully uninstalled Werkzeug-2.2.2
  Attempting uninstall: stack-data
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: stack-data 0.6.0
    Uninstalling stack-data-0.6.0:
      Successfully uninstalled stack-data-0.6.0
  Attempting uninstall: sqlalchemy
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: SQLAlchemy 1.4.43
    Uninstalling SQLAlchemy-1.4.43:
      Successfully uninstalled SQLAlchemy-1.4.43
  Attempting uninstall: marshmallow
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: marshmallow 3.18.0
    Uninstalling marshmallow-3.18.0:
      Successfully uninstalled marshmallow-3.18.0
  Attempting uninstall: mako
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: Mako 1.2.3
    Uninstalling Mako-1.2.3:
      Successfully uninstalled Mako-1.2.3
  Attempting uninstall: limits
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: limits 2.7.1
    Uninstalling limits-2.7.1:
      Successfully uninstalled limits-2.7.1
  Attempting uninstall: jsonschema
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: jsonschema 4.17.0
    Uninstalling jsonschema-4.17.0:
      Successfully uninstalled jsonschema-4.17.0
  Attempting uninstall: cryptography
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: cryptography 38.0.3
    Uninstalling cryptography-38.0.3:
      Successfully uninstalled cryptography-38.0.3
  Attempting uninstall: rich
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: rich 12.6.0
    Uninstalling rich-12.6.0:
      Successfully uninstalled rich-12.6.0
  Attempting uninstall: marshmallow-dataclass
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: marshmallow-dataclass 8.5.9
    Uninstalling marshmallow-dataclass-8.5.9:
      Successfully uninstalled marshmallow-dataclass-8.5.9
  Attempting uninstall: ipython
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: ipython 8.6.0
    Uninstalling ipython-8.6.0:
      Successfully uninstalled ipython-8.6.0
  Attempting uninstall: flask
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: Flask 2.2.2
    Uninstalling Flask-2.2.2:
      Successfully uninstalled Flask-2.2.2
  Attempting uninstall: authlib
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: Authlib 1.1.0
    Uninstalling Authlib-1.1.0:
      Successfully uninstalled Authlib-1.1.0
  Attempting uninstall: alembic
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: alembic 1.8.1
    Uninstalling alembic-1.8.1:
      Successfully uninstalled alembic-1.8.1
  Attempting uninstall: flask-wtf
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: Flask-WTF 1.0.1
    Uninstalling Flask-WTF-1.0.1:
      Successfully uninstalled Flask-WTF-1.0.1
  Attempting uninstall: flask-limiter
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: Flask-Limiter 2.7.0
    Uninstalling Flask-Limiter-2.7.0:
      Successfully uninstalled Flask-Limiter-2.7.0
  Attempting uninstall: flask-caching
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: Flask-Caching 2.0.1
    Uninstalling Flask-Caching-2.0.1:
      Successfully uninstalled Flask-Caching-2.0.1
  Attempting uninstall: flask-migrate
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: Flask-Migrate 3.1.0
    Uninstalling Flask-Migrate-3.1.0:
      Successfully uninstalled Flask-Migrate-3.1.0
  Attempting uninstall: indico
    WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
    Found existing installation: indico 3.2.2
    Uninstalling indico-3.2.2:
      Successfully uninstalled indico-3.2.2
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
Successfully installed alembic-1.9.4 asttokens-2.2.1 attrs-22.2.0 authlib-1.2.0 bleach-6.0.0 cryptography-39.0.1 dnspython-2.3.0 flask-2.2.3 flask-caching-2.0.2 flask-limiter-3.2.0 flask-migrate-4.0.4 flask-wtf-1.1.1 greenlet-2.0.2 hiredis-2.2.2 importlib-metadata-6.0.0 indico-3.2.3 ipython-8.10.0 jedi-0.18.2 jsonschema-4.17.3 limits-3.2.0 lxml-4.9.2 mako-1.2.4 markdown-it-py-2.2.0 markupsafe-2.1.2 marshmallow-3.19.0 marshmallow-dataclass-8.5.11 mdurl-0.1.2 mypy-extensions-1.0.0 ordered-set-4.1.0 packaging-23.0 rich-13.3.1 sqlalchemy-1.4.46 stack-data-0.6.2 werkzeug-2.2.3
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)
WARNING: Ignoring invalid distribution -illow (/opt/indico/.venv/lib/python3.9/site-packages)

[notice] A new release of pip is available: 23.0 -> 23.0.1
[notice] To update, run: pip install --upgrade pip

Python itself seems fine:

indico setup upgrade-python
updating pyenv
Already running on preferred version (3.9.16)

Do you know what the warnings mean? Is Indico messed up or still okay to use? The site does come up after the services are started. Thanks.

4

ERROR: Could not install packages due to an OSError: [Errno 16] Device or resource busy: '.nfs000000005c192fd30000047f'

I think it’s pretty clear that there’s something wrong with your NFS-based setup. None of us will be able to help you debug this besides making guesses.

My recommendation would be a rm -rf ~/.venv and then recreating the venv and pip install indico in there again. Anything important (config etc) isn’t within the venv anyway.

PS: It’s quite strange to have the venv on a network share. Since it’s completely disposable (unlike config files or attachments or possibly logs) it’d make more sense to have it locally.

5

These directories were inside /opt/indico/.venv/lib/python3.9/site-packages.

~illow-9.3.0.dist-info
~illow.libs
~implejson

They might have been left behind due to the NFS errors and caused the warning messages so I deleted them.

Thank you for your help.