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@sanjaysrikakulam sanjaysrikakulam commented Jul 27, 2025

@bgruening during testing found the following

root@sn09:/data/jwd05e/main/086/589/86589397$ cat galaxy_86589397.e
Could not find platform independent libraries <prefix>
Could not find platform dependent libraries <exec_prefix>
Python path configuration:
  PYTHONHOME = (not set)
  PYTHONPATH = '/opt/galaxy/server/lib:/opt/galaxy/server/lib/galaxy/jobs/rules'
  program name = 'python'
  isolated = 0
  environment = 1
  user site = 1
  safe_path = 0
  import site = 1
  is in build tree = 0
  stdlib dir = '/opt/miniconda/envs/_galaxy_/lib/python3.11'
  sys._base_executable = '/opt/miniconda/envs/_galaxy_/bin/python'
  sys.base_prefix = '/opt/miniconda/envs/_galaxy_'
  sys.base_exec_prefix = '/opt/miniconda/envs/_galaxy_'
  sys.platlibdir = 'lib'
  sys.executable = '/opt/galaxy/venv/bin/python'
  sys.prefix = '/opt/miniconda/envs/_galaxy_'
  sys.exec_prefix = '/opt/miniconda/envs/_galaxy_'
  sys.path = [
    '/opt/galaxy/server/lib',
    '/opt/galaxy/server/lib/galaxy/jobs/rules',
    '/opt/miniconda/envs/_galaxy_/lib/python311.zip',
    '/opt/miniconda/envs/_galaxy_/lib/python3.11',
    '/opt/miniconda/envs/_galaxy_/lib/python3.11/lib-dynload',
  ]
Fatal Python error: init_fs_encoding: failed to get the Python codec of the filesystem encoding
Python runtime state: core initialized
ModuleNotFoundError: No module named 'encodings'

Current thread 0x0000147227d48740 (most recent call first):
  <no Python frame>

This is because the /opt/miniconda/ is not available on the workers. The above shows references to the source where this Python is installed from (e.g., /opt/miniconda) and obviously this is not present on any worker nodes, so I switched it to use the /usr/local/tools/_conda.... and this is already an NFS share and is mounted on all the workers under the same path.

Xref:

  1. https://github.com/usegalaxy-eu/issues/issues/754
  2. WIP: add sn09 playbook and group vars #1575

@sanjaysrikakulam sanjaysrikakulam merged commit be8d196 into usegalaxy-eu:master Jul 27, 2025
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2 participants