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NVME purges break conda installations #598

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welucas2 opened this issue Apr 19, 2024 · 1 comment · Fixed by #599
Open

NVME purges break conda installations #598

welucas2 opened this issue Apr 19, 2024 · 1 comment · Fixed by #599
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@welucas2
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Every 24 hours a purge is run on all files on NVME which haven't been accessed for 28 days. When installing conda (confirmed with Anaconda and Miniconda) archives are extracted which preserve timestamps on critical files in the installation. These timestamps extend far enough into the past that within 24 hours of installing conda, large portions of the installation will automatically be deleted again, leaving a broken installation that produces errors of this kind when attempting to activate the base environment:

Could not find platform independent libraries <prefix>
Python path configuration:
  PYTHONHOME = (not set)
  PYTHONPATH = '/work/y07/shared/utils/core/bolt/0.8/modules'
  program name = '/mnt/lustre/a2fs-nvme/work/z19/z19/wlucas/opt/miniconda3/bin/python'
  isolated = 0
  environment = 1
  user site = 1
  safe_path = 0
  import site = 1
  is in build tree = 0
  stdlib dir = '/mnt/lustre/a2fs-nvme/work/z19/z19/wlucas/opt/miniconda3/lib/python3.12'
  sys._base_executable = '/mnt/lustre/a2fs-nvme/work/z19/z19/wlucas/opt/miniconda3/bin/python'
  sys.base_prefix = '/mnt/lustre/a2fs-nvme/work/z19/z19/wlucas/opt/miniconda3'
  sys.base_exec_prefix = '/mnt/lustre/a2fs-nvme/work/z19/z19/wlucas/opt/miniconda3'
  sys.platlibdir = 'lib'
  sys.executable = '/mnt/lustre/a2fs-nvme/work/z19/z19/wlucas/opt/miniconda3/bin/python'
  sys.prefix = '/mnt/lustre/a2fs-nvme/work/z19/z19/wlucas/opt/miniconda3'
  sys.exec_prefix = '/mnt/lustre/a2fs-nvme/work/z19/z19/wlucas/opt/miniconda3'
  sys.path = [
    '/work/y07/shared/utils/core/bolt/0.8/modules',
    '/mnt/lustre/a2fs-nvme/work/z19/z19/wlucas/opt/miniconda3/lib/python312.zip',
    '/mnt/lustre/a2fs-nvme/work/z19/z19/wlucas/opt/miniconda3/lib/python3.12',
    '/mnt/lustre/a2fs-nvme/work/z19/z19/wlucas/opt/miniconda3/lib/python3.12/lib-dynload',
  ]
Fatal Python error: init_fs_encoding: failed to get the Python codec of the filesystem encoding
Python runtime state: core initialized
LookupError: no codec search functions registered: can't find encoding

Current thread 0x00007fe7c3f3c740 (most recent call first):
  <no Python frame>

Our current documentation states that conda should be installed to NVME, but this clearly isn't workable at the moment as all installations will break within a day. For the time being we should remove this guidance and determine then provide an alternative.

@welucas2
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Replacement documentation proving conda installation guidance still required.

@welucas2 welucas2 reopened this Apr 24, 2024
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