prehensilecode / alphafold_singularity

Singularity recipe for AlphaFold
GNU General Public License v3.0
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`IsADirectoryError` when building image #13

Closed multimeric closed 1 year ago

multimeric commented 2 years ago

Hi. When I try to build the image from the .def file, the commands succeed until the following:

+ bash /tmp/Miniconda3-py37_4.12.0-Linux-x86_64.sh -b -p /opt/conda
PREFIX=/opt/conda
Unpacking payload ...
concurrent.futures.process._RemoteTraceback:
"""
Traceback (most recent call last):
  File "concurrent/futures/process.py", line 243, in _process_worker
  File "concurrent/futures/process.py", line 202, in _process_chunk
  File "concurrent/futures/process.py", line 202, in <listcomp>
  File "site-packages/conda_package_handling/api.py", line 58, in extract
  File "site-packages/conda_package_handling/conda_fmt.py", line 59, in extract
  File "site-packages/conda_package_handling/conda_fmt.py", line 40, in _extract_component
  File "zipfile.py", line 1616, in extract
  File "zipfile.py", line 1687, in _extract_member
IsADirectoryError: [Errno 21] Is a directory: '/opt/conda/pkgs/pysocks-1.7.1-py37_1u7jrvhn3/pkg-pysocks-1.7.1-py37_1.tar.zst'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "entry_point.py", line 69, in <module>
  File "concurrent/futures/process.py", line 559, in _chain_from_iterable_of_lists
  File "concurrent/futures/_base.py", line 608, in result_iterator
  File "concurrent/futures/_base.py", line 438, in result
  File "concurrent/futures/_base.py", line 390, in __get_result
IsADirectoryError: [Errno 21] Is a directory: '/opt/conda/pkgs/pysocks-1.7.1-py37_1u7jrvhn3/pkg-pysocks-1.7.1-py37_1.tar.zst'
[21356] Failed to execute script entry_point
prehensilecode commented 2 years ago

How much space do you have in your /tmp and/or build directory? The build process requires up to 15 GB.

Also, what version of Singularity or Apptainer are you using to build?