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neuronets / kwyk

Knowing what you know - Bayesian brain parcellation
https://doi.org/10.3389/fninf.2019.00067
Apache License 2.0
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the kwyk container with master-gpu tag has errors #33

Open Hoda1394 opened 2 years ago

Hoda1394 commented 2 years ago

when running the container with the master-gpu tag, I am getting the TensorFlow import error.

command: singularity run -B $(pwd):/data -W /data kwyk_master-gpu.sif --help

error:

Traceback (most recent call last):
  File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
    from tensorflow.python.pywrap_tensorflow_internal import *
  File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
    _pywrap_tensorflow_internal = swig_import_helper()
  File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
    _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
  File "/usr/lib/python3.5/imp.py", line 242, in load_module
    return load_dynamic(name, filename, file)
  File "/usr/lib/python3.5/imp.py", line 342, in load_dynamic
    return _load(spec)
ImportError: libcuda.so.1: cannot open shared object file: No such file or directory

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/lib/python3.5/dist-packages/nobrainer/__init__.py", line 9, in <module>
    import tensorflow
  File "/usr/local/lib/python3.5/dist-packages/tensorflow/__init__.py", line 24, in <module>
    from tensorflow.python import pywrap_tensorflow  # pylint: disable=unused-import
  File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/__init__.py", line 49, in <module>
    from tensorflow.python import pywrap_tensorflow
  File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/pywrap_tensorflow.py", line 74, in <module>
    raise ImportError(msg)
ImportError: Traceback (most recent call last):
  File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/pywrap_tensorflow.py", line 58, in <module>
    from tensorflow.python.pywrap_tensorflow_internal import *
  File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 28, in <module>
    _pywrap_tensorflow_internal = swig_import_helper()
  File "/usr/local/lib/python3.5/dist-packages/tensorflow/python/pywrap_tensorflow_internal.py", line 24, in swig_import_helper
    _mod = imp.load_module('_pywrap_tensorflow_internal', fp, pathname, description)
  File "/usr/lib/python3.5/imp.py", line 242, in load_module
    return load_dynamic(name, filename, file)
  File "/usr/lib/python3.5/imp.py", line 342, in load_dynamic
    return _load(spec)
ImportError: libcuda.so.1: cannot open shared object file: No such file or directory

Failed to load the native TensorFlow runtime.

See https://www.tensorflow.org/install/errors

for some common reasons and solutions.  Include the entire stack trace
above this error message when asking for help.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/usr/local/bin/kwyk", line 33, in <module>
    sys.exit(load_entry_point('kwyk', 'console_scripts', 'kwyk')())
  File "/usr/local/bin/kwyk", line 25, in importlib_load_entry_point
    return next(matches).load()
  File "/usr/local/lib/python3.5/dist-packages/importlib_metadata/__init__.py", line 105, in load
    module = import_module(match.group('module'))
  File "/usr/lib/python3.5/importlib/__init__.py", line 126, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "<frozen importlib._bootstrap>", line 986, in _gcd_import
  File "<frozen importlib._bootstrap>", line 969, in _find_and_load
  File "<frozen importlib._bootstrap>", line 958, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 673, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 665, in exec_module
  File "<frozen importlib._bootstrap>", line 222, in _call_with_frames_removed
  File "/opt/kwyk/kwyk/cli.py", line 10, in <module>
    from nobrainer.predict import _get_predictor
  File "/usr/local/lib/python3.5/dist-packages/nobrainer/__init__.py", line 12, in <module>
    "TensorFlow cannot be found. Please re-install nobrainer with either"
ImportError: TensorFlow cannot be found. Please re-install nobrainer with either the [cpu] or [gpu] extras, or install TensorFlow separately. Please see https://www.tensorflow.org/install/ for installation instructions.
satra commented 2 years ago

don't you need --nv to run the gpu version?