Stuck on an issue?

Lightrun Answers was designed to reduce the constant googling that comes with debugging 3rd party libraries. It collects links to all the places you might be looking at while hunting down a tough bug.

And, if you’re still stuck at the end, we’re happy to hop on a call to see how we can help out.

Memmap cannot use existing file handles

See original GitHub issue

I obtained Phy from the latest dev (2.0a0), and after clustering with spyking-circus, I get the error below.

I would so much appreciate some help!

(python3) segundo.martinez@pcl-imba-3:spyking-circus$ phy template-gui phy/params.py 
Traceback (most recent call last):
  File "/home/segundo.martinez/miniconda3/envs/python3/bin/phy", line 11, in <module>
    load_entry_point('phy', 'console_scripts', 'phy')()
  File "/home/segundo.martinez/miniconda3/envs/python3/lib/python3.5/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/home/segundo.martinez/miniconda3/envs/python3/lib/python3.5/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/home/segundo.martinez/miniconda3/envs/python3/lib/python3.5/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/segundo.martinez/miniconda3/envs/python3/lib/python3.5/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/segundo.martinez/miniconda3/envs/python3/lib/python3.5/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/home/segundo.martinez/miniconda3/envs/python3/lib/python3.5/site-packages/click/decorators.py", line 17, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/home/segundo.martinez/git/phy/phy/apps/__init__.py", line 112, in cli_template_gui
    template_gui(params_path)
  File "/home/segundo.martinez/git/phy/phy/apps/template/gui.py", line 829, in template_gui
    controller = TemplateController(**params)
  File "/home/segundo.martinez/git/phy/phy/apps/template/gui.py", line 87, in __init__
    self.model = TemplateModel(dat_path, **kwargs)
  File "/home/segundo.martinez/miniconda3/envs/python3/lib/python3.5/site-packages/phylib/io/model.py", line 193, in __init__
    self._load_data()
  File "/home/segundo.martinez/miniconda3/envs/python3/lib/python3.5/site-packages/phylib/io/model.py", line 217, in _load_data
    self.spike_samples = self._load_spike_samples()
  File "/home/segundo.martinez/miniconda3/envs/python3/lib/python3.5/site-packages/phylib/io/model.py", line 431, in _load_spike_samples
    return self._read_array(path)
  File "/home/segundo.martinez/miniconda3/envs/python3/lib/python3.5/site-packages/phylib/io/model.py", line 316, in _read_array
    return read_array(path).squeeze()
  File "/home/segundo.martinez/miniconda3/envs/python3/lib/python3.5/site-packages/phylib/io/model.py", line 43, in read_array
    return np.load(path, mmap_mode='r')
  File "/home/segundo.martinez/miniconda3/envs/python3/lib/python3.5/site-packages/numpy/lib/npyio.py", line 430, in load
    return format.open_memmap(file, mode=mmap_mode)
  File "/home/segundo.martinez/miniconda3/envs/python3/lib/python3.5/site-packages/numpy/lib/format.py", line 754, in open_memmap
    raise ValueError("Filename must be a string.  Memmap cannot use"
ValueError: Filename must be a string.  Memmap cannot use existing file handles.

Issue Analytics

State:
Created 4 years ago
Comments:6 (3 by maintainers)

Top GitHub Comments

1reaction

rossantcommented, May 31, 2019

are you able to do some quick and dirty debugging for me? Open /home/segundo.martinez/miniconda3/envs/python3/lib/python3.5/site-packages/phylib/io/model.py in a text editor, go to line 43, and replace the line by:

print(path)
return np.load(str(path), mmap_mode='r')

try again and send me the output. Thanks!

0reactions

JoseGuzmancommented, Jun 3, 2019

Hi @rossant ,

Thank you very much for your help!. It took me the whole weekend to play around this

I’ve just installed phylib and my conda environment moves from python3.5 to python3.7. The memory map issue is gone after updating to phylib. To run phy required only few updates (pyOpenGL, colorcet).

Thank you very much for your great assistance!

Top Results From Across the Web

Memmap cannot use existing file handles. #3143 - GitHub

ValueError: Filename must be a string. Memmap cannot use existing file handles. However, numpy.memmap is more than happy to work with files.

Filename must be a string or a path-like object. Memmap ...

Filename must be a string or a path-like object. Memmap cannot use existing file handles. Package: numpy logo numpy. github stars 18118. Exception...

python - Why isn't mmap closing associated file (getting ...

This will not close the open file. The memory mapping is independent of the file handle. You can use the file handle as...

numpy.memmap — NumPy v1.24 Manual

Create or overwrite existing file for reading and writing. 'c'. Copy-on-write: assignments affect data in memory, but changes are not saved to disk....

mmap — Memory-mapped file support — Python 3.11.1 ...

If you wish to map an existing Python file object, use its fileno() method ... from the file specified by the file handle...