Issue with the Miniconda Docker image or using Conda in Singularity in general

[Bili Dong]

Hello all,

I'm writing to request some help on an issue I encountered that I couldn't solve by myself.

I'm using Singularity 2.4. To reproduce the error, do the following:

```

singularity shell docker://continuumio/miniconda3:4.3.27

```

then within Singularity, do:

```

python -c "import multiprocessing as mp; mp.Queue()"

```

which results in the following error:

```

Traceback (most recent call last):

  File "<string>", line 1, in <module>

  File "/opt/conda/lib/python3.6/multiprocessing/context.py", line 102, in Queue

    return Queue(maxsize, ctx=self.get_context())

  File "/opt/conda/lib/python3.6/multiprocessing/queues.py", line 42, in __init__

    self._rlock = ctx.Lock()

  File "/opt/conda/lib/python3.6/multiprocessing/context.py", line 67, in Lock

    return Lock(ctx=self.get_context())

  File "/opt/conda/lib/python3.6/multiprocessing/synchronize.py", line 163, in __init__

    SemLock.__init__(self, SEMAPHORE, 1, 1, ctx=ctx)

  File "/opt/conda/lib/python3.6/multiprocessing/synchronize.py", line 60, in __init__

    unlink_now)

FileNotFoundError: [Errno 2] No such file or directory

```

The same code would work inside a Docker container. So I expected it to work in the corresponding Singularity container too. But it doesn't.

Thanks very much for your time!

Best,

Bili

[Chris Gorgolewski]

This seems to be related: https://github.com/poldracklab/fmriprep/issues/780

Best,

Chris

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[Bili Dong]

Thanks Chris. This does look like the same issue.

Best,

Bili

Best,

Chris

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[Bili Dong]

So this is a known issue, and the current workaround is to add /run as a bind path, like this:

```

singularity shell -B /run docker://continuumio/miniconda3:4.3.27

```

See the following links for previous discussions:

https://groups.google.com/a/lbl.gov/forum/#!topic/singularity/71MhNumuMbs/discussion

https://github.com/singularityware/singularity/issues/875