"leaked semaphore" error when running voila

[Max Ferretti]

Hello, 

I have installed Majiq on a Mac (OSX 11 Big Sur) and can run voila -v to get the version, but when I try to use view, I get an error.

I have a previous version of majiq/voila installed on another computer running Ubuntu I can open/view these files just fine with that version, so I do not think the problem is with the files themselves.

Any advice is appreciated!

Here's the error:

(majiq_env) tamannas@modv-ve703-01167 MAJIQ_09162021 % voila view splicegraph.sql WT_TAOall_KD_TAOall.deltapsi.voila 

2021-10-07 11:19:48,128 (PID:4425) - INFO - Command: /Users/tamannas/opt/anaconda3/envs/majiq_env/bin/voila view splicegraph.sql WT_TAOall_KD_TAOall.deltapsi.voila

2021-10-07 11:19:48,128 (PID:4425) - INFO - Voila v2.2.0

2021-10-07 11:19:48,128 (PID:4425) - INFO - config file: /var/folders/vw/qwm8whvd6v1586xgyytn34dw0000gq/T/tmpprzdaz5f

2021-10-07 11:19:48,134 (PID:4425) - INFO - Creating index: /Users/tamannas/Documents/Rotations/MAJIQ_09162021/WT_TAOall_KD_TAOall.deltapsi.voila

Indexing LSV IDs: 0 / 59879

2021-10-07 11:19:51,851 (PID:4425) - INFO - Writing index: /Users/tamannas/Documents/Rotations/MAJIQ_09162021/WT_TAOall_KD_TAOall.deltapsi.voila

2021-10-07 11:19:51,852 (PID:4425) - ERROR - 'FILES'

multiprocessing.pool.RemoteTraceback: 

"""

Traceback (most recent call last):

  File "/Users/tamannas/opt/anaconda3/envs/majiq_env/lib/python3.8/multiprocessing/pool.py", line 125, in worker

    result = (True, func(*args, **kwds))

  File "/Users/tamannas/opt/anaconda3/envs/majiq_env/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar

    return list(map(*args))

  File "/Users/tamannas/opt/anaconda3/envs/majiq_env/lib/python3.8/site-packages/rna_voila/index.py", line 242, in _deltapsi_pool_add_index

    with ViewDeltaPsi() as m:

  File "/Users/tamannas/opt/anaconda3/envs/majiq_env/lib/python3.8/site-packages/rna_voila/api/view_matrix.py", line 434, in __init__

    self.config = ViewConfig()

  File "/Users/tamannas/opt/anaconda3/envs/majiq_env/lib/python3.8/site-packages/rna_voila/config.py", line 303, in __new__

    'voila_files': config_parser['FILES']['voila'].split('\n'),

  File "/Users/tamannas/opt/anaconda3/envs/majiq_env/lib/python3.8/configparser.py", line 960, in __getitem__

    raise KeyError(key)

KeyError: 'FILES'

"""

 

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

 

Traceback (most recent call last):

  File "/Users/tamannas/opt/anaconda3/envs/majiq_env/lib/python3.8/site-packages/rna_voila/run_voila.py", line 346, in main

    args.func()

  File "/Users/tamannas/opt/anaconda3/envs/majiq_env/lib/python3.8/site-packages/rna_voila/view/views.py", line 78, in run_service

    run_app = get_app()

  File "/Users/tamannas/opt/anaconda3/envs/majiq_env/lib/python3.8/site-packages/rna_voila/view/views.py", line 102, in get_app

    Index()

  File "/Users/tamannas/opt/anaconda3/envs/majiq_env/lib/python3.8/site-packages/rna_voila/index.py", line 49, in __init__

    index()

  File "/Users/tamannas/opt/anaconda3/envs/majiq_env/lib/python3.8/site-packages/rna_voila/index.py", line 316, in _deltapsi

    voila_index = voila_index.get()

  File "/Users/tamannas/opt/anaconda3/envs/majiq_env/lib/python3.8/multiprocessing/pool.py", line 771, in get

    raise self._value

KeyError: 'FILES'

(majiq_env) tamannas@modv-ve703-01167 MAJIQ_09162021 % /Users/tamannas/opt/anaconda3/envs/majiq_env/lib/python3.8/multiprocessing/resource_tracker.py:216: UserWarning: resource_tracker: There appear to be 7 leaked semaphore objects to clean up at shutdown

  warnings.warn('resource_tracker: There appear to be %d '

[Paul Jewell]

Hello Max,

I've noticed some versions of OSX / conda have some kind of issue with python's multithreading. (Multiprocessing)

Could you please try to run the program with the argument " -j 1 " to disable the multiprocessing?

Thanks!

[Max Ferretti]

This worked great, thanks so much!