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[Errno 28] No space left on device when importing SigProfilerExtractor

See original GitHub issue

Issue Description

Hi,

I ran across this error when importing SigProfilerExtractor

>>> from SigProfilerExtractor import sigpro as sig /home/hannan/anaconda3/lib/python3.7/site-packages/joblib/_multiprocessing_helpers.py:53: UserWarning: [Errno 28] No space left on device. joblib will operate in serial mode warnings.warn('%s. joblib will operate in serial mode' % (e,))

I checked both the memory and disk space and there is sufficient memory on both of them.

Screenshot from 2021-09-20 11-37-30

Here is the traceback when I tried to run the tool

Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/hannan/anaconda3/lib/python3.7/site-packages/SigProfilerExtractor/sigpro.py", line 823, in sigProfilerExtractor i = i) File "/home/hannan/anaconda3/lib/python3.7/site-packages/SigProfilerExtractor/subroutines.py", line 789, in decipher_signatures results = parallel_runs(excecution_parameters, genomes=genomes, totalProcesses=totalProcesses, verbose = False) File "/home/hannan/anaconda3/lib/python3.7/site-packages/SigProfilerExtractor/subroutines.py", line 685, in parallel_runs pool = multiprocessing.Pool() File "/home/hannan/anaconda3/lib/python3.7/multiprocessing/context.py", line 119, in Pool context=self.get_context()) File "/home/hannan/anaconda3/lib/python3.7/multiprocessing/pool.py", line 158, in __init__ self._setup_queues() File "/home/hannan/anaconda3/lib/python3.7/multiprocessing/pool.py", line 251, in _setup_queues self._inqueue = self._ctx.SimpleQueue() File "/home/hannan/anaconda3/lib/python3.7/multiprocessing/context.py", line 112, in SimpleQueue return SimpleQueue(ctx=self.get_context()) File "/home/hannan/anaconda3/lib/python3.7/multiprocessing/queues.py", line 332, in __init__ self._rlock = ctx.Lock() File "/home/hannan/anaconda3/lib/python3.7/multiprocessing/context.py", line 67, in Lock return Lock(ctx=self.get_context()) File "/home/hannan/anaconda3/lib/python3.7/multiprocessing/synchronize.py", line 162, in __init__ SemLock.__init__(self, SEMAPHORE, 1, 1, ctx=ctx) File "/home/hannan/anaconda3/lib/python3.7/multiprocessing/synchronize.py", line 59, in __init__ unlink_now) OSError: [Errno 28] No space left on device

I was wondering if this error could be coming from the SigProfiler package or from the joblib/multiprocessing package? Any suggestions/insights would be much appreciated, thanks!

Warmest regards, Hannan

Issue Analytics

  • State:closed
  • Created a year ago
  • Comments:6

github_iconTop GitHub Comments

1reaction
hannanwcommented, Sep 24, 2021

Hi Marcos,

Thanks! That suggestion worked, I am able to import and run SigProfilerExtractor now without issue.

Warmest regards, Hannan

0reactions
marcos-diazgcommented, Sep 23, 2021

Hi again Hannan!

Please have a look at the first answer here. That should solve your issue since it seems that your /dev/shm is full. Hope that helps.

Best wishes,

Marcos

Read more comments on GitHub >

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