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kad-ecoli / rna3db

maintain local copy of RNA structure database
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Unable to run e2efold #5

Closed marc-harary closed 4 years ago

marc-harary commented 4 years ago

I have cloned into the e2efold repo but when running the script in e2efold/experiment_rnastralign, I got the following error:


  File "/Users/marcharary/anaconda3/lib/python3.8/multiprocessing/spawn.py", line 116, in spawn_main
    exitcode = _main(fd, parent_sentinel)
  File "/Users/marcharary/anaconda3/lib/python3.8/multiprocessing/spawn.py", line 125, in _main
    prepare(preparation_data)
  File "/Users/marcharary/anaconda3/lib/python3.8/multiprocessing/spawn.py", line 236, in prepare
    _fixup_main_from_path(data['init_main_from_path'])
  File "/Users/marcharary/anaconda3/lib/python3.8/multiprocessing/spawn.py", line 287, in _fixup_main_from_path
    main_content = runpy.run_path(main_path,
  File "/Users/marcharary/anaconda3/lib/python3.8/runpy.py", line 265, in run_path
    return _run_module_code(code, init_globals, run_name,
  File "/Users/marcharary/anaconda3/lib/python3.8/runpy.py", line 97, in _run_module_code
    _run_code(code, mod_globals, init_globals,
  File "/Users/marcharary/anaconda3/lib/python3.8/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/Users/marcharary/Pyle/e2efold/experiment_rnastralign/e2e_learning_stage1.py", line 51, in <module>
    train_data = RNASSDataGenerator('../data/{}/'.format(data_type), 'train', True)
  File "/Users/marcharary/Pyle/e2efold/e2efold/data_generator.py", line 19, in __init__
    self.load_data()
  File "/Users/marcharary/Pyle/e2efold/e2efold/data_generator.py", line 24, in load_data
    p = Pool()
  File "/Users/marcharary/anaconda3/lib/python3.8/multiprocessing/context.py", line 119, in Pool
    return Pool(processes, initializer, initargs, maxtasksperchild,
  File "/Users/marcharary/anaconda3/lib/python3.8/multiprocessing/pool.py", line 212, in __init__
    self._repopulate_pool()
  File "/Users/marcharary/anaconda3/lib/python3.8/multiprocessing/pool.py", line 303, in _repopulate_pool
    return self._repopulate_pool_static(self._ctx, self.Process,
  File "/Users/marcharary/anaconda3/lib/python3.8/multiprocessing/pool.py", line 326, in _repopulate_pool_static
    w.start()
  File "/Users/marcharary/anaconda3/lib/python3.8/multiprocessing/process.py", line 121, in start
    self._popen = self._Popen(self)
  File "/Users/marcharary/anaconda3/lib/python3.8/multiprocessing/context.py", line 283, in _Popen
    return Popen(process_obj)
  File "/Users/marcharary/anaconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 32, in __init__
    super().__init__(process_obj)
  File "/Users/marcharary/anaconda3/lib/python3.8/multiprocessing/popen_fork.py", line 19, in __init__
    self._launch(process_obj)
  File "/Users/marcharary/anaconda3/lib/python3.8/multiprocessing/popen_spawn_posix.py", line 42, in _launch
    prep_data = spawn.get_preparation_data(process_obj._name)
  File "/Users/marcharary/anaconda3/lib/python3.8/multiprocessing/spawn.py", line 154, in get_preparation_data
    _check_not_importing_main()
  File "/Users/marcharary/anaconda3/lib/python3.8/multiprocessing/spawn.py", line 134, in _check_not_importing_main
    raise RuntimeError('''
RuntimeError: 
        An attempt has been made to start a new process before the
        current process has finished its bootstrapping phase.

        This probably means that you are not using fork to start your
        child processes and you have forgotten to use the proper idiom
        in the main module:

            if __name__ == '__main__':
                freeze_support()
                ...

        The "freeze_support()" line can be omitted if the program
        is not going to be frozen to produce an executable.```
kad-ecoli commented 4 years ago

You should not use e2efold/experiment_rnastralign, which runs e2efold on its own dataset called rnastralign. rnastralign is an extremely poorly design dataset. You should modify the scripts at https://github.com/ml4bio/e2efold/tree/master/e2efold_productive to run e2efold on your own dataset.