Unable to open database file in parallel running of verification experiment

[Saeed Sarfjoo]

Hi Everyone,

For running the verification experiment with the mobio-audio-male dataset with the following command:

verify.py -d mobio-audio-male -p mod-4hz -e mfcc-60 -a gmm -s ubm_gmm_local --groups {dev,eval} --parallel 4 -vv --temp-directory /[address]/mobio/temp --result-directory /[address]/mobio/result

I got the following error:

 -- ERROR: During the execution, an exception was raised: (sqlite3.OperationalError) unable to open database file

Traceback (most recent call last):

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 2147, in _wrap_pool_connect

    return fn()

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/pool.py", line 387, in connect

    return _ConnectionFairy._checkout(self)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/pool.py", line 766, in _checkout

    fairy = _ConnectionRecord.checkout(pool)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/pool.py", line 516, in checkout

    rec = pool._do_get()

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/pool.py", line 1229, in _do_get

    return self._create_connection()

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/pool.py", line 333, in _create_connection

    return _ConnectionRecord(self)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/pool.py", line 461, in __init__

    self.__connect(first_connect_check=True)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/pool.py", line 651, in __connect

    connection = pool._invoke_creator(self)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/engine/strategies.py", line 105, in connect

    return dialect.connect(*cargs, **cparams)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/engine/default.py", line 393, in connect

    return self.dbapi.connect(*cargs, **cparams)

sqlite3.OperationalError: unable to open database file

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

Traceback (most recent call last):

  File "/bob/envs/v300py36/bin/verify.py", line 6, in <module>

    sys.exit(bob.bio.base.script.verify.main())

  File "/bob/envs/v300py36/lib/python3.6/site-packages/bob/bio/base/script/verify.py", line 435, in main

    verify(args, command_line_parameters)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/bob/bio/base/script/verify.py", line 388, in verify

    retval = add_jobs(args, submitter)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/bob/bio/base/script/verify.py", line 65, in add_jobs

    **args.grid.preprocessing_queue)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/bob/bio/base/tools/grid.py", line 108, in submit

    **kwargs

  File "/bob/envs/v300py36/lib/python3.6/site-packages/gridtk/local.py", line 48, in submit

    self.lock()

  File "/bob/envs/v300py36/lib/python3.6/site-packages/gridtk/manager.py", line 80, in lock

    self._create()

  File "/bob/envs/v300py36/lib/python3.6/site-packages/gridtk/manager.py", line 105, in _create

    Base.metadata.create_all(self._engine)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/sql/schema.py", line 3885, in create_all

    tables=tables)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 1928, in _run_visitor

    with self._optional_conn_ctx_manager(connection) as conn:

  File "/bob/envs/v300py36/lib/python3.6/contextlib.py", line 81, in __enter__

    return next(self.gen)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 1921, in _optional_conn_ctx_manager

    with self.contextual_connect() as conn:

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 2112, in contextual_connect

    self._wrap_pool_connect(self.pool.connect, None),

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 2151, in _wrap_pool_connect

    e, dialect, self)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 1465, in _handle_dbapi_exception_noconnection

    exc_info

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/util/compat.py", line 203, in raise_from_cause

    reraise(type(exception), exception, tb=exc_tb, cause=cause)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/util/compat.py", line 186, in reraise

    raise value.with_traceback(tb)

  File "/idiap/resource/software/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 2147, in _wrap_pool_connect

    return fn()

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/pool.py", line 387, in connect

    return _ConnectionFairy._checkout(self)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/pool.py", line 766, in _checkout

    fairy = _ConnectionRecord.checkout(pool)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/pool.py", line 516, in checkout

    rec = pool._do_get()

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/pool.py", line 1229, in _do_get

    return self._create_connection()

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/pool.py", line 333, in _create_connection

    return _ConnectionRecord(self)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/pool.py", line 461, in __init__

    self.__connect(first_connect_check=True)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/pool.py", line 651, in __connect

    connection = pool._invoke_creator(self)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/engine/strategies.py", line 105, in connect

    return dialect.connect(*cargs, **cparams)

  File "/bob/envs/v300py36/lib/python3.6/site-packages/sqlalchemy/engine/default.py", line 393, in connect

    return self.dbapi.connect(*cargs, **cparams)

sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) unable to open database file

I have the same problem when I run the experiment on SGE grid. The experiment was run on the v300py36 conda environment.  When I removed the --parallel 4 from the commands, the experiment can start running without any problem:

bob.bio.base@2018-04-09 09:35:21,706 -- INFO: - Preprocessing: processing 13924 data files from directory '/mobio/AUDIO_16k/' to directory '[address]/mobio/temp/ubm_gmm_local/preprocessed'

bob.bio.spear@2018-04-09 09:35:25,587 -- INFO: After Mod-4Hz based VAD there are 572 frames remaining over 1259

bob.bio.spear@2018-04-09 09:35:25,919 -- INFO: After Mod-4Hz based VAD there are 681 frames remaining over 1788

bob.bio.spear@2018-04-09 09:35:26,271 -- INFO: After Mod-4Hz based VAD there are 614 frames remaining over 1340

bob.bio.spear@2018-04-09 09:35:26,596 -- INFO: After Mod-4Hz based VAD there are 520 frames remaining over 1709

...

The .bob_bio_databases.txt file in the home directory contains the address to the /mobio/AUDIO_16k wav directory. The experiment was run on Debian8 x64 system. Any help would be appreciated.

Thanks in advance,

Saeed

[Amir Mohammadi]

Hi Saeed,

Your error is not about the .bob_bio_databases.txt file.

You probably have a broken file (or folder) named submitted.sql3

try to delete that first.

Thanks,

Amir

--
-- You received this message because you are subscribed to the Google Groups bob-devel group. To post to this group, send email to bob-...@googlegroups.com. To unsubscribe from this group, send email to bob-devel+...@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/bob-devel or directly the project website at http://idiap.github.com/bob/
---
You received this message because you are subscribed to the Google Groups "bob-devel" group.
To unsubscribe from this group and stop receiving emails from it, send an email to bob-devel+...@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Saeed Sarfjoo]

Hi Amir,

Thanks for answering. The problem was on writing permission for creating temp sql3 file.

Regards,
Saeed