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jbjorne / TEES

Turku Event Extraction System
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Does -c PBS option in train.py actually work? #18

Closed ngiordani closed 7 years ago

ngiordani commented 8 years ago

I tried to use this option with value PBS, as documented here, but I got an error:

New local connection connection=PBS:debug=False Traceback (most recent call last): File "train.py", line 502, in connection=options.connection, subset=options.subset, folds=options.folds) File "train.py", line 86, in train connection = getConnection(connection) File "/juicier/scr107/scr/natalias/TEES/TEES/Utils/Connection/Connection.py", line 31, in getConnection exec "ConnectionClass = " + connection["connection"] + "Connection" File "", line 1, in NameError: name 'PBSConnection' is not defined

Looking at the code in Util.Connections.Connection, it doesn't seem like this value receives any special handling. I'm wondering if this can be expected to work and whether there is an easy fix that will get in working.

jbjorne commented 8 years ago

Unfortunately, the cluster where I used PBS has been replaced with a newer one using SLURM, so I cannot test the PBS code anymore. However, it might be possible that the old PBS code still works, or at least it would be possible to get it working again.

To test the connection, first you need to add the "from PBSConnection import PBSConnection" line to Utils.Connection.Connection. Then, you may need to update the PBSConnection class to work with your PBS environment. Running the connection with "debug=True" may be helpful if it doesn't work. I think it was working when I last used it, but that was several years ago, and I have no idea how similar PBS environments on different clusters are.