[developers] Trouble Seeing Test Suite Instances

CLMS help (David Brodbeck) linghelp at uw.edu
Tue Sep 9 01:39:19 CEST 2014 

It's probably an AppArmor problem.  I thought I'd disabled it in recent
builds but it may not have worked.  If you're comfortable changing kernel
boot parameters, try adding 'apparmor=0' and see if that helps.

On Mon, Sep 8, 2014 at 3:02 PM, Emily M. Bender <ebender at uw.edu> wrote:

> [Again, adding developers back to the cc.]
>
> Joshua, I think you just established that there's nothing wrong with the
> skeleton, but that's not too surprising.  The problem seems to be with
> [incr tsdb()]'s ability to "see" certain directories on the UbuntuLKB
> distro.  I'm cc-ing David B. in the hopes that he might have some time to
> look at this with Alec and/or some ideas.
>
> Emily
>
>
>
>
> On Sun, Sep 7, 2014 at 9:33 AM, Alexander Sugar <sugara at uw.edu> wrote:
>
>> Joshua,
>>
>>      Somehow in updating my VirtualBox, I lost previous test suite
>> instances. If I point my database root at the opt/delphin/... path
>> that's set as a default, I am able to see those profiles in the podium
>> after I create them (and I get the same "unable to write history file
>> message", so that's definitely not the issue).
>>
>>     I'm using version 2.0 (16-jun-13; beta) of [incr tsdb()] on UbuntuLKB
>> 17.
>>
>> - Alec
>>
>> On 9/6/14, Joshua Crowgey <jcrowgey at u.washington.edu> wrote:
>> > Hi Alec,
>> >
>> > I doubt that .tsdb_history is the issue.  In Unix-like systems, many
>> > programs will store config info or other user-settings in files that
>> > start with "." in the user's home directory.  If you say (in a shell):
>> >
>> > $ ls -la ~/
>> >
>> > You'll see several such files, probably at least .emacs, .bashrc.  In my
>> > own system, I suppose that .tsdb_history stores your tsdb commands so
>> > that (maybe?) you can press "up" and see the previous command, or
>> > something like that.  I found a .tsdb_history with these lines:
>> >
>> > jcrowgey at citrus:~$ cat .tsdb_history
>> > do "/tmp/.tsdb.io.jcrowgey.11333.118378".
>> > do "/tmp/.tsdb.io.jcrowgey.11333.118384".
>> >
>> > Because I've restarted my system since I last used tsdb, the /tmp
>> > directory has been cleared and I'm not sure what was in those
>> > /tmp/.tsdb.io.jcrowgey.* files.   My guess is those were a record of my
>> > sessions this morning when I was playing around with your item and
>> > relations files.
>> >
>> > Anyway, the fact that the files were created is interesting, I think.
>> > It suggests that tsdb can create the new files, but we still don't know
>> > why it can't read those files and display them in the podium.
>> >
>> > This makes me thing of another troubleshooting/debugging test.  Can you
>> > see other existing testsuite instances?  That is, if you already had a
>> > profile with results and such, and you point your database root at that
>> > dir, do those profiles show up in the podium?
>> >
>> > Sorry I don't really have good answers for you.  I just thought I'd jump
>> > in and give you some stuff to try out.  By the way, are you using the
>> > knoppix+lkb distro?  What are the details of your platform?
>> >
>> > --Joshua
>> >
>> > On 09/06/2014 05:53 PM, Alexander Sugar wrote:
>> >> Hi Joshua,
>> >>
>> >>       I think the reason I didn't see anything printed out in emacs
>> >> was because I had previously 'created' an instance. When I cleared out
>> >> the files inside of the home folder, I saw the same lines printed as
>> >> you, except in the end:
>> >>
>> >> initialize(): creating empty data file for `score'.
>> >> main(): no history file `.tsdb_history'.
>> >>
>> >> And of course no instance showed up in the podium. I'm guessing the
>> >> '.tsdb_history' line is the source of the problem. Is there a quick
>> >> fix for it? If so, that's great but I'm sorry to have put you through
>> >> so much trouble just now...
>> >>
>> >> - Alec
>> >>
>> >> On 9/6/14, Joshua Crowgey <jcrowgey at u.washington.edu> wrote:
>> >>> Hi Alec,
>> >>>
>> >>> I put your item and relations files into a dir and pointed my itsdb at
>> >>> them and as far as I can tell, they loaded without a problem---ie,
>> tsdb
>> >>> was able to create a new instance and I see it appear in the podium
>> >>> window.
>> >>>
>> >>> As to stderr, I think if you start tsdb in emacs then all of the
>> >>> messages get printed there.  When I click to create a new instance of
>> >>> your item and relations files, I see:
>> >>>
>> >>> LKB(2): initialize(): creating empty data file for `analysis'.
>> >>> initialize(): creating empty data file for `phenomenon'.
>> >>> initialize(): creating empty data file for `parameter'.
>> >>> initialize(): creating empty data file for `set'.
>> >>> initialize(): creating empty data file for `item-phenomenon'.
>> >>> initialize(): creating empty data file for `item-set'.
>> >>> initialize(): creating empty data file for `run'.
>> >>> initialize(): creating empty data file for `parse'.
>> >>> initialize(): creating empty data file for `result'.
>> >>> initialize(): creating empty data file for `rule'.
>> >>> initialize(): creating empty data file for `output'.
>> >>> initialize(): creating empty data file for `edge'.
>> >>> initialize(): creating empty data file for `tree'.
>> >>> initialize(): creating empty data file for `decision'.
>> >>> initialize(): creating empty data file for `preference'.
>> >>> initialize(): creating empty data file for `update'.
>> >>> initialize(): creating empty data file for `fold'.
>> >>> initialize(): creating empty data file for `score'.
>> >>> close-connection():
>> >>> `/home/jcrowgey/Desktop/alexsugar/tsdb/anonymous/alex/14-09-06/lkb1/'
>> >>> expiry
>> >>>
>> >>> You don't see anything happening there, eh?  I'm not sure it would
>> help,
>> >>> but it might be interesting to try this:
>> >>>
>> >>> Since all the tsdb instance is (before you use it) is just a set of
>> >>> empty files + copies of the item and relations files, you could simply
>> >>> make the instance yourself on the command line and then see if tsdb
>> can
>> >>> recognize and already created one.  Perhaps this would give a clue as
>> to
>> >>> whether the issue is in creating files or if reading files is affected
>> >>> too.
>> >>>
>> >>> I think the usual directory structure is:
>> >>>
>> >>> $DATABASEROOT/NAME_OF_GRAMMAR/NAME_OF_TS/DATE/lkb/
>> >>>
>> >>> Then, inside that final dir, you just put a copy of item and relations
>> >>> plus empty files with the following names:
>> >>>
>> >>> jcrowgey at citrus:~/Desktop/alexsugar/tsdb$ ls -la
>> >>> anonymous/alex/14-09-06/lkb
>> >>> total 56
>> >>> drwxr-xr-x 2 jcrowgey jcrowgey  4096 Sep  6 13:14 .
>> >>> drwxr-xr-x 4 jcrowgey jcrowgey  4096 Sep  6 13:15 ..
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 analysis
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 decision
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 edge
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 fold
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey 36234 Sep  6 13:14 item
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 item-phenomenon
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 item-set
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 output
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 parameter
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 parse
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 phenomenon
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 preference
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey  9746 Sep  6 13:14 relations
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 result
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 rule
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 run
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 score
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 set
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 tree
>> >>> -rw-r--r-- 1 jcrowgey jcrowgey     0 Sep  6 13:14 update
>> >>>
>> >>> I don't know if it will help, but if you can initialize your own
>> >>> instance and tsdb is able to read it, that might help you go ahead
>> with
>> >>> your grammar testing and it might help "developers" get an idea of
>> what
>> >>> part of the program is going wrong.
>> >>>
>> >>> Sorry I don't have anything better for you,
>> >>>
>> >>> --Joshua
>> >>>
>> >>> On 09/05/2014 05:01 PM, Alexander Sugar wrote:
>> >>>> I don't see any error messages appearing either in STDERR (which I
>> >>>> assume is the bar at the bottom-right of the [tsdb()] window) or
>> emacs
>> >>>> (which I used to start tsdb).
>> >>>>
>> >>>> I'm attaching my 'item' and 'relations' files. Thanks a lot for
>> looking
>> >>>> at
>> >>>> them.
>>
>> >>>> - Alec
>> >>>>
>> >>>> On 9/5/14, Joshua Crowgey <jcrowgey at u.washington.edu> wrote:
>> >>>>> I see.  In fact, now that I think about it, the fact that your
>> >>>>> testsuite
>> >>>>> appears under File > Create seems to indicate that skeletons and
>> >>>>> Index.lisp are correct.
>> >>>>>
>> >>>>> When you click on your testsuite under File > Create and nothing
>> >>>>> appears
>> >>>>> in the window, is there any text or error messages that appear in
>> >>>>> STDERR
>> >>>>> or in emacs (if you started tsdb using the emacs interface)?
>> >>>>>
>> >>>>> Also, if you want to send me your 'item' and 'relations' files I can
>> >>>>> try
>> >>>>> to replicate your error on my system.
>> >>>>>
>> >>>>> --Joshua
>> >>>>>
>> >>>>> On 09/05/2014 03:37 PM, Alexander Sugar wrote:
>> >>>>>> Hi Joshua,
>> >>>>>>
>> >>>>>>      Thanks for offering your help. I just double checked, and my
>> >>>>>> skeletons directory indeed has Relations (with a capital 'R') and
>> >>>>>> Index.lisp. The latter points to the folders 'testsuite' and
>> >>>>>> 'testcorpus', which each contain an 'item' and 'relations' file.
>> >>>>>>
>> >>>>>> - Alec
>> >>>>>>
>> >>>>>> On 9/5/14, Joshua Crowgey <jcrowgey at u.washington.edu> wrote:
>> >>>>>>> Hi Alex,
>> >>>>>>>
>> >>>>>>> I'm not super-fluent with tsdb, but just to make sure you tried
>> it:
>> >>>>>>> have
>> >>>>>>> you double-checked that the skeletons root is set correctly?  It
>> >>>>>>> should
>> >>>>>>> be pointing to a directory that contains Relations and Index.lisp
>> >>>>>>> where
>> >>>>>>> Relations gives the schema for the fields in the tsdb profiles and
>> >>>>>>> Index.lisp gives paths to testsuites.
>> >>>>>>>
>> >>>>>>> --Joshua
>> >>>>>>>
>> >>>>>>> On 09/05/2014 12:01 PM, Alexander Sugar wrote:
>> >>>>>>>> To whom it may concern,
>> >>>>>>>>
>> >>>>>>>>      I am a graduate student at the University of Washington
>> >>>>>>>> learning
>> >>>>>>>> how to use Delph-in tools like [incr tsdb()]. Recently, when I
>> try
>> >>>>>>>> to
>> >>>>>>>> process my small uig grammar in [incr tsdb()], I see my test
>> suite
>> >>>>>>>> and
>> >>>>>>>> one test corpus under File > Create. After clicking 'create',
>> >>>>>>>> however,
>> >>>>>>>> no test suite instances appear in my window. Could you please
>> help
>> >>>>>>>> me
>> >>>>>>>> fix this problem?
>> >>>>>>>>
>> >>>>>>>> Thank you,
>> >>>>>>>> Alexander Sugar
>> >>>>>>>>
>> >>>>>>>
>> >>>>>
>> >>>
>> >
>>
>
>
>
> --
> Emily M. Bender
> Associate Professor
> Department of Linguistics
> Check out CLMS on facebook! http://www.facebook.com/uwclma
>



-- 
David Brodbeck
System Administrator, Linguistics
University of Washington
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