[developers] Trouble Seeing Test Suite Instances

Alexander Sugar sugara at uw.edu
Thu Sep 11 22:59:10 CEST 2014 

Joshua resolved the problem! Emily was right that it was a matter of
where the database root was pointed, but not in the way I thought.
Moving the /home or /tsdb/home folder(s) up or down before opening
[incr tsdb()] and pointing the database root to that new location
didn't have an effect. When we set the database root to the default
/opt/delphin/lkb/src/tsdb/home, the instance showed up in the podium.
After that, when we created in a new instance in the
~/Uyghur/tsdb/home location I had originally wanted, the instance
appeared in the podium there as well.

-- Update, after getting home and restarting my computer, I am once
again able to create a visible instance in the /opt/delphin/... path,
but unlike earlier I was unsuccessful at doing so in my own folder.
The source of this problem seems quite mysterious and I'd love to know
what it is, but for now I'm happy to be able to create browsable
instances somewhere and check coverage of my grammar.

Thank you,
Alec

On 9/10/14, Alexander Sugar <sugara at uw.edu> wrote:
> I'm seeing Joshua tomorrow am, so maybe he'll find the error somewhere in
> my folders/files.
>
> Thanks again for looking at it, David.
>
> Emily M. Bender <ebender at uw.edu>于2014年9月10日星期三写道：
>
>> Thanks, David.  I think there is something in the interaction between
>> [incr tsdb()] and UbuntuLkb---we saw something similar in 567 last year,
>> but then it was possible to work around by just changing where in the
>> directory tree the database root was.  Alec says that didn't help in his
>> case, though, so I'm not sure this is the same thing.
>>
>> Emiliy
>>
>>
>> On Wed, Sep 10, 2014 at 10:16 AM, CLMS help (David Brodbeck) <
>> linghelp at uw.edu <javascript:_e(%7B%7D,'cvml','linghelp at uw.edu');>> wrote:
>>
>>> I tried booting Alec's VM with 'apparmor=0' set, and it made no
>>> difference.  I'm also not seeing any "permission denied" type errors,
>>> which
>>> would be typical if AppArmor were the culprit.  I'm starting to suspect
>>> an
>>> issue with tsdb, since there are no error messages at all, but I don't
>>> know
>>> enough about its internals to diagnose it.
>>>
>>> On Mon, Sep 8, 2014 at 4:39 PM, CLMS help (David Brodbeck) <
>>> linghelp at uw.edu <javascript:_e(%7B%7D,'cvml','linghelp at uw.edu');>>
>>> wrote:
>>>
>>>> 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
>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>
>>>
>>>
>>>
>>> --
>>> David Brodbeck
>>> System Administrator, Linguistics
>>> University of Washington
>>>
>>
>>
>>
>> --
>> Emily M. Bender
>> Associate Professor
>> Department of Linguistics
>> Check out CLMS on facebook! http://www.facebook.com/uwclma
>>
>

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