<div dir="ltr">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.</div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Sep 8, 2014 at 4:39 PM, CLMS help (David Brodbeck) <span dir="ltr"><<a href="mailto:linghelp@uw.edu" target="_blank">linghelp@uw.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">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.</div><div class="gmail_extra"><div><div class="h5"><br><div class="gmail_quote">On Mon, Sep 8, 2014 at 3:02 PM, Emily M. Bender <span dir="ltr"><<a href="mailto:ebender@uw.edu" target="_blank">ebender@uw.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">[Again, adding developers back to the cc.]<div><br></div><div>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.</div><div><br></div><div>Emily</div><div><br></div><div><div><br></div><div><br></div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Sun, Sep 7, 2014 at 9:33 AM, Alexander Sugar <span dir="ltr"><<a href="mailto:sugara@uw.edu" target="_blank">sugara@uw.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Joshua,<br>
<br>
Somehow in updating my VirtualBox, I lost previous test suite<br>
instances. If I point my database root at the opt/delphin/... path<br>
that's set as a default, I am able to see those profiles in the podium<br>
after I create them (and I get the same "unable to write history file<br>
message", so that's definitely not the issue).<br>
<br>
I'm using version 2.0 (16-jun-13; beta) of [incr tsdb()] on UbuntuLKB 17.<br>
<div><div><br>
- Alec<br>
<br>
On 9/6/14, Joshua Crowgey <<a href="mailto:jcrowgey@u.washington.edu" target="_blank">jcrowgey@u.washington.edu</a>> wrote:<br>
> Hi Alec,<br>
><br>
> I doubt that .tsdb_history is the issue. In Unix-like systems, many<br>
> programs will store config info or other user-settings in files that<br>
> start with "." in the user's home directory. If you say (in a shell):<br>
><br>
> $ ls -la ~/<br>
><br>
> You'll see several such files, probably at least .emacs, .bashrc. In my<br>
> own system, I suppose that .tsdb_history stores your tsdb commands so<br>
> that (maybe?) you can press "up" and see the previous command, or<br>
> something like that. I found a .tsdb_history with these lines:<br>
><br>
> jcrowgey@citrus:~$ cat .tsdb_history<br>
> do "/tmp/.tsdb.io.jcrowgey.11333.118378".<br>
> do "/tmp/.tsdb.io.jcrowgey.11333.118384".<br>
><br>
> Because I've restarted my system since I last used tsdb, the /tmp<br>
> directory has been cleared and I'm not sure what was in those<br>
> /tmp/.tsdb.io.jcrowgey.* files. My guess is those were a record of my<br>
> sessions this morning when I was playing around with your item and<br>
> relations files.<br>
><br>
> Anyway, the fact that the files were created is interesting, I think.<br>
> It suggests that tsdb can create the new files, but we still don't know<br>
> why it can't read those files and display them in the podium.<br>
><br>
> This makes me thing of another troubleshooting/debugging test. Can you<br>
> see other existing testsuite instances? That is, if you already had a<br>
> profile with results and such, and you point your database root at that<br>
> dir, do those profiles show up in the podium?<br>
><br>
> Sorry I don't really have good answers for you. I just thought I'd jump<br>
> in and give you some stuff to try out. By the way, are you using the<br>
> knoppix+lkb distro? What are the details of your platform?<br>
><br>
> --Joshua<span><br>
><br>
> On 09/06/2014 05:53 PM, Alexander Sugar wrote:<br>
>> Hi Joshua,<br>
>><br></span>
>> I think the reason I didn't see anything printed out in emacs<br>
>> was because I had previously 'created' an instance. When I cleared out<br>
>> the files inside of the home folder, I saw the same lines printed as<br>
>> you, except in the end:<br>
>><br>
>> initialize(): creating empty data file for `score'.<br>
>> main(): no history file `.tsdb_history'.<br>
>><br>
>> And of course no instance showed up in the podium. I'm guessing the<br>
>> '.tsdb_history' line is the source of the problem. Is there a quick<br>
>> fix for it? If so, that's great but I'm sorry to have put you through<br>
>> so much trouble just now...<br>
>><br>
>> - Alec<br>
>><br>
>> On 9/6/14, Joshua Crowgey <<a href="mailto:jcrowgey@u.washington.edu" target="_blank">jcrowgey@u.washington.edu</a>> wrote:<br>
>>> Hi Alec,<br>
>>><br>
>>> I put your item and relations files into a dir and pointed my itsdb at<br>
>>> them and as far as I can tell, they loaded without a problem---ie, tsdb<br>
>>> was able to create a new instance and I see it appear in the podium<br>
>>> window.<br>
>>><br>
>>> As to stderr, I think if you start tsdb in emacs then all of the<br>
>>> messages get printed there. When I click to create a new instance of<br>
>>> your item and relations files, I see:<br>
>>><br>
>>> LKB(2): initialize(): creating empty data file for `analysis'.<br>
>>> initialize(): creating empty data file for `phenomenon'.<br>
>>> initialize(): creating empty data file for `parameter'.<br>
>>> initialize(): creating empty data file for `set'.<br>
>>> initialize(): creating empty data file for `item-phenomenon'.<br>
>>> initialize(): creating empty data file for `item-set'.<br>
>>> initialize(): creating empty data file for `run'.<br>
>>> initialize(): creating empty data file for `parse'.<br>
>>> initialize(): creating empty data file for `result'.<br>
>>> initialize(): creating empty data file for `rule'.<br>
>>> initialize(): creating empty data file for `output'.<br>
>>> initialize(): creating empty data file for `edge'.<br>
>>> initialize(): creating empty data file for `tree'.<br>
>>> initialize(): creating empty data file for `decision'.<br>
>>> initialize(): creating empty data file for `preference'.<br>
>>> initialize(): creating empty data file for `update'.<br>
>>> initialize(): creating empty data file for `fold'.<br>
>>> initialize(): creating empty data file for `score'.<br>
>>> close-connection():<br>
>>> `/home/jcrowgey/Desktop/alexsugar/tsdb/anonymous/alex/14-09-06/lkb1/'<br>
>>> expiry<br>
>>><br>
>>> You don't see anything happening there, eh? I'm not sure it would help,<br>
>>> but it might be interesting to try this:<br>
>>><br>
>>> Since all the tsdb instance is (before you use it) is just a set of<br>
>>> empty files + copies of the item and relations files, you could simply<br>
>>> make the instance yourself on the command line and then see if tsdb can<br>
>>> recognize and already created one. Perhaps this would give a clue as to<br>
>>> whether the issue is in creating files or if reading files is affected<br>
>>> too.<br>
>>><br>
>>> I think the usual directory structure is:<br>
>>><br>
>>> $DATABASEROOT/NAME_OF_GRAMMAR/NAME_OF_TS/DATE/lkb/<br>
>>><br>
>>> Then, inside that final dir, you just put a copy of item and relations<br>
>>> plus empty files with the following names:<br>
>>><br>
>>> jcrowgey@citrus:~/Desktop/alexsugar/tsdb$ ls -la<br>
>>> anonymous/alex/14-09-06/lkb<br>
>>> total 56<br>
>>> drwxr-xr-x 2 jcrowgey jcrowgey 4096 Sep 6 13:14 .<br>
>>> drwxr-xr-x 4 jcrowgey jcrowgey 4096 Sep 6 13:15 ..<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 analysis<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 decision<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 edge<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 fold<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 36234 Sep 6 13:14 item<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 item-phenomenon<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 item-set<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 output<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 parameter<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 parse<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 phenomenon<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 preference<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 9746 Sep 6 13:14 relations<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 result<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 rule<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 run<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 score<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 set<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 tree<br>
>>> -rw-r--r-- 1 jcrowgey jcrowgey 0 Sep 6 13:14 update<br>
>>><br>
>>> I don't know if it will help, but if you can initialize your own<br>
>>> instance and tsdb is able to read it, that might help you go ahead with<br>
>>> your grammar testing and it might help "developers" get an idea of what<br>
>>> part of the program is going wrong.<br>
>>><br>
>>> Sorry I don't have anything better for you,<br>
>>><br>
>>> --Joshua<br>
>>><br>
>>> On 09/05/2014 05:01 PM, Alexander Sugar wrote:<br>
>>>> I don't see any error messages appearing either in STDERR (which I<br>
>>>> assume is the bar at the bottom-right of the [tsdb()] window) or emacs<br>
>>>> (which I used to start tsdb).<br>
>>>><br>
>>>> I'm attaching my 'item' and 'relations' files. Thanks a lot for looking<br>
>>>> at<br>
>>>> them.<div><div><br>
>>>> - Alec<br>
>>>><br>
>>>> On 9/5/14, Joshua Crowgey <<a href="mailto:jcrowgey@u.washington.edu" target="_blank">jcrowgey@u.washington.edu</a>> wrote:<br>
>>>>> I see. In fact, now that I think about it, the fact that your<br>
>>>>> testsuite<br>
>>>>> appears under File > Create seems to indicate that skeletons and<br>
>>>>> Index.lisp are correct.<br>
>>>>><br>
>>>>> When you click on your testsuite under File > Create and nothing<br>
>>>>> appears<br>
>>>>> in the window, is there any text or error messages that appear in<br>
>>>>> STDERR<br>
>>>>> or in emacs (if you started tsdb using the emacs interface)?<br>
>>>>><br>
>>>>> Also, if you want to send me your 'item' and 'relations' files I can<br>
>>>>> try<br>
>>>>> to replicate your error on my system.<br>
>>>>><br>
>>>>> --Joshua<br>
>>>>><br>
>>>>> On 09/05/2014 03:37 PM, Alexander Sugar wrote:<br>
>>>>>> Hi Joshua,<br>
>>>>>><br>
>>>>>> Thanks for offering your help. I just double checked, and my<br>
>>>>>> skeletons directory indeed has Relations (with a capital 'R') and<br>
>>>>>> Index.lisp. The latter points to the folders 'testsuite' and<br>
>>>>>> 'testcorpus', which each contain an 'item' and 'relations' file.<br>
>>>>>><br>
>>>>>> - Alec<br>
>>>>>><br>
>>>>>> On 9/5/14, Joshua Crowgey <<a href="mailto:jcrowgey@u.washington.edu" target="_blank">jcrowgey@u.washington.edu</a>> wrote:<br>
>>>>>>> Hi Alex,<br>
>>>>>>><br>
>>>>>>> I'm not super-fluent with tsdb, but just to make sure you tried it:<br>
>>>>>>> have<br>
>>>>>>> you double-checked that the skeletons root is set correctly? It<br>
>>>>>>> should<br>
>>>>>>> be pointing to a directory that contains Relations and Index.lisp<br>
>>>>>>> where<br>
>>>>>>> Relations gives the schema for the fields in the tsdb profiles and<br>
>>>>>>> Index.lisp gives paths to testsuites.<br>
>>>>>>><br>
>>>>>>> --Joshua<br>
>>>>>>><br>
>>>>>>> On 09/05/2014 12:01 PM, Alexander Sugar wrote:<br></div></div><div><div>
>>>>>>>> To whom it may concern,<br>
>>>>>>>><br>
>>>>>>>> I am a graduate student at the University of Washington<br>
>>>>>>>> learning<br>
>>>>>>>> how to use Delph-in tools like [incr tsdb()]. Recently, when I try<br>
>>>>>>>> to<br>
>>>>>>>> process my small uig grammar in [incr tsdb()], I see my test suite<br>
>>>>>>>> and<br>
>>>>>>>> one test corpus under File > Create. After clicking 'create',<br>
>>>>>>>> however,<br>
>>>>>>>> no test suite instances appear in my window. Could you please help<br>
>>>>>>>> me<br>
>>>>>>>> fix this problem?<br>
>>>>>>>><br>
>>>>>>>> Thank you,<br>
>>>>>>>> Alexander Sugar<br>
>>>>>>>><br>
>>>>>>><br>
>>>>><br>
>>><br>
><br>
</div></div></div></div></blockquote></div><br><br clear="all"><span><div><br></div>-- <br>Emily M. Bender<br>Associate Professor<br>Department of Linguistics<br>Check out CLMS on facebook! <a href="http://www.facebook.com/uwclma" target="_blank">http://www.facebook.com/uwclma</a><br>
</span></div>
</blockquote></div><br><br clear="all"><div><br></div></div></div><span class="HOEnZb"><font color="#888888">-- <br><span style="font-size:12px"><span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div>David Brodbeck</div><div>System Administrator, Linguistics</div><div>University of Washington</div></span></span></span>
</font></span></div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><span style="font-size:12px"><span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><span style="border-collapse:separate;color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><div>David Brodbeck</div><div>System Administrator, Linguistics</div><div>University of Washington</div></span></span></span>
</div>