[yt-users] Merger Tree

Brian Crosby crosby.bd at gmail.com
Thu Jul 8 13:50:43 PDT 2010


Matt,

Here's what I came across:

Failed to find the necessary bits to build these modules:
_sqlite3           bsddb185           dl              
gdbm               imageop            sunaudiodev     
To find the necessary bits, look in setup.py in detect_modules() for the module's name.

I looked this routine up, but unfortunately can't make sense of how to change it to solve the problem.

-Brian

On Jul 8, 2010, at 4:30 PM, Matthew Turk wrote:

> Hi Brian,
> 
> Just before that line, it should say those are the modules that
> weren't build.  I'd suggest making sure your LD_LIBRARY_PATH is
> correct, going into the src/Python-2.6.4 (or 2.6.1 or whatever)
> directory in your yt build path, doing a "make clean" and "make
> install" and watching to see if it says *why* _sqlite3 wasn't built.
> 
> -Matt
> 
> On Thu, Jul 8, 2010 at 1:28 PM, Brian Crosby <crosby.bd at gmail.com> wrote:
>> Matt,
>> 
>> Everything in yt_install.log is either shown as "compiling" or "listing" except for the last line, which is simply
>> _sqlite3           bsddb185           dl
>> 
>> I'm not sure what that one means.
>> 
>> Thanks,
>> Brian
>> 
>> On Jul 8, 2010, at 4:22 PM, Matthew Turk wrote:
>> 
>>> Hi Brian,
>>> 
>>> Do you still have your yt_install.log file?  It looks like _sqlite3
>>> might simply not have been built.  If you grep through yt_install.log,
>>> do you see anything saying it was not built?
>>> 
>>> -Matt
>>> 
>>> On Thu, Jul 8, 2010 at 1:20 PM, Brian Crosby <crosby.bd at gmail.com> wrote:
>>>> Rick,
>>>> 
>>>> After checking those paths, I found both libsqlite3.so.0 and libsqlite3.so.0.8.6 in /usr/lib64.  If I'm reading your message correctly, this would mean that something else is causing my problem.  Any clue why it can't import sqlite3 in that case?
>>>> 
>>>> Thanks,
>>>> Brian
>>>> 
>>>> 
>>>> On Jul 8, 2010, at 3:44 PM, Rick Wagner wrote:
>>>> 
>>>>> Hi Brian,
>>>>> 
>>>>> The directory you mention is actually for the package that's part of Python's standard library. If you're getting LD_LIBRARY_PATH errors, it's more than likely looking for the SQLite library, which will have a name like, libsqlite3.so, libsqlite3.so.0, or libsqlite3.so.0.8.6.
>>>>> 
>>>>> If this is part of your operating system's distribution, the library will be in /usr/lib or /usr/lib64, and you won't need the LD_LIBRARY_PATH environment variable. However, if you installed SQLite yourself, you'll need to tell the Python sqlite3 package where to find the library.
>>>>> 
>>>>> --Rick
>>>>> 
>>>>> On Jul 8, 2010, at 12:32 PM, Brian Crosby wrote:
>>>>> 
>>>>>> Hi all,
>>>>>> 
>>>>>> I've been trying to make a merger tree for Enzo simulation, am having some trouble.  I think that the problem stems from sqlite3, or my misuse of it, but I'm not certain.  I keep getting an error that LD_LIBRARY_PATH is undefined, but I currently have it set to $HOME/yt-x86_64/lib/python2.6/sqlite3/ so that may suggest that sqlite3 is not actually the culprit here.
>>>>>> 
>>>>>> The script and output are both attached, any help or suggestions would be very appreciated.
>>>>>> 
>>>>>> Thanks,
>>>>>> Brian Crosby
>>>>>> 
>>>>>> <Merger_Tree.o1461174><MergerTree.py>_______________________________________________
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