Hi Milos, Please, let's keep using the mailing list for this discussion.
A Friday 15 August 2008, escriguéreu: > Hi Jan, > > thanks for your reply once again. I got it to work by going back to > HDF5 version 1.6.7 and pytables 2.0.2. Some of the tests for pytables > are failing now, but everything seems to be working fine. I am on > vacation and can't send the output with the test failures, but I > saved it and will send them soon (it is on another computer). Thanks > again, > > Milos > > P.S. Here is what I did figure out about the problem I was having, I > think it has to do with zlib, because compress2 is a function in the > zlib compression library, at least that's what I found online, so > there may have been an issue with how pytables 2.0.4 or HDF5 1.8.1 > was interacting with my version of zlib, but this is just > speculation. Hmm, PyTables does not directly interact with zlib and its use is completely deferred to the HDF5 library. So my guess is that it should be a problem with HDF5. Try to run the tests that come with the HDF5 library to see if the problem is on that side. If those tests run fine, please provide us the information about your compiler and a detailed description of your compilation process as well (for both PyTables and HDF5). Francesc > > On Thu, Aug 14, 2008 at 10:01 PM, Jan Strube <[EMAIL PROTECTED]> wrote: > > Hi Milos, > > hmm. I'm sorry, but I must admit I am at the end of my knowledge > > here. I hope somebody else is able to help you further. > > Good luck, > > Jan > > > > On Aug 08, 2008, at 21:24 PM, Milos Ilak wrote: > > > > On Fri, Aug 8, 2008 at 3:15 PM, Jan Strube <[EMAIL PROTECTED]> wrote: > >> ** > >> > >> Hi Milos > >> > >> > >> Traceback (most recent call last): > >> File "<stdin>", line 1, in <module> > >> File "tables/__init__.py", line 56, in <module> > >> from tables.utilsExtension import getPyTablesVersion, > >> getHDF5Version ImportError: dlopen(tables/utilsExtension.so, 2): > >> Symbol not found: _compress2 > >> Referenced from: > >> /Users/milos/Work/python/pytables-2.0.4/tables/utilsExtension.so > >> Expected in: dynamic lookup > >> > >> I am not sure what this means, but I am guessing that it doesn't > >> have to do with the libraries. Do you have an idea what may be > >> going on? Thanks, > >> > >> could you try an > >> otool -L > >> /Users/milos/Work/python/pytables-2.0.4/tables/utilsExtension.so > >> and see if all libraries referenced there are found? If not, your > >> LD_LIBRARY_PATH or $DYLD_LIBRARY_PATH needs some adjustments. (But > >> I don't think that's the problem...) > > > > Sure, here's the output: > > > > dynamic-oit-vapornet-c-682:~ milos$ otool -L > > /Users/milos/Work/python/pytables-2.0.4/tables/utilsExtension.so > > /Users/milos/Work/python/pytables-2.0.4/tables/utilsExtension.so: > > /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, > > current version 88.3.6) > > > >> ImportError: dlopen(tables/utilsExtension.so, 2): Symbol not > >> found: _compress2 > >> > >> I can't really help here, but you get the symbols in a shared > >> library with nm > >> (man nm) > >> > >> I have tried a few things to find where that symbol could be > >> referenced or defined, unfortunately without success. But I run > >> the same version on Mac OS X 10.4.11 and it's just fine here. > > > > I find the following: > > > > dynamic-oit-vapornet-c-682:~ milos$ nm > > /Users/milos/Work/python/pytables-2.0.4/tables/utilsExtension.so | > > grep -n _compress2 > > 5593: U _compress2 > > > > It is also there in the other .so files: > > > > dynamic-oit-vapornet-c-682:~ milos$ nm > > /Users/milos/Work/python/pytables-2.0.4/tables/hdf5Extension.so | > > grep -n _compress2 > > 5710: U _compress2 > > dynamic-oit-vapornet-c-682:~ milos$ nm > > /Users/milos/Work/python/pytables-2.0.4/tables/tableExtension.so | > > grep -n _compress2 > > 5635: U _compress2 > > > > But I am not sure what this is telling me. I have tried the whole > > process again with a newly re-compiled HDF5 library (I needed that > > to make a fortran code work with the compiler I have) and I get the > > same error. Thanks, > > > > Milos > > > >> > I am sending this just to you first, since it is an installation > >> > > >>> > issue, so I don't want to bother the whole user group. > >> > >> Please don't! Always bother the group with everything, unless you > >> are already iterating specific problems with somebody. The chances > >> of somebody having a similar problem before or after you are > >> infinitely higher if you post to the list. Unfortunately I am not > >> being a great help here, but please don't let that discourage you. > >> > >> Good luck, > >> Jan > >> > >> > >> > >> ------------------------------------------------------------------ > >>------- This SF.Net email is sponsored by the Moblin Your Move > >> Developer's challenge > >> Build the coolest Linux based applications with Moblin SDK & win > >> great prizes > >> Grand prize is a trip for two to an Open Source event anywhere in > >> the world > >> http://moblin-contest.org/redirect.php?banner_id=100&url=/ > >> _______________________________________________ > >> Pytables-users mailing list > >> [email protected] > >> https://lists.sourceforge.net/lists/listinfo/pytables-users -- Francesc Alted Freelance developer Tel +34-964-282-249 ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Pytables-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/pytables-users
