Thanks for the reply. I've been digging around and trying some things and I think the architectural issue might be it after all.
You're right that the Uname info is what's reported by uname -a. Mac OS 10.6 does use a 32-bit kernel, but nevertheless lots of stuff in userland runs in 64-bit. I am running 64-bit Python, and will be using HDF5 with PyTables, so I presume that I do indeed need a 64-bit build. Anyway, I was able to get it to configure for x86_64 by doing this sudo env ARCHFLAGS="-arch x86_64" LDFLAGS="-arch x86_64" ./configure --build=x86_64-apple-darwin10 --target=x86_64-apple-darwin10 --prefix=/usr/local/hdf5 --with-szlib=/usr/local/src/szip-2.1/szip --with-zlib=/usr/local/include,/usr/local/lib Note that I opted for the overkill approach. Setting ARCHFLAGS did not work by itself. I didn't try the rest of the options alone, so I don't know which of LDFLAGS or the ./configure --build or --target options did the trick. Well, we'll see if it did the trick. I am making now and will report back. ... On Fri, Aug 20, 2010 at 6:01 PM, George N. White III <[email protected]>wrote: > On Fri, Aug 20, 2010 at 12:59 PM, Eric Pashman <[email protected]> > wrote: > > > To add to my previous message, I've just noticed in running through the > HDF5 > > build process again that ./ configure returns this configuration: > > General Information: > > ------------------- > > HDF5 Version: 1.8.5 > > Configured on: Fri Aug 20 16:25:11 BST 2010 > > Configured by: [email protected] > > Configure mode: production > > Host system: i386-apple-darwin10.4.0 > > Uname information: Darwin my.domain 10.4.0 Darwin Kernel Version > > 10.4.0: Fri Apr 23 18:28:53 PDT 2010; root:xnu-1504.7.4~1/RELEASE_I386 > i386 > > I assume the uname information is just copied from the 'uname -a' > output. Maybe > your kernel is running in 32-bit mode, which might be necessary with > older hardware > (e.g., lacking 64-bit drivers). In principle you can still run 64-bit > apps, but it may take > extra effort to convince 'configure' scripts to built 64-bit versions. > You can try > running configure after something like: > > export CFLAGS='-m64' > or > export CFLAGS='-arch x86_64' > > > > > > > > Byte sex: little-endian > > Libraries: > > Installation point: /usr/local/hdf5 > > > > That configuration is incorrect. I am running Mac OS 10.6 on an x86_64 > > architecture. ./configure shows at various steps that it's found a 64-bit > > architecture, it's looking at the gcc linker at > > /usr/libexec/gcc/i686-apple-darwin10/4.2.1/ld (which is correct), but > also > > reports > > checking dynamic linker characteristics... darwin10.4.0 dyld > > which possibly is incorrect. I say possibly because Apple's version of > the > > gcc linker takes multi-architecture input files and then output just one > > file for the correct architecture. Though I don't know why it would > report > > as above. I've also tried prefacing make with sudo env ARCHFLAGS="-arch > > x86_64", but the end result is the same. > > The tests shouldn't pass if it were building for the wrong architecture, > > anyway, so this is probably all a red herring. (Recall that I also tried > the > > binaries on the website.) Has anyone installed HDF5 on Mac OS 10.6 lately > > and seen this behavior? > > Regards, > > Eric > > > > On Fri, Aug 20, 2010 at 4:10 PM, Eric Pashman <[email protected]> > > wrote: > >> > >> I'm having all kinds of problems installing PyTables, whose developer > >> suggested I seek help here, as the problem seems related to my HDF5 > >> installation or its use of SZIP. > >> First, my system configuration: > >> Mac OS 10.6.4 > >> Intel Core 2 Duo (64-bit) > >> Python 2.7 (binaries from python.org) > >> Numpy 1.5.0b1 (binaries from scipy.org) > >> I've installed all of Pytables's dependencies, and those dependencies' > >> dependencies: Numexpr (1.4, via easy_install), bzip2 (1.0.5, built from > >> source), SZIP (2.1, built from source), LZO (2.03, built from source), > zlib > >> (1.2.5, built from source), all without apparent problems. The stuff I > built > >> from source passed all tests in make check/test. > >> I tried installing the HDF5 1.8.5 binaries available on the website, and > >> when that didn't work I built it from source. The tests in make > check/test > >> all PASS, except a couple are SKIPPED. But when I try to install > PyTables > >> (both via easy_install and via setup.py), things go wrong. This first > step > >> yields no errors, but there's a scary warning about not finding > >> the HDF5 runtime): > >> tables-2.2 myuser$ sudo python setup.py build_ext --inplace > >> * Found numpy 1.5.0b1 package installed. > >> * Found numexpr 1.4 package installed. > >> * Found HDF5 headers at ``/usr/local/include``, library at > >> ``/usr/local/lib``. > >> .. WARNING:: Could not find the HDF5 runtime. > >> The HDF5 shared library was *not* found in the default library > >> paths. In case of runtime problems, please remember to install it. > >> * Found LZO 2 headers at ``/usr/local/include``, library at > >> ``/usr/local/lib``. > >> * Skipping detection of LZO 1 since LZO 2 has already been found. > >> * Found bzip2 headers at ``/usr/include``, library at ``/usr/lib``. > >> * Found pthreads headers at ``/usr/include``, library at ``/usr/lib``. > >> running build_ext > >> cythoning tables/linkExtension.pyx to tables/linkExtension.c > >> building 'tables.linkExtension' extension > >> The same thing happens if I use the --hdf5=whatever command. There's > more > >> output that includes a bunch of architectural warnings, but no errors. > That > >> looks OK to me because the errors are all for ppc and i386 > architectures, > >> and I should need the x86_64 stuff. Then if I run Python and try to load > >> Pytables, I get this error: > >> >> import tables > >> Traceback (most recent call last): > >> File "<stdin>", line 1, in <module> > >> File "tables/__init__.py", line 63, in <module> > >> from tables.utilsExtension import getPyTablesVersion, getHDF5Version > >> ImportError: dlopen(tables/utilsExtension.so, 2): Symbol not found: > >> _SZ_BufftoBuffCompress > >> Referenced from: /usr/local/src/tables-2.2/tables/utilsExtension.so > >> Expected in: flat namespace > >> in /usr/local/src/tables-2.2/tables/utilsExtension.so > >> I've ended up with the same error through every permutation of the > >> installation process that I've tried. I rebuilt HDF5 several times, and > I > >> verified that it was finding the SZIP libraries; The HDF5 ./configure > even > >> outputted this line: > >> checking for SZ_BufftoBuffCompress in -lsz... yes > >> Yet that seems to be the stumbling block. Does anyone know anything > about > >> SZ_BufftoBuffCompress? Very little shows up on Google, and nothing on > this > >> mailing list. I assume from the name that it is a SZIP thing, so I tried > >> reinstalling that several times, building HDF5 with and without the SZIP > >> flag, etc., all to no avail. > >> I'd be grateful for any pointers. > >> Regards, > >> Eric > > > > _______________________________________________ > > Hdf-forum is for HDF software users discussion. > > [email protected] > > http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org > > > > > > > > -- > George N. White III <[email protected]> > Head of St. Margarets Bay, Nova Scotia > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org >
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