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 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 >
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