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From: Josh M. <jos...@gm...> - 2012-06-22 14:47:09
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On Jun 19, 2012, at 4:37 AM, David Donovan wrote: > Hi Anthony, > > Thanks for the response. Installed HDF5 1.8.9 using the following > flags for configure. > > `./configure --prefix=/usr/local > --with-szlib=/Library/Frameworks/Python.framework/Versions/Current > CPPFLAGS=-I/Library/Frameworks/Python.framework/Versions/Current/include > LDFLAGS=-L/Library/Frameworks/Python.framework/Versions/Current/lib` > > Also, I had to modify the optimization flag for gcc-4 in order to pass > the make check part (as noted on the HDF5 page). > `Conversion Tests fail on Mac OS X 10.7 (Lion) Users have reported > that when building HDF5, the conversion tests failed (make check) in > dt_arith.chk. A workaround is to edit ./< HDF5source >> /config/gnu-flags, search for PROD_CFLAGS under "gcc-4.*", and change > the value for PROD_CFLAGS to "-O0".` > > Then: > 'make' > 'make check' > 'sudo make install' > > Is there a better way? Is tables somehow having a hard time finding > the HDF5 library do you think? Hi David, I always use homebrew for any of my prerequisites: http://mxcl.github.com/homebrew/ Cheers ~Josh > Thanks! > > Best Regards, > David > > > > On Sat, Jun 16, 2012 at 12:57 AM, Anthony Scopatz <sc...@gm...> wrote: >> Hi David, >> >> How did you build / install HDF5? >> >> Be Well >> Anthony >> >> On Fri, Jun 15, 2012 at 7:14 PM, David Donovan <don...@gm...> wrote: >>> >>> Hi Everyone, >>> >>> I am having problems running the tests for PyTables on Mac OS X Lion. >>> I have tried HDF5 version 1.8.5 as well, but I still get the same issue. >>> >>> Any thoughts would be helpful... >>> >>> Thanks for any help you can provide. >>> >>> Best Regards, >>> David Donovan >>> >>> >>> impPython 2.7.1 (r271:86832, Jul 31 2011, 19:30:53) >>> [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on >>> darwin >>> Type "help", "copyright", "credits" or "license" for more information. >>>>>> import tables >>> table>>> tables.test() >>> >>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= >>> PyTables version: 2.3.1 >>> HDF5 version: 1.8.9 >>> NumPy version: 1.7.0.dev-0c5f480 >>> Numexpr version: 2.0.1 (not using Intel's VML/MKL) >>> Zlib version: 1.2.5 (in Python interpreter) >>> LZO version: 2.06 (Aug 12 2011) >>> BZIP2 version: 1.0.6 (6-Sept-2010) >>> Blosc version: 1.1.2 (2010-11-04) >>> Cython version: 0.16 >>> Python version: 2.7.1 (r271:86832, Jul 31 2011, 19:30:53) >>> [GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] >>> Platform: darwin-i386 >>> Byte-ordering: little >>> Detected cores: 2 >>> >>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= >>> Performing only a light (yet comprehensive) subset of the test suite. >>> If you want a more complete test, try passing the --heavy flag to this >>> script >>> (or set the 'heavy' parameter in case you are using tables.test() call). >>> The whole suite will take more than 4 hours to complete on a relatively >>> modern CPU and around 512 MB of main memory. >>> >>> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= >>> >>> .....................................................................................................................................FSegmentation >>> fault: 11 >>> |