Re: [Pytables-users] segmentation fault on Mac OS X Lion when running tables.test()
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 scop...@gmail.com wrote: Hi David, How did you build / install HDF5? Be Well Anthony On Fri, Jun 15, 2012 at 7:14 PM, David Donovan donov...@gmail.com 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
Re: [Pytables-users] segmentation fault on Mac OS X Lion when running tables.test()
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? Thanks! Best Regards, David On Sat, Jun 16, 2012 at 12:57 AM, Anthony Scopatz scop...@gmail.com wrote: Hi David, How did you build / install HDF5? Be Well Anthony On Fri, Jun 15, 2012 at 7:14 PM, David Donovan donov...@gmail.com 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users
Re: [Pytables-users] segmentation fault on Mac OS X Lion when running tables.test()
Hmmm That all looks correct. Have you tried linking PyTables against the HDF5 from MacPorts? This has worked for me in the past... On Mon, Jun 18, 2012 at 9:37 PM, David Donovan donov...@gmail.com 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? Thanks! Best Regards, David On Sat, Jun 16, 2012 at 12:57 AM, Anthony Scopatz scop...@gmail.com wrote: Hi David, How did you build / install HDF5? Be Well Anthony On Fri, Jun 15, 2012 at 7:14 PM, David Donovan donov...@gmail.com 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 -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Pytables-users mailing list Pytables-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pytables-users -- Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ ___ Pytables-users mailing list Pytables-users@lists.sourceforge.net
