Hi Scot, On Oct 20, 2012, at 3:59 PM, Scott Sides wrote:
> Albert, > > I'm unclear how this is different from what I've done. We cannot reproduce the error with h5dump we built. Could you please try h5dump that Albert provided? It will help us to understand what the next steps in our investigation will be (and will give you a working binary ;-) > You believe that some of the cmake configure options are > breaking the binary build? Yes, this is the theory. Thank you in helping us to investigate the issue. Elena > Or just that the cmake build > itself is failing? (so then reverting to the autotools build is the 'fix') > > Scott > > On 10/19/12 1:18 PM, Albert Cheng wrote: >> >> Hi Scott, >> >> We are not using cmake to build HDF5 library in our Mac systems, yet. >> I have a built of h5dump in my Mountain Lion system and used it >> to dump the file you provided. It worked fine (see output h5dump.out >> in the ftp space below.) >> >> Here is my "solution", for now: >> 1. I have deposited my h5dump executable and your hdf5 data file in my >> FTP outgoing directories as below. Please downloaded it and try it out. >> ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/acheng/h5dump/ >> >> mdsum output to verify you got the right files. >> da2f13df506878b406146524eff7d3da diblock2s_History.h5 >> 8fe01cd79b43ba6f528ee7be314da2b1 h5dump >> 7d1047e6339ad415f3a2cecc8c3aa4ab h5dump.out >> >> 2. If my executable works in your system, try use the following >> steps to build your own and see if it works. >> ./configure; make; make check; make install; .... >> >> Let me know if this "solution" works for you, for now. >> >> -Albert Cheng >> >> On 10/17/12 5:37 PM, Scott Sides wrote: >>> thanks a lot. Let me know if you find a solution and >>> if you need any more info. >>> >>> Scott >>> >>> On 10/17/12 4:31 PM, Peter Cao wrote: >>>> >>>> Hi Scott, >>>> >>>> Thank you for the information and the sample file. We will build 1.8.10 >>>> with >>>> the same configuration and try to reproduce the problem. >>>> >>>> Thanks >>>> --pc >>>> >>>> On 10/17/2012 3:27 PM, Scott Sides wrote: >>>>> Here's the info from our build/configure system for hdf5-1.8.10. >>>>> I didnt do the 'make check' test. h5dump seg faults when trying to access >>>>> file. >>>>> >>>>> Scott >>>>> >>>>> #!/bin/bash >>>>> >>>>> # Clear cmake cache to ensure a clean configure. >>>>> rm -rf CMakeFiles CMakeCache.txt >>>>> >>>>> '/Users/swsides/contrib/cmake/bin/cmake' \ >>>>> -DCMAKE_INSTALL_PREFIX:PATH=/Users/swsides/contrib/hdf5-1.8.10-pre1-ser >>>>> \ >>>>> -DCMAKE_BUILD_TYPE:STRING=Release \ >>>>> -DCMAKE_COLOR_MAKEFILE:BOOL=FALSE \ >>>>> -DCMAKE_VERBOSE_MAKEFILE:BOOL=TRUE \ >>>>> -DCMAKE_C_COMPILER:FILEPATH='/usr/bin/gcc' \ >>>>> -DCMAKE_CXX_COMPILER:FILEPATH='/usr/bin/g++' \ >>>>> -DCMAKE_Fortran_COMPILER:FILEPATH='/usr/local/bin/gfortran' \ >>>>> -DCMAKE_C_FLAGS:STRING='-pipe -fPIC' \ >>>>> -DCMAKE_CXX_FLAGS:STRING='-pipe -fPIC' \ >>>>> -DCMAKE_Fortran_FLAGS:STRING='-fPIC' \ >>>>> -DHDF5_BUILD_TOOLS:BOOL=ON \ >>>>> -DHDF5_BUILD_HL_LIB:BOOL=ON \ >>>>> -DHDF5_BUILD_FORTRAN:BOOL=ON \ >>>>> /Users/swsides/chompstall/builds/hdf5-1.8.10-pre1 >>>>> >>>>> >>>>> this is the command I used for looking at the file thats attached. >>>>> /Users/swsides/contrib/hdf5-1.8.10-pre1-ser/bin/h5dump >>>>> diblock2s_History.h5 >>>>> >>>>> Thanks! >>>>> Scott >>>>> >>>>> >>>>> >>>>> >>>>> On 10/17/12 2:19 PM, Albert Cheng wrote: >>>>>> Hi Scot, >>>>>> >>>>>> I would like to ask for some more information about h5dump seg fault >>>>>> in your Mountain Lion system. >>>>>> >>>>>> Did you also use gcc compilers to build hdf5 v1.8.10 pre-release in your >>>>>> mountain lion system? >>>>>> >>>>>> What configure option(s) did you use to build the library and tools? >>>>>> >>>>>> How does h5dump seg fault on you? >>>>>> Did it seg fault during "make check"? >>>>>> Or did it seg fault when you used it to access your own HDF5 data files? >>>>>> >>>>>> If the former (during make check), can you please send me whatever >>>>>> output it shows when it seg faulted. >>>>>> >>>>>> If the latter, any chance I may get a copy of your HDF5 files and >>>>>> the command you used? >>>>>> >>>>>> Thanks. >>>>>> >>>>>> -Albert >>>>>> >>>>>> On 10/17/12 11:28 AM, Scott Sides wrote: >>>>>>> Dave, thanks for pointing that out. I had two windows open. >>>>>>> Here are the results for my Mac Lion. >>>>>>> >>>>>>> polymer:~ swsides$ gfortran --version ;gcc --version ; uname -a >>>>>>> GNU Fortran (GCC) 4.6.2 20111019 (prerelease) >>>>>>> Copyright (C) 2011 Free Software Foundation, Inc. >>>>>>> >>>>>>> GNU Fortran comes with NO WARRANTY, to the extent permitted by law. >>>>>>> You may redistribute copies of GNU Fortran >>>>>>> under the terms of the GNU General Public License. >>>>>>> For more information about these matters, see the file named COPYING >>>>>>> >>>>>>> i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build >>>>>>> 5658) (LLVM build 2336.1.00) >>>>>>> Copyright (C) 2007 Free Software Foundation, Inc. >>>>>>> This is free software; see the source for copying conditions. There is >>>>>>> NO >>>>>>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR >>>>>>> PURPOSE. >>>>>>> >>>>>>> Darwin polymer.txcorp.com 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug >>>>>>> 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 >>>>>>> >>>>>>> >>>>>>> >>>>>>> On 10/17/12 10:23 AM, Scott Sides wrote: >>>>>>>> [swsides@volt lists]$ gfortran --version ; gcc --version ; uname -a >>>>>>>> GNU Fortran (GCC) 4.4.4 20100726 (Red Hat 4.4.4-13) >>>>>>>> Copyright (C) 2010 Free Software Foundation, Inc. >>>>>>>> >>>>>>>> GNU Fortran comes with NO WARRANTY, to the extent permitted by law. >>>>>>>> You may redistribute copies of GNU Fortran >>>>>>>> under the terms of the GNU General Public License. >>>>>>>> For more information about these matters, see the file named COPYING >>>>>>>> >>>>>>>> gcc (GCC) 4.4.4 20100726 (Red Hat 4.4.4-13) >>>>>>>> Copyright (C) 2010 Free Software Foundation, Inc. >>>>>>>> This is free software; see the source for copying conditions. There is >>>>>>>> NO >>>>>>>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR >>>>>>>> PURPOSE. >>>>>>>> >>>>>>>> Linux volt.txcorp.com 2.6.32-71.29.1.el6.x86_64 #1 SMP Mon Jun 27 >>>>>>>> 19:49:27 BST 2011 x86_64 x86_64 x86_64 GNU/Linux >>>>>>>> >>>>>>>> On 10/17/12 10:14 AM, Raymond Lu wrote: >>>>>>>>> Scot, >>>>>>>>> >>>>>>>>> What compiler do you use? What version is it? Thanks. >>>>>>>>> >>>>>>>>> Ray >>>>>>>>> >>>>>>>>> On Oct 17, 2012, at 10:03 AM, Scott Sides wrote: >>>>>>>>> >>>>>>>>>> I just tried the new 1.8.10 pre-release on Mac Lion >>>>>>>>>> and the binaries do not work. In particular the h5dump binary >>>>>>>>>> seg faults. Actualy, this problem seem to be persistent across >>>>>>>>>> lion, mountain lion and snow leopard since 1.8.7. We've had >>>>>>>>>> to revert to 1.8.7 on mac for some time. Is this problem known >>>>>>>>>> and is a fix being considered? Thanks, >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> ********************************* >>>>>>>>>> Dr. Scott W. Sides >>>>>>>>>> [email protected] >>>>>>>>>> >>>>>>>>>> Tech-X Corporation >>>>>>>>>> 5621 Arapahoe Avenue, Suite A >>>>>>>>>> Boulder, CO 80303 >>>>>>>>>> office: (720) 974-1849 >>>>>>>>>> fax : (303) 448-7756 >>>>>>>>>> ********************************* >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Hdf-forum is for HDF software users discussion. >>>>>>>>>> [email protected] >>>>>>>>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> Hdf-forum is for HDF software users discussion. >>>>>>>>> [email protected] >>>>>>>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> Hdf-forum is for HDF software users discussion. >>>>>> [email protected] >>>>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org >>>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>>> Hdf-forum is for HDF software users discussion. >>>>> [email protected] >>>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org >>>>> >>>> >>>> >>>> _______________________________________________ >>>> Hdf-forum is for HDF software users discussion. >>>> [email protected] >>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org >>>> >>> >>> >>> -- >>> ********************************* >>> Dr. Scott W. Sides >>> [email protected] >>> >>> Tech-X Corporation >>> 5621 Arapahoe Avenue, Suite A >>> Boulder, CO 80303 >>> office: (720) 974-1849 >>> fax : (303) 448-7756 >>> ********************************* >>> >>> >>> _______________________________________________ >>> Hdf-forum is for HDF software users discussion. >>> [email protected] >>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org >> >> >> _______________________________________________ >> Hdf-forum is for HDF software users discussion. >> [email protected] >> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
_______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
