For those that have the time, please take a look at the 1.8 branch in our svn repo. Also, please stay tuned on for annoucement when we will have our public CDash site available!
Thanks,
Allen
> I haven't really followed the whole discussion but in our projects, we
> no longer use the FindHDF5.cmake file which comes with cmake since HDF5
> now directly defines hdf5-config.cmake, hdf5-targets.cmake etc in
> lib/cmake/hdf5-version or share/cmake/hdf5-version depending on the
> version used.
>
> We just do something like this:
> FIND_PACKAGE(HDF5 "1.8.6" REQUIRED NO_MODULE)
> IF(HDF5_FOUND)
> SET(LIBS hdf5)
> INCLUDE_DIRECTORIES(${HDF5_INCLUDE_DIR})
> ENDIF(HDF5_FOUND)
>
> Then we simply give, during the cmake configuration, the HDF5_DIR where
> all the hdf5 .cmake files are installed and that's all.
>
> Jerome
>
> On 03/15/2011 10:16 PM, Williams, Norman K wrote:
> > I just wanted to write some files so matlab could read them 
> >
> >
> > I talk nearly daily with people at Kitware about CMake -- I think part of
> > the problem is that whatever gets pushed into CMake sticks around; the HDF
> > library has a couple of commonly used major versions and active
> > development on minor versions. A really useful FindHDF5.cmake would
> > support specifying the version, and adjust according to the version
> > requested.
> >
> >
> > On 3/15/11 4:01 PM, "Michael Jackson"<mike.jackson@bluequartz.net> > wrote:
> >
> >> On the note of the FindHDF5.cmake file that comes with CMake "The HDF
> >> Group" may want to really consider taking ownership of that module so
> >> that you can synchronize the "FindHDF.cmake" with the HDF5/CMake
> >> integration and make sure they work correctly together. I also have my
> >> own version of FindHDF5.cmake that I use that works with my cmake version
> >> of HDF5 V1.6.9. I think there are more than a few versions of
> >> FindHDF5.cmake floating around.
> >>
> >> ___________________________________________________________
> >> Mike Jackson www.bluequartz.net
> >> Principal Software Engineer mike.jackson@bluequartz.net
> >> BlueQuartz Software Dayton, Ohio
> >>
> >> On Mar 15, 2011, at 4:24 PM, Allen D Byrne wrote:
> >>
> >>> Yes. I found that out as well, I have overrode that module in the 1.8.7
> >>> config/cmake folder. You might try getting the source from the 1.8
> >>> branch:
> >>> http://svn.hdfgroup.uiuc.edu/hdf5/branches/hdf5_1_8
> >>> Allen
> >>>> I'd be glad to use a snapshot, if it fixed the problems I'm seeing.
> >>>>
> >>>> The bigger problem is that the FindHDF5.cmake that's distributed with
> >>>> CMake is brain-damaged, or its interaction with the hdf5-config.cmake
> >>> file
> >>>> is dysfunctional.
> >>>>
> >>>> FindHDF5.cmake is looking for h5cc or h5pcc which aren't actually
> >>> getting
> >>>> built or installed.
> >>>> Then HDF5_INCLUDE_DIRS and HDF5_LIBRARIES are supposed to be defined
> >>> in
> >>>> hdf5-config.cmake and they aren't.
> >>>>
> >>>>
> >>>> --
> >>>> Kent Williams norman-k-williams@uiowa.edu
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>> From: Allen D Byrne<byrn@hdfgroup.org>
> >>>> Organization: HDF Group
> >>>> Date: Tue, 15 Mar 2011 14:57:06 -0500
> >>>> To: Mushly McMushmaster<norman-k-williams@uiowa.edu>
> >>>> Cc: "hdf-forum@hdfgroup.org"<hdf-forum@hdfgroup.org>
> >>>> Subject: Re: [Hdf-forum] Trying to build HDF5 1.8.6 with CMake,
> >>> getting
> >>>> undefined externals?
> >>>>
> >>>>
> >>>> Interesting. I wouldn't think you need to pass in the COMPILER args
> >>> since
> >>>> it should use the same settings as the parent project. Post 1.8.6
> >>> code has
> >>>> been tested as an external project, but with compression libs
> >>> explictly
> >>>> enabled/disabled. Have you inspected the generated files to determine
> >>> if
> >>>> they make sense. How about the log files for any clues?
> >>>> Can you use a 1.8.7 snapshot? There was significant cmake code changes
> >>>> after 1.8.6 concerning use as an External Project.
> >>>> Allen
> >>>>> I satisfy both of those expectations. If you're curious what I'm
> >>> doing
> >>>>> is:
> >>>>>
> >>>>> # External_HDF5.cmake
> >>>>> #
> >>>>> # gets C/CXX stuff from parent project
> >>>>> # BRAINS3_INSTALL_PREFIX = local install dir for prerequisites for
> >>>>> BRAINS3
> >>>>> # BUILD_SHARED_LIBS = whether or not to build shared libs. Normally
> >>> On.
> >>>>> include(ExternalProject)
> >>>>>
> >>>>> ExternalProject_add(HDF5
> >>>>> SOURCE_DIR HDF5
> >>>>> BINARY_DIR HDF5-build
> >>>>> URL
> >>> "http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.6.tar.gz"
> >>>>> URL_MD5 bd2d369dfcf7aa0437dde6aeb8460a31
> >>>>> UPDATE_COMMAND ""
> >>>>> CMAKE_ARGS
> >>>>> -DCMAKE_CXX_COMPILER:STRING=${CMAKE_CXX_COMPILER}
> >>>>> -DCMAKE_CXX_COMPILER_ARG1:STRING=${CMAKE_CXX_COMPILER_ARG1}
> >>>>> -DCMAKE_C_COMPILER:STRING=${CMAKE_C_COMPILER}
> >>>>> -DCMAKE_C_COMPILER_ARG1:STRING=${CMAKE_C_COMPILER_ARG1}
> >>>>> -DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS}
> >>>>> -DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS}
> >>>>> -DBUILD_SHARED_LIBS:BOOL=${BUILD_SHARED_LIBS}
> >>>>> -DCMAKE_INSTALL_PREFIX:PATH=${BRAINS3_INSTALL_PREFIX}
> >>>>> INSTALL_DIR ${BRAINS3_INSTALL_PREFIX}
> >>>>> )
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> From: Allen D Byrne<byrn@hdfgroup.org>
> >>>>> Organization: HDF Group
> >>>>> Date: Tue, 15 Mar 2011 14:24:06 -0500
> >>>>> To:<hdf-forum@hdfgroup.org>
> >>>>> Cc: Mushly McMushmaster<norman-k-williams@uiowa.edu>
> >>>>> Subject: Re: [Hdf-forum] Trying to build HDF5 1.8.6 with CMake,
> >>> getting
> >>>>> undefined externals?
> >>>>>
> >>>>>
> >>>>> When building with cmake there are two expectations, one is that the
> >>>>> everything will be built out of source (usually create a sub-folder
> >>>>> called
> >>>>> build) and that the source folders are clean (you did not run
> >>> configure
> >>>>> and/or build in source).
> >>>>> That has to do with the cmake part, I will need find some help for
> >>> why
> >>>>> you
> >>>>> get the following errors if the above conditions are met.
> >>>>> Allen
> >>>>>> I sure don't understand this problem. If I use CMake (on OS X
> >>> 10.6
> >>>>> with
> >>>>>> CMake 2.8.4) I get all sorts of mysterious undefined externals.
> >>>>>>
> >>>>>> When I look through the source, these appear to be used as
> >>> function
> >>>>>> points
> >>>>>> when they've never been defined. E.G.
> >>>>>>
> >>>>>> ./src/H5Osdspace.c:#define H5O_SHARED_ENCODE
> >>> H5O_sdspace_shared_encode
> >>>>>> ./src/H5Osdspace.c: H5O_sdspace_shared_encode, /* encode
> >>> message */
> >>>>>>
> >>>>>> What gives?
> >>>>>>
> >>>>>> Linking C shared library ../bin/libhdf5.dylib
> >>>>>> Undefined symbols:
> >>>>>> "_H5O_sdspace_shared_encode", referenced from:
> >>>>>> _H5O_MSG_SDSPACE in H5Osdspace.c.o
> >>>>>> "_H5O_attr_shared_size", referenced from:
> >>>>>> _H5O_MSG_ATTR in H5Oattr.c.o
> >>>>>> "_H5O_fill_shared_encode", referenced from:
> >>>>>> _H5O_MSG_FILL in H5Ofill.c.o
> >>>>>> "_H5O_pline_shared_encode", referenced from:
> >>>>>> _H5O_MSG_PLINE in H5Opline.c.o
> >>>>>> "_H5O_dtype_shared_copy_file", referenced from:
> >>>>>> _H5O_MSG_DTYPE in H5Odtype.c.o
> >>>>>> "_H5O_attr_shared_post_copy_file", referenced from:
> >>>>>> _H5O_MSG_ATTR in H5Oattr.c.o
> >>>>>> "_H5O_fill_new_shared_decode", referenced from:
> >>>>>> _H5O_MSG_FILL_NEW in H5Ofill.c.o
> >>>>>> "_H5O_fill_new_shared_debug", referenced from:
> >>>>>> _H5O_MSG_FILL_NEW in H5Ofill.c.o
> >>>>>> "_H5O_attr_shared_decode", referenced from:
> >>>>>> _H5O_MSG_ATTR in H5Oattr.c.o
> >>>>>> "_H5O_fill_new_shared_delete", referenced from:
> >>>>>> _H5O_MSG_FILL_NEW in H5Ofill.c.o
> >>>>>> "_H5O_attr_shared_delete", referenced from:
> >>>>>> _H5O_MSG_ATTR in H5Oattr.c.o
> >>>>>> "_H5O_sdspace_shared_decode", referenced from:
> >>>>>> _H5O_MSG_SDSPACE in H5Osdspace.c.o
> >>>>>> "_H5O_fill_shared_decode", referenced from:
> >>>>>> _H5O_MSG_FILL in H5Ofill.c.o
> >>>>>> "_H5O_pline_shared_decode", referenced from:
> >>>>>> _H5O_MSG_PLINE in H5Opline.c.o
> >>>>>> "_H5O_pline_shared_link", referenced from:
> >>>>>> _H5O_MSG_PLINE in H5Opline.c.o
> >>>>>> "_H5O_sdspace_shared_delete", referenced from:
> >>>>>> _H5O_MSG_SDSPACE in H5Osdspace.c.o
> >>>>>> "_H5O_fill_new_shared_link", referenced from:
> >>>>>> _H5O_MSG_FILL_NEW in H5Ofill.c.o
> >>>>>> "_H5O_fill_shared_delete", referenced from:
> >>>>>> _H5O_MSG_FILL in H5Ofill.c.o
> >>>>>> "_H5O_attr_shared_debug", referenced from:
> >>>>>> _H5O_MSG_ATTR in H5Oattr.c.o
> >>>>>> "_H5O_sdspace_shared_link", referenced from:
> >>>>>> _H5O_MSG_SDSPACE in H5Osdspace.c.o
> >>>>>> "_H5O_pline_shared_delete", referenced from:
> >>>>>> _H5O_MSG_PLINE in H5Opline.c.o
> >>>>>> "_H5O_pline_shared_size", referenced from:
> >>>>>> _H5O_MSG_PLINE in H5Opline.c.o
> >>>>>> "_H5O_pline_shared_debug", referenced from:
> >>>>>> _H5O_MSG_PLINE in H5Opline.c.o
> >>>>>> "_H5O_dtype_shared_link", referenced from:
> >>>>>> _H5O_MSG_DTYPE in H5Odtype.c.o
> >>>>>> "_H5O_fill_new_shared_size", referenced from:
> >>>>>> _H5O_MSG_FILL_NEW in H5Ofill.c.o
> >>>>>> "_H5O_sdspace_shared_size", referenced from:
> >>>>>> _H5O_MSG_SDSPACE in H5Osdspace.c.o
> >>>>>> "_H5O_attr_shared_copy_file", referenced from:
> >>>>>> _H5O_MSG_ATTR in H5Oattr.c.o
> >>>>>> "_H5O_dtype_shared_size", referenced from:
> >>>>>> _H5O_MSG_DTYPE in H5Odtype.c.o
> >>>>>> "_H5O_pline_shared_copy_file", referenced from:
> >>>>>> _H5O_MSG_PLINE in H5Opline.c.o
> >>>>>> "_H5O_dtype_shared_encode", referenced from:
> >>>>>> _H5O_MSG_DTYPE in H5Odtype.c.o
> >>>>>> "_H5O_fill_shared_debug", referenced from:
> >>>>>> _H5O_MSG_FILL in H5Ofill.c.o
> >>>>>> "_H5O_sdspace_shared_copy_file", referenced from:
> >>>>>> _H5O_MSG_SDSPACE in H5Osdspace.c.o
> >>>>>> "_H5O_sdspace_shared_debug", referenced from:
> >>>>>> _H5O_MSG_SDSPACE in H5Osdspace.c.o
> >>>>>> "_H5O_fill_shared_link", referenced from:
> >>>>>> _H5O_MSG_FILL in H5Ofill.c.o
> >>>>>> "_H5O_fill_new_shared_copy_file", referenced from:
> >>>>>> _H5O_MSG_FILL_NEW in H5Ofill.c.o
> >>>>>> "_H5O_dtype_shared_decode", referenced from:
> >>>>>> _H5O_MSG_DTYPE in H5Odtype.c.o
> >>>>>> "_H5O_fill_shared_size", referenced from:
> >>>>>> _H5O_MSG_FILL in H5Ofill.c.o
> >>>>>> "_H5O_fill_new_shared_encode", referenced from:
> >>>>>> _H5O_MSG_FILL_NEW in H5Ofill.c.o
> >>>>>> "_H5O_fill_shared_copy_file", referenced from:
> >>>>>> _H5O_MSG_FILL in H5Ofill.c.o
> >>>>>> "_H5O_attr_shared_encode", referenced from:
> >>>>>> _H5O_MSG_ATTR in H5Oattr.c.o
> >>>>>> "_H5O_dtype_shared_delete", referenced from:
> >>>>>> _H5O_MSG_DTYPE in H5Odtype.c.o
> >>>>>> "_H5O_dtype_shared_debug", referenced from:
> >>>>>> _H5O_MSG_DTYPE in H5Odtype.c.o
> >>>>>> "_H5O_attr_shared_link", referenced from:
> >>>>>> _H5O_MSG_ATTR in H5Oattr.c.o
> >>>>>> ld: symbol(s) not found
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> ________________________________
> >>>>>> Notice: This UI Health Care e-mail (including attachments) is
> >>> covered
> >>>>> by
> >>>>>> the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is
> >>>>>> confidential and may be legally privileged. If you are not the
> >>> intended
> >>>>>> recipient, you are hereby notified that any retention,
> >>> dissemination,
> >>>>>> distribution, or copying of this communication is strictly
> >>> prohibited.
> >>>>>> Please reply to the sender that you have received the message in
> >>> error,
> >>>>>> then delete it. Thank you.
> >>>>>> ________________________________
> >>>>>>
> >>>>>> _______________________________________________
> >>>>>> Hdf-forum is for HDF software users discussion.
> >>>>>> Hdf-forum@hdfgroup.org
> >>>>>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
> >>>>>>
> >>>>>
> >>>>>
> >>>>> ________________________________
> >>>>> Notice: This UI Health Care e-mail (including attachments) is
> >>> covered by
> >>>>> the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is
> >>>>> confidential and may be legally privileged. If you are not the
> >>> intended
> >>>>> recipient, you are hereby notified that any retention, dissemination,
> >>>>> distribution, or copying of this communication is strictly
> >>> prohibited.
> >>>>> Please reply to the sender that you have received the message in
> >>> error,
> >>>>> then delete it. Thank you.
> >>>>> ________________________________
> >>>>>
> >>>>
> >>>>
> >>>> ________________________________
> >>>> Notice: This UI Health Care e-mail (including attachments) is covered
> >>> by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is
> >>> confidential and may be legally privileged. If you are not the intended
> >>> recipient, you are hereby notified that any retention, dissemination,
> >>> distribution, or copying of this communication is strictly prohibited.
> >>> Please reply to the sender that you have received the message in error,
> >>> then delete it. Thank you.
> >>>> ________________________________
> >>>>
> >>> _______________________________________________
> >>> Hdf-forum is for HDF software users discussion.
> >>> Hdf-forum@hdfgroup.org
> >>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
> >>
> >> _______________________________________________
> >> Hdf-forum is for HDF software users discussion.
> >> Hdf-forum@hdfgroup.org
> >> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
> >
> >
> > ________________________________
> > Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you.
> > ________________________________
> >
> > _______________________________________________
> > Hdf-forum is for HDF software users discussion.
> > Hdf-forum@hdfgroup.org
> > http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>
>
>
