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 [email protected] 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 [email protected] > > > > > > > > > > > > > > From: Allen D Byrne <[email protected]> > > Organization: HDF Group > > Date: Tue, 15 Mar 2011 14:57:06 -0500 > > To: Mushly McMushmaster <[email protected]> > > Cc: "[email protected]" <[email protected]> > > 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 <[email protected]> > > > Organization: HDF Group > > > Date: Tue, 15 Mar 2011 14:24:06 -0500 > > > To: <[email protected]> > > > Cc: Mushly McMushmaster <[email protected]> > > > 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. > > > > [email protected] > > > > 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. > [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
