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. > ________________________________ >
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