[MOAB-dev] HDF5 CMake Troubles

[Vijay S. Mahadevan]

Paul, your patch, modified as a PR [1] has been merged to master. Just FYI.

Vijay

[1] https://bitbucket.org/fathomteam/moab/pull-requests/375/fixes-for-hdf5-configuration-with-cmake/diff

On Fri, Nov 10, 2017 at 4:16 PM, Vijay S. Mahadevan <vijay.m at gmail.com> wrote:
> Paul, we will take a look at the patch you sent and fix the issue. We
> have tested our CMake configuration with system installed HDF/NetCDF
> libraries and this didn't replicate the problems  you mentioned.
> Nevertheless, if we can improve and make the build system more robust,
> all patches welcome.
>
> If you want to submit a PR directly to our Bitbucket website in the
> future, that would also add context to such additions. I will let you
> know when we have the patch merged to master.
>
> Thanks,
> Vijay
>
> On Fri, Nov 10, 2017 at 3:34 PM, Kuberry, Paul Allen <pakuber at sandia.gov> wrote:
>>
>> Hello,
>>
>>
>> I ran into three issues while building MOAB with CMake and my own hdf5:
>>
>>
>> 1.)
>>
>>
>>    Although I had a version of hdf5 library on my PC (apt-get install ...),
>> I was trying to get MOAB to build using CMake with the hdf5 from the one
>> that I had built. It continued to pick up the system version, despite all of
>> my efforts to get it not to.
>>
>>
>> I was getting messages like:
>>
>>
>> CMake Warning at test/CMakeLists.txt:129 (add_executable):
>>   Cannot generate a safe runtime search path for target mbcn_test because
>>   files in some directories may conflict with libraries in implicit
>>   directories:
>>
>>     runtime library [libhdf5.so.7] in /usr/lib/x86_64-linux-gnu may be
>> hidden by files in:
>>       /ascldap/users/pakuber/hdf5/lib
>>
>>   Some of these libraries may not be found correctly.
>>
>> and this was resulting in bad builds (the system version wasn't parallel).
>>
>>
>> I fixed defaulting to the system version of hdf5 by amending the line in
>> FindHDF5_MOAB.cmake to:find_package(HDF5 COMPONENTS C HL NO_DEFAULT_PATH)
>>
>>
>> 2.) After fixing the libraries, with #1 and ensuring that I get the
>> libraries that I'm trying to use, I found that FindHDF5_MOAB.cmake was not
>> assigning the CMake variable HDF5_INCLUDES, which caused CMake errors.
>>
>>
>> Rebuilding hdf5 with CMake, I observed that despite finding my
>> hdf5-config.cmake, I needed to add the line:
>>
>> SET( HDF5_INCLUDES "${HDF5_INCLUDE_DIR}" )
>>
>> to FindHDF5_MOAB.cmake
>>
>>
>> as can be seen in the attached diff.patch file.
>>
>>
>> 3.) In config/MOABConfig.cmake.in,
>>
>>
>> in line 28 and 78 @HDF5_DIR@ is used, but in config/MOABConfig.cmake.cmake,
>>
>> line 28 is replaced by @HDF5_ROOT@ while line 78 remains @HDF5_DIR@, causing
>> build errors.
>>
>>
>> This is also address in the attached patch file.
>>
>>
>> Take care,
>>
>> ---------------------------------------------
>>
>> Paul Kuberry
>>
>> Sandia National Laboratories
>>
>> P.O. Box 5800, Mailstop 1320
>> Albuquerque, NM 87123-1320
>> (505) 844-3668