MantisBT - CMake
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IDProjectCategoryView StatusDate SubmittedLast Update
0015618CMakeModulespublic2015-06-16 09:302016-06-10 14:31
ReporterSebastian Wouters 
Assigned ToKitware Robot 
PrioritynormalSeveritycrashReproducibilityalways
StatusclosedResolutionmoved 
Platformx86OSlinux/debianOS Versionsid
Product VersionCMake 3.2.2 
Target VersionFixed in Version 
Summary0015618: HDF5 headers have migrated in linux/debian/sid -- FindHDF5.cmake doesn't detect them
DescriptionI got the following comment from someone who's helping me package my code for debian:

> 4. The include for HDF5 in CheMPS2/include/chemps2/MyHDF5.h is not
> working for me, there's no /usr/include/hdf5.h (anymore?). If I replace
> that with '#include <hdf5/serial/hdf5.h>', it builds fine.

I have currently used a work-around to make debuild work for sid: https://github.com/SebWouters/CheMPS2/blob/master/CheMPS2/CMakeLists.txt [^]

According to HDF5's specifications, one should include <hdf5.h>, see section 5 on the page http://www.hdfgroup.org/ftp/HDF5/current/src/unpacked/release_docs/INSTALL [^]

In sid's packaged hdf5 version, this file is installed in /usr/include/hdf5/serial/: https://packages.debian.org/sid/amd64/libhdf5-dev/filelist [^]

Would it be possible to modify the FindHDF5.cmake so that it detects the hdf5 headers on sid and correctly sets the HDF5_INCLUDE_DIRS variable?
Steps To ReproduceDownload and install debian/sid
Get cmake, libatlas3-base, libgsl0-dev, and libhdf5-dev with the package manager
Download chemps2 commit 226b04dfc07589804fbf7bf2b78b409b08d937eb, or earlier
Try to build chemps2 with cmake
Additional InformationThe discussion at debichem's mailing list:

http://lists.alioth.debian.org/pipermail/debichem-devel/2015-June/005963.html [^]
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Issue History
Date ModifiedUsernameFieldChange
2015-06-16 09:30Sebastian WoutersNew Issue
2015-06-16 09:48Brad KingNote Added: 0038934
2015-08-30 04:03Paul RomanoNote Added: 0039355
2015-08-31 13:32Sebastian WoutersNote Added: 0039360
2016-06-10 14:29Kitware RobotNote Added: 0042797
2016-06-10 14:29Kitware RobotStatusnew => resolved
2016-06-10 14:29Kitware RobotResolutionopen => moved
2016-06-10 14:29Kitware RobotAssigned To => Kitware Robot
2016-06-10 14:31Kitware RobotStatusresolved => closed

Notes
(0038934)
Brad King   
2015-06-16 09:48   
The FindHDF5 module currently has no maintainer:

 http://www.cmake.org/Wiki/CMake:Module_Maintainers [^]

so no one is actively working on issues reported against it.
(0039355)
Paul Romano   
2015-08-30 04:03   
I find that HDF5_INCLUDE_DIRS is set correctly on Ubuntu 15.04 which also has a libhdf5-dev package that puts hdf5.h in /usr/include/hdf5/serial. Looking at FindHDF5.cmake, the compile line, e.g. 'h5cc -show' is parsed to look for include directories, one of which is -I/usr/include/hdf5/serial. This is then used in HINTS when find_path(HDF5_${LANGUAGE}_INCLUDE_DIR ...) is called.

Sebastian, can you report what you get when you run 'h5cc -show'?
(0039360)
Sebastian Wouters   
2015-08-31 13:32   
I packaged chemps2 for debian on ubuntu 14.04. It was Michael Banck who tested on debian/sid and told me about the missing header files. I've sent him an e-mail to ask.
(0042797)
Kitware Robot   
2016-06-10 14:29   
Resolving issue as `moved`.

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