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0015618

CMake

Modules

public

2015-06-16 09:30

2016-06-10 14:31

Reporter

Sebastian Wouters

Assigned To

Kitware Robot

Priority

normal

Severity

crash

Reproducibility

always

Status

closed

Resolution

moved

Platform

x86

linux/debian

OS Version

sid

Product Version

CMake 3.2.2

Target Version

Fixed in Version

Summary

0015618: HDF5 headers have migrated in linux/debian/sid -- FindHDF5.cmake doesn't detect them

Description

I 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 Reproduce

Download 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 Information

The discussion at debichem's mailing list:

http://lists.alioth.debian.org/pipermail/debichem-devel/2015-June/005963.html [^]

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Notes
(0038934) Brad King (manager) 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 (reporter) 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 (reporter) 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 (administrator) 2016-06-10 14:29	Resolving issue as `moved`. This issue tracker is no longer used. Further discussion of this issue may take place in the current CMake Issues page linked in the banner at the top of this page.

Issue History
Date Modified	Username	Field	Change
2015-06-16 09:30	Sebastian Wouters	New Issue
2015-06-16 09:48	Brad King	Note Added: 0038934
2015-08-30 04:03	Paul Romano	Note Added: 0039355
2015-08-31 13:32	Sebastian Wouters	Note Added: 0039360
2016-06-10 14:29	Kitware Robot	Note Added: 0042797
2016-06-10 14:29	Kitware Robot	Status	new => resolved
2016-06-10 14:29	Kitware Robot	Resolution	open => moved
2016-06-10 14:29	Kitware Robot	Assigned To	=> Kitware Robot
2016-06-10 14:31	Kitware Robot	Status	resolved => closed