[Hdf-forum] Failure to compile HDF

Larry Knox lrknox at hdfgroup.org
Tue Aug 12 09:32:58 CDT 2014


Actually you need to run "make" before "make check".  If you still have the build, running "make" will finish building the tools includeing h5import, then "make check install" should complete without failures.  If you start again from scratch, run "make; make check install" to work around the problem.

Larry

-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces at lists.hdfgroup.org] On Behalf Of help at hdfgroup.org
Sent: Tuesday, August 12, 2014 9:22 AM
To: Syed Ahsan Ali Bokhari
Cc: HDF Helpdesk; HDF Users Discussion List
Subject: Re: [Hdf-forum] Failure to compile HDF

Hello Ahsan,

We can reproduce the issue and will enter a bug report for this.

The problem is that h5import has not been built yet when the tests are being run.

If you run 'make check' and then 'make install', then the tests should complete properly.

-Barbara
help at hdfgroup.org

On Tue, 12 Aug 2014, Syed Ahsan Ali Bokhari wrote:

> Dear George
> Thank you for your reply. I didn't have red hat subscription that is
> why I switched to CentOS6.5 and this time I upgraded gcc using
> devtoolset gcc-4.8.2. The issue is that I want to install netcdf with
> netcdf4 support which needs zlib and hdf to be compiled first. I
> installed zlib first and then I tried to compile hdf specifying the
> zlib directory ./configure --with-zlib=/opt/zlib-1.2.8/
> --prefix=/opt/hdf5-1.8.13
> (config.log) is attached.
> the make process again crashes at the end during tests. Please see
> attached make.out.
>
> Thank you for your help.
> Ahsan
>
>
> On Thu, Aug 7, 2014 at 3:47 PM, George N. White III <gnwiii at gmail.com>
> wrote:
>
>> On Thu, Aug 7, 2014 at 1:33 AM, Syed Ahsan Ali Bokhari <
>> ahsan.pmd at gmail.com> wrote:
>>
>>>
>>> I have tried different versions of HDF but compilation fails for all.
>>> Please have a look at attcched log files. Following are the commands
>>> I use to compile
>>>
>>
>> Unless you have specific software that requires an older version of
>> the
>> hdf5 libraries I suggest you spend less time trying old versions and
>> more time investigating the problems building the current version.
>> Otherwise you end up rediscovering bugs that have been fixed in more
>> recent hdf5 versions.
>>
>> You appear to have installed gcc-4.9.1.   Providing a complete development
>> environment for Red Hat systems requires more than just installing
>> the compiler.  RH has done this work for you with the devtoolset
>> software collections.  I have been using the devtoolset compilers to
>> build large systems that use hdf5 libraries with few problems and
>> excellent reliability in use.  You can get free (unsupported) clone
>> packages from CERN Scientific Linux <
>> http://linux.web.cern.ch/linux/devtoolset/>.  These rpms can be
>> installed in real RHEL 5+6, CentOS 5+6, and SL 5+6 , and probably Oracle Linux 5+6.
>>
>> I think Cmake is more robust than GNU configure.
>>
>>
>>
>>> ./configure --with-zlib=/opt/zlib-1.2.8/ --prefix=/opt/hdf5-1.8.9
>>>
>>> make check install
>>>
>>> th5s.c:734:9: error: expected expression before ?/? token
>>>          // CHECK(ret, FAIL, "H5Pset_alloc_time");
>>>          ^
>>> In file included from th5s.c:25:0:
>>> th5s.c: At top level:
>>> H5srcdir.h:38:20: warning: ?H5_get_srcdir_filename? defined but not
>>> used [-Wunused-function]  static const char
>>> *H5_get_srcdir_filename(const char *filename)
>>>                     ^
>>> H5srcdir.h:68:20: warning: ?H5_get_srcdir? defined but not used
>>> [-Wunused-function]  static const char *H5_get_srcdir(void)
>>>                     ^
>>> make[1]: *** [th5s.o] Error 1
>>> make: *** [check-recursive] Error 1
>>>
>>>
>>> Thank you for your help!
>>> --
>>>  Syed Ahsan Ali Bokhari
>>>  Electronic Engineer
>>>  Research & Development Division
>>>  Pakistan Meteorological Department H-8/2, Islamabad.
>>>  Phone # off +92519250361
>>>  Cell # +923155145014
>>>  Fax # +92519250368
>>>  www.pmd.gov.pk
>>>
>>>
>>>
>>> --
>>>  Syed Ahsan Ali Bokhari
>>>  Electronic Engineer
>>>  Research & Development Division
>>>  Pakistan Meteorological Department H-8/2, Islamabad.
>>>  Phone # off +92519250361
>>>  Cell # +923155145014
>>>  Fax # +92519250368
>>>  www.pmd.gov.pk
>>>
>>> _______________________________________________
>>> Hdf-forum is for HDF software users discussion.
>>> Hdf-forum at lists.hdfgroup.org
>>>
>>> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfg
>>> roup.org
>>> Twitter: https://twitter.com/hdf5
>>>
>>
>>
>>
>> --
>> George N. White III <aa056 at chebucto.ns.ca> Head of St. Margarets Bay,
>> Nova Scotia
>>
>> _______________________________________________
>> Hdf-forum is for HDF software users discussion.
>> Hdf-forum at lists.hdfgroup.org
>>
>> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgr
>> oup.org
>> Twitter: https://twitter.com/hdf5
>>
>
>
>
>

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