[FLASH-USERS] hdf5 for Ubuntu

[Chris Daley]

Hi Kris,

This looks like a genuine bug in hdf5:
https://bugs.launchpad.net/ubuntu/+source/hdf5/+bug/286565

Download version HDF-1.6.8:
(ftp://ftp.hdfgroup.org/HDF5/current16/src/)


http://www.hdfgroup.org/HDF5/doc1.6/ADGuide/RELEASE.txt:

Bug Fixes since HDF5-1.6.8 Release
==================================

    Tools
    -----
    - zip_perf.c had missing argument on one of the open() calls. Fixed.
      AKC - 2008/12/9


As a side note, FLASH uses HDF5 1.6 bindings.

Regards,
Chris


Kris Murawski wrote:
> Hi Chris,
>
> thank you for your prompt reply.
>
> I am using :
>
> hdf5-1.8.2
> mpich2-1.0.8
> Intel10.1.015
> Ubuntu: 9.04 (64 or 32-bit, I am not sure that)
>
> I configure with
>
> CC=gcc FC=/opt/intel/fc/10.1.015/bin/ifort ./configure 
> --prefix=/usr/local/hdf5 --enable-fortran --enable-cxx
>
> with the following output:
>
> Features:
> ---------
> Parallel HDF5: no
> High Level library: yes
> Threadsafety: no
> Default API Mapping: v18
> With Deprecated Public Symbols: yes
> I/O filters (external): deflate(zlib)
> I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
> MPE: no
> Direct VFD: no
> dmalloc: no
> Clear file buffers before write: yes
> Using memory checker: no
> Function Stack Tracing: no
> GPFS: no
> Strict File Format Checks: no
> Optimization Instrumentation: no
> Linux Large File Support (LFS): yes
>
> When I "make" I get at the end
>
> /usr/include/bits/unistd.h:39: warning: will never be executed
> /usr/include/bits/unistd.h:42: warning: will never be executed
> /usr/include/bits/unistd.h:43: warning: will never be executed
> /usr/include/bits/unistd.h:40: warning: will never be executed
> /usr/include/bits/string3.h:82: warning: will never be executed
> In function ‘open’,
> inlined from ‘do_write_test’ at zip_perf.c:552,
> inlined from ‘main’ at zip_perf.c:653:
> /usr/include/bits/fcntl2.h:51: error: call to ‘__open_missing_mode’ 
> declared with attribute error: open with O_CREAT in second argument 
> needs 3 arguments
> zip_perf.c:69:1: warning: macro "GZ_SUFFIX" is not used
> zip_perf.c:50:1: warning: macro "SET_BINARY_MODE" is not used
> zip_perf.c:91:1: warning: macro "BUFLEN" is not used
> zip_perf.c:72:1: warning: macro "SUFFIX_LEN" is not used
> zip_perf.c:92:1: warning: macro "MAX_NAME_LEN" is not used
> make[2]: *** [zip_perf.o] Error 1
> make[2]: Leaving directory `/home/kris/tmp/hdf5-1.8.2/perform'
> make[1]: *** [all-local] Error 2
> make[1]: Leaving directory `/home/kris/tmp/hdf5-1.8.2'
> make: *** [all-recursive] Error 1
>
>
> Thank you in advance for your help.
>
> Best wishes,
>
> Kris
>
> Chris Daley wrote:
>> Show us the make error messages.
>>
>> Chris
>>
>> Kris Murawski wrote:
>>> Dear All,
>>>
>>> sorry about the former mail which should read as it is
>>> now.
>>>
>>> I have problems installing the recent version of hdf5 on
>>> the recent version of Ubuntu for the recent version of
>>> Intel f90 compiler. Unfortunately, "make" shows up bugs.
>>> Has anyone come across this problem? I would appreciate
>>> your help.
>>>
>>> Best wishes,
>>>
>>> Kris
>>>
>>>
>>
>>