make check failures with gcc/4.9.0 and HDF5 1.8.13 (long double conversions)

When building with hdf5/1.8.13 with the following configure line:
./configure CC=gcc CXX=g++ FC=gfortran --disable-silent-rules --enable-fortran --enable-fortran2003 --enable-static --with-pic --disable-sharedlib-rpath --enable-shared --enable-cxx

With the gcc, g++ and gfortran resolving to gcc/4.9 I see the following failures:
grep "FAILED" gcc49.check.out
Testing hard signed char -> long double conversions *FAILED*
Testing hard unsigned char -> long double conversions *FAILED*
Testing hard short -> long double conversions *FAILED*
Testing hard unsigned short -> long double conversions *FAILED*
Testing hard int -> long double conversions *FAILED*
Testing hard unsigned int -> long double conversions *FAILED*
Testing hard long -> long double conversions *FAILED*

Has anyone else observed this ? Is there a workaround. Thanks.

Sean B.

···

From: Elena Pourmal <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>>
Reply-To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Date: Thursday, May 15, 2014 2:35 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Subject: Re: [Hdf-forum] make check-install fails with HDF5 1.8.13

Ekin,

On May 15, 2014, at 1:42 PM, Ekin Akoglu <ekin@ims.metu.edu.tr<mailto:ekin@ims.metu.edu.tr>> wrote:

Dear Elena,

Changing to the directory hdf5-1.8.13/fortran/examples and then issuing

$ h5fc -o h5_crtdat h5_crtdat.f90

works. However, the check-install complains about not being able to open h5_crtdat.o to write, which already exists. I checked the permissions of that file and they are correct: 644, so write is allowed.

Do you have an idea?

No idea at this point. We couldn't reproduce the problem here on one of our machines with Intel Fortran compiler.

Could you please try to run run-fortran-ex.sh in that directory?

./run-fortran-ex.sh

Thank you!

Elena
Thank you,

Ekin

On 15 May 2014 19:47, Elena Pourmal <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>> wrote:
Ekin,

It looks like that for some reason Fortran compiler cannot write *.o file. Could it be that you ran out of space? Is there quota on your system? Was /tmp partition full?

I would try to run make check-install the second time, or go to /usr/local/hdf5-1.8.13/share/hdf5_examples/fortran and try to run the following command

../../../bin/h5fc -o h5_crtdat h5_crtdat.f90

and see if it works.

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org<http://hdfgroup.org/>
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 10:30 AM, Ekin Akoglu <ekin@ims.metu.edu.tr<mailto:ekin@ims.metu.edu.tr>> wrote:

Dear Elena,

The OS is 64-bit Debian Wheezy 7.5. The compiler is Intel Fortran Compiler 2013 SP1 Update 3, which is exactly 14.0.3 20140422. My GCC version is 4.7.2. I built and installed HDF5 as follows:

$ ./configure --prefix=/usr/local/hdf5-1.8.13 --enable-fortran --enable-fortran2003
$ make
$ make check
# make install
$ make check-install

Everything except the "make check-install" step worked flawlessly.

Thank you.

Kind regards,

Ekin

On 15 May 2014 17:11, Elena Pourmal <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>> wrote:
Ekin,

Could you please provide OS and compiler information? It would also help if you post the outputs of the commands used to build and install the HDF5 libraries.

Thank you!

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org<http://hdfgroup.org/>
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 9:10 AM, Ekin Akoglu <ekin@ims.metu.edu.tr<mailto:ekin@ims.metu.edu.tr>> wrote:

Dear all,

I have just installed the HDF5 version 1.8.13 and the check-install process failed with:

============================
Testing run-fortran-ex.sh

################# h5_crtdat #################
error: can't open file h5_crtdat.o for write
compilation aborted for h5_crtdat.f90 (code 1)
messed up compiling h5_crtdat.f90
rm: cannot remove `*.o': No such file or directory
rm: cannot remove `*.h5': No such file or directory

make[3]: *** [installcheck-local] Error 1
make[3]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran/examples'
make[2]: *** [installcheck-local] Error 1
make[2]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran'
make[1]: *** [installcheck-recursive] Error 1
make[1]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran'
make: *** [installcheck-recursive] Error 1

Regards,

Ekin

On 15 May 2014 15:20, <help@hdfgroup.org<mailto:help@hdfgroup.org>> wrote:

To view from a browser see:
   http://www.hdfgroup.org/newsletters/newsletter140.html

--------------------------------------------------------------------------
The HDF Group Home Page: http://www.hdfgroup.org/
Support Services: http://www.hdfgroup.org/services/
--------------------------------------------------------------------------

                            Newsletter #140
                             May 15, 2014

CONTENTS
. Release of HDF5-1.8.13

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Release of HDF5 1.8.13

The HDF5-1.8.13 release is now available, and can be downloaded from the
HDF Group Downloads page:

    http://www.hdfgroup.org/downloads/

It can also be obtained directly from:

    http://www.hdfgroup.org/HDF5/release/obtain5.html

HDF5-1.8.13 is a minor release, with a few new features and changes.
Important changes include:

o The H5free_memory (C) api was added to free memory that was allocated
   by HDF5 API calls. This was added specifically for Windows, but may be
   useful anywhere that the library uses a different memory manager than
   the application.

o New wrappers were added for C++ (many) and Fortran
   (h5pset_file_image_f and h5pget_file_image_f).

o Mac OS X 10.9 Mavericks is now supported.

o Many improvements were added in support of CMake, including the
   addition of support for CMake 2.8.11.

o Improvements were added to the Core VFD (or Memory VFD).

o The following changes were made to Parallel HDF5:

   - The MPI-POSIX VFD was removed. Application developers should
     always use the MPI-IO VFD.

   - Parallel HDF5 now supports collective I/O on point selections.

o A few changes were added to the tools (h5diff, h5dump, and h5repack).

This release contains many other changes that are not listed here.
Please be sure to read the Release Notes for a comprehensive list of
new features and changes:

   http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.13-RELEASE.txt

Changes that affect maintainers of HDF5-dependent applications are
listed in "HDF5 Software Changes from Release to Release". See:

   http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html

Future Changes to Supported Platforms
-------------------------------------

Please be aware that after this release, we will be moving to
CMake 3.0, and will add testing for VS 2013. VS 2012 will remain
the standard.

In addition, we will only support Cygwin built with CMake, and will
be dropping VS 2010.

-------------------------------------------------------------
For questions regarding these or other HDF issues, contact:

   help@hdfgroup.org<mailto:help@hdfgroup.org>

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

Hi Sean,

Thank you for trying with the newly released gcc! I'll add the issue to JIRA; we will try to support gcc 4.9.* in the next release.

As a workaround please try to use different level of optimization (edit the config/gnu-flags file; search for "Production" string and then edit gcc-4.* line).

Elena

···

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 2:45 PM, Sean Byland <seanb@cray.com> wrote:

When building with hdf5/1.8.13 with the following configure line:
./configure CC=gcc CXX=g++ FC=gfortran --disable-silent-rules --enable-fortran --enable-fortran2003 --enable-static --with-pic --disable-sharedlib-rpath --enable-shared --enable-cxx

With the gcc, g++ and gfortran resolving to gcc/4.9 I see the following failures:
grep "FAILED" gcc49.check.out
Testing hard signed char -> long double conversions *FAILED*
Testing hard unsigned char -> long double conversions *FAILED*
Testing hard short -> long double conversions *FAILED*
Testing hard unsigned short -> long double conversions *FAILED*
Testing hard int -> long double conversions *FAILED*
Testing hard unsigned int -> long double conversions *FAILED*
Testing hard long -> long double conversions *FAILED*

Has anyone else observed this ? Is there a workaround. Thanks.

Sean B.

From: Elena Pourmal <epourmal@hdfgroup.org>
Reply-To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Date: Thursday, May 15, 2014 2:35 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Subject: Re: [Hdf-forum] make check-install fails with HDF5 1.8.13

Ekin,

On May 15, 2014, at 1:42 PM, Ekin Akoglu <ekin@ims.metu.edu.tr> wrote:

Dear Elena,

Changing to the directory hdf5-1.8.13/fortran/examples and then issuing

$ h5fc -o h5_crtdat h5_crtdat.f90

works. However, the check-install complains about not being able to open h5_crtdat.o to write, which already exists. I checked the permissions of that file and they are correct: 644, so write is allowed.

Do you have an idea?

No idea at this point. We couldn't reproduce the problem here on one of our machines with Intel Fortran compiler.

Could you please try to run run-fortran-ex.sh in that directory?

./run-fortran-ex.sh

Thank you!

Elena

Thank you,

Ekin

On 15 May 2014 19:47, Elena Pourmal <epourmal@hdfgroup.org> wrote:

Ekin,

It looks like that for some reason Fortran compiler cannot write *.o file. Could it be that you ran out of space? Is there quota on your system? Was /tmp partition full?

I would try to run make check-install the second time, or go to /usr/local/hdf5-1.8.13/share/hdf5_examples/fortran and try to run the following command

../../../bin/h5fc -o h5_crtdat h5_crtdat.f90

and see if it works.

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 10:30 AM, Ekin Akoglu <ekin@ims.metu.edu.tr> wrote:

Dear Elena,

The OS is 64-bit Debian Wheezy 7.5. The compiler is Intel Fortran Compiler 2013 SP1 Update 3, which is exactly 14.0.3 20140422. My GCC version is 4.7.2. I built and installed HDF5 as follows:

$ ./configure --prefix=/usr/local/hdf5-1.8.13 --enable-fortran --enable-fortran2003
$ make
$ make check
# make install
$ make check-install

Everything except the "make check-install" step worked flawlessly.

Thank you.

Kind regards,

Ekin

On 15 May 2014 17:11, Elena Pourmal <epourmal@hdfgroup.org> wrote:

Ekin,

Could you please provide OS and compiler information? It would also help if you post the outputs of the commands used to build and install the HDF5 libraries.

Thank you!

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 9:10 AM, Ekin Akoglu <ekin@ims.metu.edu.tr> wrote:

Dear all,

I have just installed the HDF5 version 1.8.13 and the check-install process failed with:

============================
Testing run-fortran-ex.sh

################# h5_crtdat #################
error: can't open file h5_crtdat.o for write
compilation aborted for h5_crtdat.f90 (code 1)
messed up compiling h5_crtdat.f90
rm: cannot remove `*.o': No such file or directory
rm: cannot remove `*.h5': No such file or directory

make[3]: *** [installcheck-local] Error 1
make[3]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran/examples'
make[2]: *** [installcheck-local] Error 1
make[2]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran'
make[1]: *** [installcheck-recursive] Error 1
make[1]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran'
make: *** [installcheck-recursive] Error 1

Regards,

Ekin

On 15 May 2014 15:20, <help@hdfgroup.org> wrote:

To view from a browser see:
   http://www.hdfgroup.org/newsletters/newsletter140.html

--------------------------------------------------------------------------
The HDF Group Home Page: http://www.hdfgroup.org/
Support Services: http://www.hdfgroup.org/services/
--------------------------------------------------------------------------

                            Newsletter #140
                             May 15, 2014

CONTENTS
. Release of HDF5-1.8.13

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Release of HDF5 1.8.13

The HDF5-1.8.13 release is now available, and can be downloaded from the
HDF Group Downloads page:

    http://www.hdfgroup.org/downloads/

It can also be obtained directly from:

    http://www.hdfgroup.org/HDF5/release/obtain5.html

HDF5-1.8.13 is a minor release, with a few new features and changes.
Important changes include:

o The H5free_memory (C) api was added to free memory that was allocated
   by HDF5 API calls. This was added specifically for Windows, but may be
   useful anywhere that the library uses a different memory manager than
   the application.

o New wrappers were added for C++ (many) and Fortran
   (h5pset_file_image_f and h5pget_file_image_f).

o Mac OS X 10.9 Mavericks is now supported.

o Many improvements were added in support of CMake, including the
   addition of support for CMake 2.8.11.

o Improvements were added to the Core VFD (or Memory VFD).

o The following changes were made to Parallel HDF5:

   - The MPI-POSIX VFD was removed. Application developers should
     always use the MPI-IO VFD.

   - Parallel HDF5 now supports collective I/O on point selections.

o A few changes were added to the tools (h5diff, h5dump, and h5repack).

This release contains many other changes that are not listed here.
Please be sure to read the Release Notes for a comprehensive list of
new features and changes:

   http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.13-RELEASE.txt

Changes that affect maintainers of HDF5-dependent applications are
listed in "HDF5 Software Changes from Release to Release". See:

   http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html

Future Changes to Supported Platforms
-------------------------------------

Please be aware that after this release, we will be moving to
CMake 3.0, and will add testing for VS 2013. VS 2012 will remain
the standard.

In addition, we will only support Cygwin built with CMake, and will
be dropping VS 2010.

-------------------------------------------------------------
For questions regarding these or other HDF issues, contact:

   help@hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

Thanks Elena,
Unfortunately it still fails regardless of the optimization level. Do you have any other suggestions ? I tried it with g++/gfortran pointing to gcc/4.9.0 and gcc pointing it to 4.8.2 (because C++ name mangling and fortran modules are often the incompatible elements) and all of the test pass but I'd prefer to use 4.9.0 for all of the compilers.

Sean

···

From: Elena Pourmal <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>>
Reply-To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Date: Thursday, May 15, 2014 5:32 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Cc: Kimberly Browning <kimmers@cray.com<mailto:kimmers@cray.com>>
Subject: Re: [Hdf-forum] make check failures with gcc/4.9.0 and HDF5 1.8.13 (long double conversions)

Hi Sean,

Thank you for trying with the newly released gcc! I'll add the issue to JIRA; we will try to support gcc 4.9.* in the next release.

As a workaround please try to use different level of optimization (edit the config/gnu-flags file; search for "Production" string and then edit gcc-4.* line).

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 2:45 PM, Sean Byland <seanb@cray.com<mailto:seanb@cray.com>> wrote:

When building with hdf5/1.8.13 with the following configure line:
./configure CC=gcc CXX=g++ FC=gfortran --disable-silent-rules --enable-fortran --enable-fortran2003 --enable-static --with-pic --disable-sharedlib-rpath --enable-shared --enable-cxx

With the gcc, g++ and gfortran resolving to gcc/4.9 I see the following failures:
grep "FAILED" gcc49.check.out
Testing hard signed char -> long double conversions *FAILED*
Testing hard unsigned char -> long double conversions *FAILED*
Testing hard short -> long double conversions *FAILED*
Testing hard unsigned short -> long double conversions *FAILED*
Testing hard int -> long double conversions *FAILED*
Testing hard unsigned int -> long double conversions *FAILED*
Testing hard long -> long double conversions *FAILED*

Has anyone else observed this ? Is there a workaround. Thanks.

Sean B.

From: Elena Pourmal <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>>
Reply-To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Date: Thursday, May 15, 2014 2:35 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Subject: Re: [Hdf-forum] make check-install fails with HDF5 1.8.13

Ekin,

On May 15, 2014, at 1:42 PM, Ekin Akoglu <ekin@ims.metu.edu.tr<mailto:ekin@ims.metu.edu.tr>> wrote:

Dear Elena,

Changing to the directory hdf5-1.8.13/fortran/examples and then issuing

$ h5fc -o h5_crtdat h5_crtdat.f90

works. However, the check-install complains about not being able to open h5_crtdat.o to write, which already exists. I checked the permissions of that file and they are correct: 644, so write is allowed.

Do you have an idea?

No idea at this point. We couldn't reproduce the problem here on one of our machines with Intel Fortran compiler.

Could you please try to run run-fortran-ex.sh in that directory?

./run-fortran-ex.sh

Thank you!

Elena
Thank you,

Ekin

On 15 May 2014 19:47, Elena Pourmal <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>> wrote:
Ekin,

It looks like that for some reason Fortran compiler cannot write *.o file. Could it be that you ran out of space? Is there quota on your system? Was /tmp partition full?

I would try to run make check-install the second time, or go to /usr/local/hdf5-1.8.13/share/hdf5_examples/fortran and try to run the following command

../../../bin/h5fc -o h5_crtdat h5_crtdat.f90

and see if it works.

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org<http://hdfgroup.org/>
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 10:30 AM, Ekin Akoglu <ekin@ims.metu.edu.tr<mailto:ekin@ims.metu.edu.tr>> wrote:

Dear Elena,

The OS is 64-bit Debian Wheezy 7.5. The compiler is Intel Fortran Compiler 2013 SP1 Update 3, which is exactly 14.0.3 20140422. My GCC version is 4.7.2. I built and installed HDF5 as follows:

$ ./configure --prefix=/usr/local/hdf5-1.8.13 --enable-fortran --enable-fortran2003
$ make
$ make check
# make install
$ make check-install

Everything except the "make check-install" step worked flawlessly.

Thank you.

Kind regards,

Ekin

On 15 May 2014 17:11, Elena Pourmal <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>> wrote:
Ekin,

Could you please provide OS and compiler information? It would also help if you post the outputs of the commands used to build and install the HDF5 libraries.

Thank you!

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org<http://hdfgroup.org/>
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 9:10 AM, Ekin Akoglu <ekin@ims.metu.edu.tr<mailto:ekin@ims.metu.edu.tr>> wrote:

Dear all,

I have just installed the HDF5 version 1.8.13 and the check-install process failed with:

============================
Testing run-fortran-ex.sh

################# h5_crtdat #################
error: can't open file h5_crtdat.o for write
compilation aborted for h5_crtdat.f90 (code 1)
messed up compiling h5_crtdat.f90
rm: cannot remove `*.o': No such file or directory
rm: cannot remove `*.h5': No such file or directory

make[3]: *** [installcheck-local] Error 1
make[3]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran/examples'
make[2]: *** [installcheck-local] Error 1
make[2]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran'
make[1]: *** [installcheck-recursive] Error 1
make[1]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran'
make: *** [installcheck-recursive] Error 1

Regards,

Ekin

On 15 May 2014 15:20, <help@hdfgroup.org<mailto:help@hdfgroup.org>> wrote:

To view from a browser see:
   http://www.hdfgroup.org/newsletters/newsletter140.html

--------------------------------------------------------------------------
The HDF Group Home Page: http://www.hdfgroup.org/
Support Services: http://www.hdfgroup.org/services/
--------------------------------------------------------------------------

                            Newsletter #140
                             May 15, 2014

CONTENTS
. Release of HDF5-1.8.13

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Release of HDF5 1.8.13

The HDF5-1.8.13 release is now available, and can be downloaded from the
HDF Group Downloads page:

    http://www.hdfgroup.org/downloads/

It can also be obtained directly from:

    http://www.hdfgroup.org/HDF5/release/obtain5.html

HDF5-1.8.13 is a minor release, with a few new features and changes.
Important changes include:

o The H5free_memory (C) api was added to free memory that was allocated
   by HDF5 API calls. This was added specifically for Windows, but may be
   useful anywhere that the library uses a different memory manager than
   the application.

o New wrappers were added for C++ (many) and Fortran
   (h5pset_file_image_f and h5pget_file_image_f).

o Mac OS X 10.9 Mavericks is now supported.

o Many improvements were added in support of CMake, including the
   addition of support for CMake 2.8.11.

o Improvements were added to the Core VFD (or Memory VFD).

o The following changes were made to Parallel HDF5:

   - The MPI-POSIX VFD was removed. Application developers should
     always use the MPI-IO VFD.

   - Parallel HDF5 now supports collective I/O on point selections.

o A few changes were added to the tools (h5diff, h5dump, and h5repack).

This release contains many other changes that are not listed here.
Please be sure to read the Release Notes for a comprehensive list of
new features and changes:

   http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.13-RELEASE.txt

Changes that affect maintainers of HDF5-dependent applications are
listed in "HDF5 Software Changes from Release to Release". See:

   http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html

Future Changes to Supported Platforms
-------------------------------------

Please be aware that after this release, we will be moving to
CMake 3.0, and will add testing for VS 2013. VS 2012 will remain
the standard.

In addition, we will only support Cygwin built with CMake, and will
be dropping VS 2010.

-------------------------------------------------------------
For questions regarding these or other HDF issues, contact:

   help@hdfgroup.org<mailto:help@hdfgroup.org>

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

Sean,

Thanks Elena,
Unfortunately it still fails regardless of the optimization level. Do you have any other suggestions ?

Unfortunately, no. We will need to investigate. Hopefully, this is a problem with the tests and not with the library.

One thing you may try is to store some data of each of those types signed/unsigned char, short, int, long as long double in HDF5 (see http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/hdf5-examples/1_8/C/H5T/h5ex_t_int.c ) and see if the problem is still there.

Elena

···

On May 16, 2014, at 10:43 AM, Sean Byland <seanb@cray.com> wrote:

I tried it with g++/gfortran pointing to gcc/4.9.0 and gcc pointing it to 4.8.2 (because C++ name mangling and fortran modules are often the incompatible elements) and all of the test pass but I'd prefer to use 4.9.0 for all of the compilers.

Sean

From: Elena Pourmal <epourmal@hdfgroup.org>
Reply-To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Date: Thursday, May 15, 2014 5:32 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Cc: Kimberly Browning <kimmers@cray.com>
Subject: Re: [Hdf-forum] make check failures with gcc/4.9.0 and HDF5 1.8.13 (long double conversions)

Hi Sean,

Thank you for trying with the newly released gcc! I'll add the issue to JIRA; we will try to support gcc 4.9.* in the next release.

As a workaround please try to use different level of optimization (edit the config/gnu-flags file; search for "Production" string and then edit gcc-4.* line).

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 2:45 PM, Sean Byland <seanb@cray.com> wrote:

When building with hdf5/1.8.13 with the following configure line:
./configure CC=gcc CXX=g++ FC=gfortran --disable-silent-rules --enable-fortran --enable-fortran2003 --enable-static --with-pic --disable-sharedlib-rpath --enable-shared --enable-cxx

With the gcc, g++ and gfortran resolving to gcc/4.9 I see the following failures:
grep "FAILED" gcc49.check.out
Testing hard signed char -> long double conversions *FAILED*
Testing hard unsigned char -> long double conversions *FAILED*
Testing hard short -> long double conversions *FAILED*
Testing hard unsigned short -> long double conversions *FAILED*
Testing hard int -> long double conversions *FAILED*
Testing hard unsigned int -> long double conversions *FAILED*
Testing hard long -> long double conversions *FAILED*

Has anyone else observed this ? Is there a workaround. Thanks.

Sean B.

From: Elena Pourmal <epourmal@hdfgroup.org>
Reply-To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Date: Thursday, May 15, 2014 2:35 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Subject: Re: [Hdf-forum] make check-install fails with HDF5 1.8.13

Ekin,

On May 15, 2014, at 1:42 PM, Ekin Akoglu <ekin@ims.metu.edu.tr> wrote:

Dear Elena,

Changing to the directory hdf5-1.8.13/fortran/examples and then issuing

$ h5fc -o h5_crtdat h5_crtdat.f90

works. However, the check-install complains about not being able to open h5_crtdat.o to write, which already exists. I checked the permissions of that file and they are correct: 644, so write is allowed.

Do you have an idea?

No idea at this point. We couldn't reproduce the problem here on one of our machines with Intel Fortran compiler.

Could you please try to run run-fortran-ex.sh in that directory?

./run-fortran-ex.sh

Thank you!

Elena

Thank you,

Ekin

On 15 May 2014 19:47, Elena Pourmal <epourmal@hdfgroup.org> wrote:

Ekin,

It looks like that for some reason Fortran compiler cannot write *.o file. Could it be that you ran out of space? Is there quota on your system? Was /tmp partition full?

I would try to run make check-install the second time, or go to /usr/local/hdf5-1.8.13/share/hdf5_examples/fortran and try to run the following command

../../../bin/h5fc -o h5_crtdat h5_crtdat.f90

and see if it works.

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 10:30 AM, Ekin Akoglu <ekin@ims.metu.edu.tr> wrote:

Dear Elena,

The OS is 64-bit Debian Wheezy 7.5. The compiler is Intel Fortran Compiler 2013 SP1 Update 3, which is exactly 14.0.3 20140422. My GCC version is 4.7.2. I built and installed HDF5 as follows:

$ ./configure --prefix=/usr/local/hdf5-1.8.13 --enable-fortran --enable-fortran2003
$ make
$ make check
# make install
$ make check-install

Everything except the "make check-install" step worked flawlessly.

Thank you.

Kind regards,

Ekin

On 15 May 2014 17:11, Elena Pourmal <epourmal@hdfgroup.org> wrote:

Ekin,

Could you please provide OS and compiler information? It would also help if you post the outputs of the commands used to build and install the HDF5 libraries.

Thank you!

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 9:10 AM, Ekin Akoglu <ekin@ims.metu.edu.tr> wrote:

Dear all,

I have just installed the HDF5 version 1.8.13 and the check-install process failed with:

============================
Testing run-fortran-ex.sh

################# h5_crtdat #################
error: can't open file h5_crtdat.o for write
compilation aborted for h5_crtdat.f90 (code 1)
messed up compiling h5_crtdat.f90
rm: cannot remove `*.o': No such file or directory
rm: cannot remove `*.h5': No such file or directory

make[3]: *** [installcheck-local] Error 1
make[3]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran/examples'
make[2]: *** [installcheck-local] Error 1
make[2]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran'
make[1]: *** [installcheck-recursive] Error 1
make[1]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran'
make: *** [installcheck-recursive] Error 1

Regards,

Ekin

On 15 May 2014 15:20, <help@hdfgroup.org> wrote:

To view from a browser see:
   http://www.hdfgroup.org/newsletters/newsletter140.html

--------------------------------------------------------------------------
The HDF Group Home Page: http://www.hdfgroup.org/
Support Services: http://www.hdfgroup.org/services/
--------------------------------------------------------------------------

                            Newsletter #140
                             May 15, 2014

CONTENTS
. Release of HDF5-1.8.13

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Release of HDF5 1.8.13

The HDF5-1.8.13 release is now available, and can be downloaded from the
HDF Group Downloads page:

    http://www.hdfgroup.org/downloads/

It can also be obtained directly from:

    http://www.hdfgroup.org/HDF5/release/obtain5.html

HDF5-1.8.13 is a minor release, with a few new features and changes.
Important changes include:

o The H5free_memory (C) api was added to free memory that was allocated
   by HDF5 API calls. This was added specifically for Windows, but may be
   useful anywhere that the library uses a different memory manager than
   the application.

o New wrappers were added for C++ (many) and Fortran
   (h5pset_file_image_f and h5pget_file_image_f).

o Mac OS X 10.9 Mavericks is now supported.

o Many improvements were added in support of CMake, including the
   addition of support for CMake 2.8.11.

o Improvements were added to the Core VFD (or Memory VFD).

o The following changes were made to Parallel HDF5:

   - The MPI-POSIX VFD was removed. Application developers should
     always use the MPI-IO VFD.

   - Parallel HDF5 now supports collective I/O on point selections.

o A few changes were added to the tools (h5diff, h5dump, and h5repack).

This release contains many other changes that are not listed here.
Please be sure to read the Release Notes for a comprehensive list of
new features and changes:

   http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.13-RELEASE.txt

Changes that affect maintainers of HDF5-dependent applications are
listed in "HDF5 Software Changes from Release to Release". See:

   http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html

Future Changes to Supported Platforms
-------------------------------------

Please be aware that after this release, we will be moving to
CMake 3.0, and will add testing for VS 2013. VS 2012 will remain
the standard.

In addition, we will only support Cygwin built with CMake, and will
be dropping VS 2010.

-------------------------------------------------------------
For questions regarding these or other HDF issues, contact:

   help@hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

Elena,
FWIW, I changed the example you linked to:
    dset = H5Dcreate (file, DATASET, H5T_NATIVE_LDOUBLE, space, H5P_DEFAULT,
                H5P_DEFAULT, H5P_DEFAULT);
    status = H5Dwrite (dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
                wdata[0]);

To check the following test failure:
Testing hard int -> long double conversions *FAILED*

And visual inspection showed:
[ 0 -1 -2 -3 -4 -5 -6]
[ 0 0 0 0 0 0 0]
[ 0 1 2 3 4 5 6]
[ 0 2 4 6 8 10 12]

To be the same output as before, so I suspect the library might me fine.

Sean B.

···

From: Elena Pourmal <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>>
Reply-To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Date: Friday, May 16, 2014 9:30 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Cc: Kimberly Browning <kimmers@cray.com<mailto:kimmers@cray.com>>
Subject: Re: [Hdf-forum] make check failures with gcc/4.9.0 and HDF5 1.8.13 (long double conversions)

Sean,

On May 16, 2014, at 10:43 AM, Sean Byland <seanb@cray.com<mailto:seanb@cray.com>> wrote:

Thanks Elena,
Unfortunately it still fails regardless of the optimization level. Do you have any other suggestions ?

Unfortunately, no. We will need to investigate. Hopefully, this is a problem with the tests and not with the library.

One thing you may try is to store some data of each of those types signed/unsigned char, short, int, long as long double in HDF5 (see http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/hdf5-examples/1_8/C/H5T/h5ex_t_int.c ) and see if the problem is still there.

Elena

I tried it with g++/gfortran pointing to gcc/4.9.0 and gcc pointing it to 4.8.2 (because C++ name mangling and fortran modules are often the incompatible elements) and all of the test pass but I'd prefer to use 4.9.0 for all of the compilers.

Sean

From: Elena Pourmal <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>>
Reply-To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Date: Thursday, May 15, 2014 5:32 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Cc: Kimberly Browning <kimmers@cray.com<mailto:kimmers@cray.com>>
Subject: Re: [Hdf-forum] make check failures with gcc/4.9.0 and HDF5 1.8.13 (long double conversions)

Hi Sean,

Thank you for trying with the newly released gcc! I'll add the issue to JIRA; we will try to support gcc 4.9.* in the next release.

As a workaround please try to use different level of optimization (edit the config/gnu-flags file; search for "Production" string and then edit gcc-4.* line).

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org<http://hdfgroup.org/>
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 2:45 PM, Sean Byland <seanb@cray.com<mailto:seanb@cray.com>> wrote:

When building with hdf5/1.8.13 with the following configure line:
./configure CC=gcc CXX=g++ FC=gfortran --disable-silent-rules --enable-fortran --enable-fortran2003 --enable-static --with-pic --disable-sharedlib-rpath --enable-shared --enable-cxx

With the gcc, g++ and gfortran resolving to gcc/4.9 I see the following failures:
grep "FAILED" gcc49.check.out
Testing hard signed char -> long double conversions *FAILED*
Testing hard unsigned char -> long double conversions *FAILED*
Testing hard short -> long double conversions *FAILED*
Testing hard unsigned short -> long double conversions *FAILED*
Testing hard int -> long double conversions *FAILED*
Testing hard unsigned int -> long double conversions *FAILED*
Testing hard long -> long double conversions *FAILED*

Has anyone else observed this ? Is there a workaround. Thanks.

Sean B.

From: Elena Pourmal <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>>
Reply-To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Date: Thursday, May 15, 2014 2:35 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org<mailto:hdf-forum@lists.hdfgroup.org>>
Subject: Re: [Hdf-forum] make check-install fails with HDF5 1.8.13

Ekin,

On May 15, 2014, at 1:42 PM, Ekin Akoglu <ekin@ims.metu.edu.tr<mailto:ekin@ims.metu.edu.tr>> wrote:

Dear Elena,

Changing to the directory hdf5-1.8.13/fortran/examples and then issuing

$ h5fc -o h5_crtdat h5_crtdat.f90

works. However, the check-install complains about not being able to open h5_crtdat.o to write, which already exists. I checked the permissions of that file and they are correct: 644, so write is allowed.

Do you have an idea?

No idea at this point. We couldn't reproduce the problem here on one of our machines with Intel Fortran compiler.

Could you please try to run run-fortran-ex.sh in that directory?

./run-fortran-ex.sh

Thank you!

Elena
Thank you,

Ekin

On 15 May 2014 19:47, Elena Pourmal <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>> wrote:
Ekin,

It looks like that for some reason Fortran compiler cannot write *.o file. Could it be that you ran out of space? Is there quota on your system? Was /tmp partition full?

I would try to run make check-install the second time, or go to /usr/local/hdf5-1.8.13/share/hdf5_examples/fortran and try to run the following command

../../../bin/h5fc -o h5_crtdat h5_crtdat.f90

and see if it works.

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org<http://hdfgroup.org/>
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 10:30 AM, Ekin Akoglu <ekin@ims.metu.edu.tr<mailto:ekin@ims.metu.edu.tr>> wrote:

Dear Elena,

The OS is 64-bit Debian Wheezy 7.5. The compiler is Intel Fortran Compiler 2013 SP1 Update 3, which is exactly 14.0.3 20140422. My GCC version is 4.7.2. I built and installed HDF5 as follows:

$ ./configure --prefix=/usr/local/hdf5-1.8.13 --enable-fortran --enable-fortran2003
$ make
$ make check
# make install
$ make check-install

Everything except the "make check-install" step worked flawlessly.

Thank you.

Kind regards,

Ekin

On 15 May 2014 17:11, Elena Pourmal <epourmal@hdfgroup.org<mailto:epourmal@hdfgroup.org>> wrote:
Ekin,

Could you please provide OS and compiler information? It would also help if you post the outputs of the commands used to build and install the HDF5 libraries.

Thank you!

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org<http://hdfgroup.org/>
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 9:10 AM, Ekin Akoglu <ekin@ims.metu.edu.tr<mailto:ekin@ims.metu.edu.tr>> wrote:

Dear all,

I have just installed the HDF5 version 1.8.13 and the check-install process failed with:

============================
Testing run-fortran-ex.sh

################# h5_crtdat #################
error: can't open file h5_crtdat.o for write
compilation aborted for h5_crtdat.f90 (code 1)
messed up compiling h5_crtdat.f90
rm: cannot remove `*.o': No such file or directory
rm: cannot remove `*.h5': No such file or directory

make[3]: *** [installcheck-local] Error 1
make[3]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran/examples'
make[2]: *** [installcheck-local] Error 1
make[2]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran'
make[1]: *** [installcheck-recursive] Error 1
make[1]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran'
make: *** [installcheck-recursive] Error 1

Regards,

Ekin

On 15 May 2014 15:20, <help@hdfgroup.org<mailto:help@hdfgroup.org>> wrote:

To view from a browser see:
   http://www.hdfgroup.org/newsletters/newsletter140.html

--------------------------------------------------------------------------
The HDF Group Home Page: http://www.hdfgroup.org/
Support Services: http://www.hdfgroup.org/services/
--------------------------------------------------------------------------

                            Newsletter #140
                             May 15, 2014

CONTENTS
. Release of HDF5-1.8.13

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Release of HDF5 1.8.13

The HDF5-1.8.13 release is now available, and can be downloaded from the
HDF Group Downloads page:

    http://www.hdfgroup.org/downloads/

It can also be obtained directly from:

    http://www.hdfgroup.org/HDF5/release/obtain5.html

HDF5-1.8.13 is a minor release, with a few new features and changes.
Important changes include:

o The H5free_memory (C) api was added to free memory that was allocated
   by HDF5 API calls. This was added specifically for Windows, but may be
   useful anywhere that the library uses a different memory manager than
   the application.

o New wrappers were added for C++ (many) and Fortran
   (h5pset_file_image_f and h5pget_file_image_f).

o Mac OS X 10.9 Mavericks is now supported.

o Many improvements were added in support of CMake, including the
   addition of support for CMake 2.8.11.

o Improvements were added to the Core VFD (or Memory VFD).

o The following changes were made to Parallel HDF5:

   - The MPI-POSIX VFD was removed. Application developers should
     always use the MPI-IO VFD.

   - Parallel HDF5 now supports collective I/O on point selections.

o A few changes were added to the tools (h5diff, h5dump, and h5repack).

This release contains many other changes that are not listed here.
Please be sure to read the Release Notes for a comprehensive list of
new features and changes:

   http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.13-RELEASE.txt

Changes that affect maintainers of HDF5-dependent applications are
listed in "HDF5 Software Changes from Release to Release". See:

   http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html

Future Changes to Supported Platforms
-------------------------------------

Please be aware that after this release, we will be moving to
CMake 3.0, and will add testing for VS 2013. VS 2012 will remain
the standard.

In addition, we will only support Cygwin built with CMake, and will
be dropping VS 2010.

-------------------------------------------------------------
For questions regarding these or other HDF issues, contact:

   help@hdfgroup.org<mailto:help@hdfgroup.org>

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org<mailto:Hdf-forum@lists.hdfgroup.org>
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org

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Thank you for checking!

Elena

···

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 19, 2014, at 10:59 AM, Sean Byland <seanb@cray.com> wrote:

Elena,
FWIW, I changed the example you linked to:
    dset = H5Dcreate (file, DATASET, H5T_NATIVE_LDOUBLE, space, H5P_DEFAULT,
                H5P_DEFAULT, H5P_DEFAULT);
    status = H5Dwrite (dset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT,
                wdata[0]);

To check the following test failure:
Testing hard int -> long double conversions *FAILED*

And visual inspection showed:
[ 0 -1 -2 -3 -4 -5 -6]
[ 0 0 0 0 0 0 0]
[ 0 1 2 3 4 5 6]
[ 0 2 4 6 8 10 12]

To be the same output as before, so I suspect the library might me fine.

Sean B.

From: Elena Pourmal <epourmal@hdfgroup.org>
Reply-To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Date: Friday, May 16, 2014 9:30 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Cc: Kimberly Browning <kimmers@cray.com>
Subject: Re: [Hdf-forum] make check failures with gcc/4.9.0 and HDF5 1.8.13 (long double conversions)

Sean,

On May 16, 2014, at 10:43 AM, Sean Byland <seanb@cray.com> wrote:

Thanks Elena,
Unfortunately it still fails regardless of the optimization level. Do you have any other suggestions ?

Unfortunately, no. We will need to investigate. Hopefully, this is a problem with the tests and not with the library.

One thing you may try is to store some data of each of those types signed/unsigned char, short, int, long as long double in HDF5 (see http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/hdf5-examples/1_8/C/H5T/h5ex_t_int.c ) and see if the problem is still there.

Elena

I tried it with g++/gfortran pointing to gcc/4.9.0 and gcc pointing it to 4.8.2 (because C++ name mangling and fortran modules are often the incompatible elements) and all of the test pass but I'd prefer to use 4.9.0 for all of the compilers.

Sean

From: Elena Pourmal <epourmal@hdfgroup.org>
Reply-To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Date: Thursday, May 15, 2014 5:32 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Cc: Kimberly Browning <kimmers@cray.com>
Subject: Re: [Hdf-forum] make check failures with gcc/4.9.0 and HDF5 1.8.13 (long double conversions)

Hi Sean,

Thank you for trying with the newly released gcc! I'll add the issue to JIRA; we will try to support gcc 4.9.* in the next release.

As a workaround please try to use different level of optimization (edit the config/gnu-flags file; search for "Production" string and then edit gcc-4.* line).

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 2:45 PM, Sean Byland <seanb@cray.com> wrote:

When building with hdf5/1.8.13 with the following configure line:
./configure CC=gcc CXX=g++ FC=gfortran --disable-silent-rules --enable-fortran --enable-fortran2003 --enable-static --with-pic --disable-sharedlib-rpath --enable-shared --enable-cxx

With the gcc, g++ and gfortran resolving to gcc/4.9 I see the following failures:
grep "FAILED" gcc49.check.out
Testing hard signed char -> long double conversions *FAILED*
Testing hard unsigned char -> long double conversions *FAILED*
Testing hard short -> long double conversions *FAILED*
Testing hard unsigned short -> long double conversions *FAILED*
Testing hard int -> long double conversions *FAILED*
Testing hard unsigned int -> long double conversions *FAILED*
Testing hard long -> long double conversions *FAILED*

Has anyone else observed this ? Is there a workaround. Thanks.

Sean B.

From: Elena Pourmal <epourmal@hdfgroup.org>
Reply-To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Date: Thursday, May 15, 2014 2:35 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Subject: Re: [Hdf-forum] make check-install fails with HDF5 1.8.13

Ekin,

On May 15, 2014, at 1:42 PM, Ekin Akoglu <ekin@ims.metu.edu.tr> wrote:

Dear Elena,

Changing to the directory hdf5-1.8.13/fortran/examples and then issuing

$ h5fc -o h5_crtdat h5_crtdat.f90

works. However, the check-install complains about not being able to open h5_crtdat.o to write, which already exists. I checked the permissions of that file and they are correct: 644, so write is allowed.

Do you have an idea?

No idea at this point. We couldn't reproduce the problem here on one of our machines with Intel Fortran compiler.

Could you please try to run run-fortran-ex.sh in that directory?

./run-fortran-ex.sh

Thank you!

Elena

Thank you,

Ekin

On 15 May 2014 19:47, Elena Pourmal <epourmal@hdfgroup.org> wrote:

Ekin,

It looks like that for some reason Fortran compiler cannot write *.o file. Could it be that you ran out of space? Is there quota on your system? Was /tmp partition full?

I would try to run make check-install the second time, or go to /usr/local/hdf5-1.8.13/share/hdf5_examples/fortran and try to run the following command

../../../bin/h5fc -o h5_crtdat h5_crtdat.f90

and see if it works.

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 10:30 AM, Ekin Akoglu <ekin@ims.metu.edu.tr> wrote:

Dear Elena,

The OS is 64-bit Debian Wheezy 7.5. The compiler is Intel Fortran Compiler 2013 SP1 Update 3, which is exactly 14.0.3 20140422. My GCC version is 4.7.2. I built and installed HDF5 as follows:

$ ./configure --prefix=/usr/local/hdf5-1.8.13 --enable-fortran --enable-fortran2003
$ make
$ make check
# make install
$ make check-install

Everything except the "make check-install" step worked flawlessly.

Thank you.

Kind regards,

Ekin

On 15 May 2014 17:11, Elena Pourmal <epourmal@hdfgroup.org> wrote:

Ekin,

Could you please provide OS and compiler information? It would also help if you post the outputs of the commands used to build and install the HDF5 libraries.

Thank you!

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

On May 15, 2014, at 9:10 AM, Ekin Akoglu <ekin@ims.metu.edu.tr> wrote:

Dear all,

I have just installed the HDF5 version 1.8.13 and the check-install process failed with:

============================
Testing run-fortran-ex.sh

################# h5_crtdat #################
error: can't open file h5_crtdat.o for write
compilation aborted for h5_crtdat.f90 (code 1)
messed up compiling h5_crtdat.f90
rm: cannot remove `*.o': No such file or directory
rm: cannot remove `*.h5': No such file or directory

make[3]: *** [installcheck-local] Error 1
make[3]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran/examples'
make[2]: *** [installcheck-local] Error 1
make[2]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran'
make[1]: *** [installcheck-recursive] Error 1
make[1]: Leaving directory `/home/ekin/Tools/hdf5-1.8.13/fortran'
make: *** [installcheck-recursive] Error 1

Regards,

Ekin

On 15 May 2014 15:20, <help@hdfgroup.org> wrote:

To view from a browser see:
   http://www.hdfgroup.org/newsletters/newsletter140.html

--------------------------------------------------------------------------
The HDF Group Home Page: http://www.hdfgroup.org/
Support Services: http://www.hdfgroup.org/services/
--------------------------------------------------------------------------

                            Newsletter #140
                             May 15, 2014

CONTENTS
. Release of HDF5-1.8.13

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Release of HDF5 1.8.13

The HDF5-1.8.13 release is now available, and can be downloaded from the
HDF Group Downloads page:

    http://www.hdfgroup.org/downloads/

It can also be obtained directly from:

    http://www.hdfgroup.org/HDF5/release/obtain5.html

HDF5-1.8.13 is a minor release, with a few new features and changes.
Important changes include:

o The H5free_memory (C) api was added to free memory that was allocated
   by HDF5 API calls. This was added specifically for Windows, but may be
   useful anywhere that the library uses a different memory manager than
   the application.

o New wrappers were added for C++ (many) and Fortran
   (h5pset_file_image_f and h5pget_file_image_f).

o Mac OS X 10.9 Mavericks is now supported.

o Many improvements were added in support of CMake, including the
   addition of support for CMake 2.8.11.

o Improvements were added to the Core VFD (or Memory VFD).

o The following changes were made to Parallel HDF5:

   - The MPI-POSIX VFD was removed. Application developers should
     always use the MPI-IO VFD.

   - Parallel HDF5 now supports collective I/O on point selections.

o A few changes were added to the tools (h5diff, h5dump, and h5repack).

This release contains many other changes that are not listed here.
Please be sure to read the Release Notes for a comprehensive list of
new features and changes:

   http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-1.8.13-RELEASE.txt

Changes that affect maintainers of HDF5-dependent applications are
listed in "HDF5 Software Changes from Release to Release". See:

   http://www.hdfgroup.org/HDF5/doc/ADGuide/Changes.html

Future Changes to Supported Platforms
-------------------------------------

Please be aware that after this release, we will be moving to
CMake 3.0, and will add testing for VS 2013. VS 2012 will remain
the standard.

In addition, we will only support Cygwin built with CMake, and will
be dropping VS 2010.

-------------------------------------------------------------
For questions regarding these or other HDF issues, contact:

   help@hdfgroup.org

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