If you have some time to test this, we would greatly appreciate it. While we test on a wide variety of platforms, there are many systems and setups that we are unable to test on, and feedback from the user community is quite welcome.
Of particular interest in this maintenance release is the introduction of several additions to the Fortran interface:
-- Fortran interface was enhanced to support the Fortran 2003 standard. The release provides a wider set of Fortran and
HDF5 datatypes such as
- any kind of INTEGER or REAL
- Fortran derived types
- Fortran and HDF5 enumeration
- HDF5 variable-length datatypes
- HDF5 compound datatypes of any complexity
It also contains new subroutines corresponding to the C functions with the callback functions as parameters. For general overview and information
on how to enable these new features please see "New Features in the HDF5 Fortran Library: Adding support for the Fortran 2003 standard" paper posted
at http://www.hdfgroup.org/HDF5/doc_test/H51.8docs/fortran/index.html. You may download HDF5 Fortran 2003 examples (names have F03 suffix) from http://www.hdfgroup.org/ftp/HDF5/examples/examples-by-api/api18-fortran.html
We would appreciate feedback from the community on these additions.
Please note that while the release notes contained in the pre-release are reflective of the new features and bug fixes present in this release, the platforms tested and tested configurations sections still need to be updated with our current testing configurations and are not reflective of this pre-release candidate at this time.
We plan to release HDF5 1.8.8 mid-November barring the discovery of any critical issues.
Testing big file with the Family Driver
Checking if file system is adequate for this test...
Testing Huge dataset write
PASSED #000 0x0000002416144964nknownx
HDF5-DIAG: Error detected in HDF5 (1.8.8-snap1) thread 0: #000: H5Dio.c line 153 in H5Dread(): selection+offset not within extent
major: Dataspace
minor: Out of range
*FAILED*
at big.c:523 in reader()...
HDF5-DIAG: Error detected in HDF5 (1.8.8-snap1) thread 0: #000: H5Dio.c line 153 in H5Dread(): selection+offset not within extent
major: Dataspace
minor: Out of range
*** TEST FAILED ***
"""
I tracked down the test failure is happend due to adding "-lbsd-compat"
in r20898 and can be fixed by applying the patch attached (which reverts
one line from r20898).
I need to note that I'm using a special build setup:
The build machine is CentOS 4.6 and I have bootstrapped GCC 4.6.2
myself. The regression does not occur when using a bootstrapped GCC
4.2.4 instead of GCC 4.6.2. Unfortunately I have no distribution handy
that ships with GCC 4.6 as the system compiler (like openSUSE 12.1
will). It is entirely possible that the issue I am reporting is specific
to the combo RHEL4/GCC4.6.
Best regards,
Bernd
On 11-10-27 17:46, Mike McGreevy wrote:
Hi all,
A pre-release candidate version of HDF5 1.8.8 is available for testing
and can be downloaded at the following link:
If you have some time to test this, we would greatly appreciate it.
While we test on a wide variety of platforms, there are many systems and
setups that we are unable to test on, and feedback from the user
community is quite welcome.
Of particular interest in this maintenance release is the introduction
of several additions to the Fortran interface:
-- Fortran interface was enhanced to support the Fortran 2003
standard. The release provides a wider set of Fortran and
HDF5 datatypes such as
- any kind of INTEGER or REAL
- Fortran derived types
- Fortran and HDF5 enumeration
- HDF5 variable-length datatypes
- HDF5 compound datatypes of any complexity
It also contains new subroutines corresponding to the C functions
with the callback functions as parameters. For general overview and
information
on how to enable these new features please see "New Features in the
HDF5 Fortran Library: Adding support for the Fortran 2003 standard"
paper posted
at http://www.hdfgroup.org/HDF5/doc_test/H51.8docs/fortran/index.html\. You
may download HDF5 Fortran 2003 examples (names have F03 suffix) from
We would appreciate feedback from the community on these additions.
Please note that while the release notes contained in the pre-release
are reflective of the new features and bug fixes present in this
release, the platforms tested and tested configurations sections still
need to be updated with our current testing configurations and are not
reflective of this pre-release candidate at this time.
We plan to release HDF5 1.8.8 mid-November barring the discovery of any
critical issues.
Thank you very much for this report (and subversion detective work)! We will take a look before the release and evaluate this revision and the failing test.
- Mike
Bernd Rinn wrote:
···
Hi Mike,
I'd like to report a regression of 1.8.8-pre1 (compared to 1.8.7) on
Linux i386 with GCC 4.6.2. I get the following test failure (excerpt):
"""
Testing big
big Test Log
Testing big file with the Family Driver
Checking if file system is adequate for this test...
Testing Huge dataset write
PASSED #000 0x0000002416144964nknownx
HDF5-DIAG: Error detected in HDF5 (1.8.8-snap1) thread 0: #000: H5Dio.c line 153 in H5Dread(): selection+offset not within extent
major: Dataspace
minor: Out of range
*FAILED*
at big.c:523 in reader()...
HDF5-DIAG: Error detected in HDF5 (1.8.8-snap1) thread 0: #000: H5Dio.c line 153 in H5Dread(): selection+offset not within extent
major: Dataspace
minor: Out of range
*** TEST FAILED ***
"""
I tracked down the test failure is happend due to adding "-lbsd-compat"
in r20898 and can be fixed by applying the patch attached (which reverts
one line from r20898).
I need to note that I'm using a special build setup:
The build machine is CentOS 4.6 and I have bootstrapped GCC 4.6.2
myself. The regression does not occur when using a bootstrapped GCC
4.2.4 instead of GCC 4.6.2. Unfortunately I have no distribution handy
that ships with GCC 4.6 as the system compiler (like openSUSE 12.1
will). It is entirely possible that the issue I am reporting is specific
to the combo RHEL4/GCC4.6.
Best regards,
Bernd
On 11-10-27 17:46, Mike McGreevy wrote:
Hi all,
A pre-release candidate version of HDF5 1.8.8 is available for testing
and can be downloaded at the following link:
If you have some time to test this, we would greatly appreciate it.
While we test on a wide variety of platforms, there are many systems and
setups that we are unable to test on, and feedback from the user
community is quite welcome.
Of particular interest in this maintenance release is the introduction
of several additions to the Fortran interface:
-- Fortran interface was enhanced to support the Fortran 2003
standard. The release provides a wider set of Fortran and
HDF5 datatypes such as
- any kind of INTEGER or REAL
- Fortran derived types
- Fortran and HDF5 enumeration
- HDF5 variable-length datatypes
- HDF5 compound datatypes of any complexity
We would appreciate feedback from the community on these additions.
Please note that while the release notes contained in the pre-release
are reflective of the new features and bug fixes present in this
release, the platforms tested and tested configurations sections still
need to be updated with our current testing configurations and are not
reflective of this pre-release candidate at this time.
We plan to release HDF5 1.8.8 mid-November barring the discovery of any
critical issues.
The reason I added -lbsd-compat is that it should be linked when
-D_BSD_SOURCE is defined, which has been true in the library for a
long time. See the GNU libc recommendations here here:
I do not know if we use any features from 4.3 BSD that conflict with
the POSIX 1 standard (the purpose of the symbol is to resolve the
conflicts in favor of BSD), though I doubt that we do. If one goes,
the other should go as well.
If we are going to yank -D_BSD_SOURCE and -lbsd-compat this for the
release, I can test this on the BSD VMs tonight. Those would be the
most likely systems to have issues.
Cheers,
Dana
···
On Mon, Oct 31, 2011 at 4:58 AM, Bernd Rinn <bernd.rinn@bsse.ethz.ch> wrote:
Hi Mike,
I'd like to report a regression of 1.8.8-pre1 (compared to 1.8.7) on
Linux i386 with GCC 4.6.2. I get the following test failure (excerpt):
"""
Testing big
big Test Log
Testing big file with the Family Driver
Checking if file system is adequate for this test...
Testing Huge dataset write
PASSED #000 0x0000002416144964nknownx
HDF5-DIAG: Error detected in HDF5 (1.8.8-snap1) thread 0: #000: H5Dio.c line 153 in H5Dread(): selection+offset not within extent
major: Dataspace
minor: Out of range
*FAILED*
at big.c:523 in reader()...
HDF5-DIAG: Error detected in HDF5 (1.8.8-snap1) thread 0: #000: H5Dio.c line 153 in H5Dread(): selection+offset not within extent
major: Dataspace
minor: Out of range
*** TEST FAILED ***
"""
I tracked down the test failure is happend due to adding "-lbsd-compat"
in r20898 and can be fixed by applying the patch attached (which reverts
one line from r20898).
I need to note that I'm using a special build setup:
The build machine is CentOS 4.6 and I have bootstrapped GCC 4.6.2
myself. The regression does not occur when using a bootstrapped GCC
4.2.4 instead of GCC 4.6.2. Unfortunately I have no distribution handy
that ships with GCC 4.6 as the system compiler (like openSUSE 12.1
will). It is entirely possible that the issue I am reporting is specific
to the combo RHEL4/GCC4.6.
Best regards,
Bernd
On 11-10-27 17:46, Mike McGreevy wrote:
Hi all,
A pre-release candidate version of HDF5 1.8.8 is available for testing
and can be downloaded at the following link:
If you have some time to test this, we would greatly appreciate it.
While we test on a wide variety of platforms, there are many systems and
setups that we are unable to test on, and feedback from the user
community is quite welcome.
Of particular interest in this maintenance release is the introduction
of several additions to the Fortran interface:
-- Fortran interface was enhanced to support the Fortran 2003
standard. The release provides a wider set of Fortran and
HDF5 datatypes such as
- any kind of INTEGER or REAL
- Fortran derived types
- Fortran and HDF5 enumeration
- HDF5 variable-length datatypes
- HDF5 compound datatypes of any complexity
It also contains new subroutines corresponding to the C functions
with the callback functions as parameters. For general overview and
information
on how to enable these new features please see "New Features in the
HDF5 Fortran Library: Adding support for the Fortran 2003 standard"
paper posted
at http://www.hdfgroup.org/HDF5/doc_test/H51.8docs/fortran/index.html. You
may download HDF5 Fortran 2003 examples (names have F03 suffix) from
We would appreciate feedback from the community on these additions.
Please note that while the release notes contained in the pre-release
are reflective of the new features and bug fixes present in this
release, the platforms tested and tested configurations sections still
need to be updated with our current testing configurations and are not
reflective of this pre-release candidate at this time.
We plan to release HDF5 1.8.8 mid-November barring the discovery of any
critical issues.
On Mon, Oct 31, 2011 at 4:58 AM, Bernd Rinn <bernd.rinn@bsse.ethz.ch> wrote:
Hi Mike,
I'd like to report a regression of 1.8.8-pre1 (compared to 1.8.7) on
Linux i386 with GCC 4.6.2. I get the following test failure (excerpt):
"""
Testing big
big Test Log
Testing big file with the Family Driver
Checking if file system is adequate for this test...
Testing Huge dataset write
PASSED #000 0x0000002416144964nknownx
HDF5-DIAG: Error detected in HDF5 (1.8.8-snap1) thread 0: #000: H5Dio.c line 153 in H5Dread(): selection+offset not within extent
major: Dataspace
minor: Out of range
*FAILED*
at big.c:523 in reader()...
HDF5-DIAG: Error detected in HDF5 (1.8.8-snap1) thread 0: #000: H5Dio.c line 153 in H5Dread(): selection+offset not within extent
major: Dataspace
minor: Out of range
*** TEST FAILED ***
"""
I tracked down the test failure is happend due to adding "-lbsd-compat"
in r20898 and can be fixed by applying the patch attached (which reverts
one line from r20898).
I need to note that I'm using a special build setup:
The build machine is CentOS 4.6 and I have bootstrapped GCC 4.6.2
myself. The regression does not occur when using a bootstrapped GCC
4.2.4 instead of GCC 4.6.2. Unfortunately I have no distribution handy
that ships with GCC 4.6 as the system compiler (like openSUSE 12.1
will). It is entirely possible that the issue I am reporting is specific
to the combo RHEL4/GCC4.6.
Best regards,
Bernd
I'm looking into this, but I've been unable to reproduce the big test
failure on any of our machines or VMs. I'm downloading Centos 4.6
i386 today to try building HDF5 with gcc 4.6.2. I'll post the results
when I'm done.
Regarding the _BSD_SOURCE and -lbsd-compat issues, we are going to be
reverting to the original behavior for the 1.8.8 release. The old
behavior was to define _BSD_SOURCE but not link to the bsd-compat
library.
Note that this only affects linux systems. _BSD_SOURCE is not defined
on other platforms.
BTW, _BSD_SOURCE and -lbsd-compat are only specified for linux systems
(they are set up in a linux-specific section of configure.in). Mac OS
X, BSD, Solaris, etc. are unaffected.
On Mon, Oct 31, 2011 at 4:58 AM, Bernd Rinn <bernd.rinn@bsse.ethz.ch> wrote:
Hi Mike,
I'd like to report a regression of 1.8.8-pre1 (compared to 1.8.7) on
Linux i386 with GCC 4.6.2. I get the following test failure (excerpt):
"""
Testing big
big Test Log
Testing big file with the Family Driver
Checking if file system is adequate for this test...
Testing Huge dataset write
PASSED #000 0x0000002416144964nknownx
HDF5-DIAG: Error detected in HDF5 (1.8.8-snap1) thread 0: #000: H5Dio.c line 153 in H5Dread(): selection+offset not within extent
major: Dataspace
minor: Out of range
*FAILED*
at big.c:523 in reader()...
HDF5-DIAG: Error detected in HDF5 (1.8.8-snap1) thread 0: #000: H5Dio.c line 153 in H5Dread(): selection+offset not within extent
major: Dataspace
minor: Out of range
*** TEST FAILED ***
"""
I tracked down the test failure is happend due to adding "-lbsd-compat"
in r20898 and can be fixed by applying the patch attached (which reverts
one line from r20898).
I need to note that I'm using a special build setup:
The build machine is CentOS 4.6 and I have bootstrapped GCC 4.6.2
myself. The regression does not occur when using a bootstrapped GCC
4.2.4 instead of GCC 4.6.2. Unfortunately I have no distribution handy
that ships with GCC 4.6 as the system compiler (like openSUSE 12.1
will). It is entirely possible that the issue I am reporting is specific
to the combo RHEL4/GCC4.6.
Best regards,
Bernd
I'm looking into this, but I've been unable to reproduce the big test
failure on any of our machines or VMs. I'm downloading Centos 4.6
i386 today to try building HDF5 with gcc 4.6.2. I'll post the results
when I'm done.
This is exactly the kind of situation where it is handy to have daily build results reported to a dashboard. It would be nice if the HDF5 dashboard had more submissions. The 'big' test has been failing on one of my machines for days:
<http://cdash.hdfgroup.uiuc.edu/index.php?project=HDF518>
···
On Wed, 2 Nov 2011 08:55:54 -0500, Dana Robinson said:
I'm looking into this, but I've been unable to reproduce the big test
failure on any of our machines or VMs. I'm downloading Centos 4.6
i386 today to try building HDF5 with gcc 4.6.2. I'll post the results
when I'm done.
--
____________________________________________________________
Sean McBride, B. Eng sean@rogue-research.com
Rogue Research www.rogue-research.com
Mac Software Developer Montréal, Québec, Canada
This is exactly the kind of situation where it is handy to have daily build results reported to a dashboard. It would be nice if the HDF5 dashboard had more submissions. The 'big' test has been failing on one of my machines for days:
<http://cdash.hdfgroup.uiuc.edu/index.php?project=HDF518>
Hi Sean,
I can't speak to the dashboard issue, but the stdio VFD test that is
failing is not that surprising. The stdio VFD is intended to be a
demo ("how to write a VFD using the VFD API") driver and is not as
well tested as the production VFDs. Making the stdio VFD more robust,
especially for large files, is on my to-do list.
Sounds like a great idea. But, how do I submit these results? If the information needed was included in the build/install instructions, perhaps more people would do it, as a part of the build process? (Or perhaps I just didn't find the info.) For other projects using cdash that I've seen, the trick was "make Experimental" or something like that; no such make target seems to exist.
Cheers
Paul
···
On 2. nov. 2011, at 15:13, Sean McBride wrote:
On Wed, 2 Nov 2011 08:55:54 -0500, Dana Robinson said:
I'm looking into this, but I've been unable to reproduce the big test
failure on any of our machines or VMs. I'm downloading Centos 4.6
i386 today to try building HDF5 with gcc 4.6.2. I'll post the results
when I'm done.
This is exactly the kind of situation where it is handy to have daily build results reported to a dashboard. It would be nice if the HDF5 dashboard had more submissions. The 'big' test has been failing on one of my machines for days:
<http://cdash.hdfgroup.uiuc.edu/index.php?project=HDF518>
--
____________________________________________________________
Sean McBride, B. Eng sean@rogue-research.com
Rogue Research www.rogue-research.com
Mac Software Developer Montréal, Québec, Canada
Hi Mike,
tested the hdf5-1.8.8 and it is working perfectly.
The cygwin package I just prepared it is the first one
that has no need of any source patches.
It is configured as
--with-zlib \
--with-gnu-ld \
--enable-shared \
--enable-threadsafe \
--with-pthread \
FC=gfortran-4 \
Only test failures are:
Testing MDC/FILE related API calls *FAILED*
check_file_mdc_api_calls(): failure_mssg = "Unexpected internal config #3.".
Testing MDC/FILE related API input errors HDF5-DIAG: Error detected in HDF5 (1.8.8) thread 2147483704: #000: /pub/devel/hdf5/hdf5-1.8.8-1/src/hdf5-1.8.8/src/H5F.c line 1440 in H5Fcreate(): unable to create file
major: File accessability
minor: Unable to open file #001: /pub/devel/hdf5/hdf5-1.8.8-1/src/hdf5-1.8.8/src/H5F.c line 1243 in H5F_open(): unable to truncate a file which is already open
major: File accessability
minor: Unable to open file
*FAILED*
check_file_mdc_api_errs(): failure_mssg = "H5Fcreate() failed.
".
Testing query functions of compiler conversion *FAILED*
Can't query conversion function
Regards
Marco
···
On 11/10/2011 11:37 PM, Mike McGreevy wrote:
Hi Marco,
I was able to reproduce your findings on an installation of CYGWIN
v1.7.7, and I believe I have found the problem. Can you try the
following patched tar-ball and let me know if this fixes the regression
failure you reported? If so, it's an easy enough fix that we can include
it in the 1.8.8 release.
We encourage submissions, however please provide configuration information and if there are errors, provide support to HDF to identify the problem. Please use the "Experimental" ctest option as necessary. If your submission is configured consistently each day then use the "Nightly" option. Use the latest release or the "CMake" branch of hdf5 svn: http://svn.hdfgroup.uiuc.edu/hdf5/branches/hdf5_1_8_cmake.
Simple example commands for those who need them:
In a build subfolder on linux ->
However, if you have actual ctest scripts, please use those. Also Windows requires that you add the build configuration (Release/Debug) to the command lines.
Any other questions? Please ask.
Allen
···
On 2. nov. 2011, at 15:13, Sean McBride wrote:
> On Wed, 2 Nov 2011 08:55:54 -0500, Dana Robinson said:
>
>> I'm looking into this, but I've been unable to reproduce the big test
>> failure on any of our machines or VMs. I'm downloading Centos 4.6
>> i386 today to try building HDF5 with gcc 4.6.2. I'll post the results
>> when I'm done.
>
> This is exactly the kind of situation where it is handy to have daily build results reported to a dashboard. It would be nice if the HDF5 dashboard had more submissions. The 'big' test has been failing on one of my machines for days:
> <http://cdash.hdfgroup.uiuc.edu/index.php?project=HDF518>
>
Sounds like a great idea. But, how do I submit these results? If the information needed was included in the build/install instructions, perhaps more people would do it, as a part of the build process? (Or perhaps I just didn't find the info.) For other projects using cdash that I've seen, the trick was "make Experimental" or something like that; no such make target seems to exist.
