Release of HDF5-1.10.0-pre2

Hdf-forum archives
1

Release of HDF5-1.10.0-pre2

···

===========================

The HDF5-1.10.0-pre2 release is now available for anyone who would like to
try it.

It can be obtained from The HDF Group Downloads page:

   https://www.hdfgroup.org/downloads/

It can also be obtained directly from:

   https://www.hdfgroup.org/HDF5/release/obtain5110.html

This version contains a fix for an issue which occurred when building HDF5
within the source code directory. A script run by "make check" removed the
java/lib files, including the source jar files.

We are still on target for releasing HDF5-1.10.0 next week. Let us know if
you have any comments!

2

Could you please provide a direct link to the actual source distro (either bzipped or gzipped).

Cheers,
Rob

···

-----Original Message----- From: help@hdfgroup.org
Sent: Thursday, March 24, 2016 5:45 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] Release of HDF5-1.10.0-pre2

Release of HDF5-1.10.0-pre2

The HDF5-1.10.0-pre2 release is now available for anyone who would like to try it.

It can be obtained from The HDF Group Downloads page:

  https://www.hdfgroup.org/downloads/

It can also be obtained directly from:

  https://www.hdfgroup.org/HDF5/release/obtain5110.html

3

On Windows 7, (mingw-w64 port of) gcc-4.9.2, building in msys shell using autotools.
I start with:

$ ./configure --disable-shared --enable-static CFLAGS=-DH5_HAVE_WIN32_API CPPFLAGS=-IC:/_32/msys_492/1.0/local/include LDFLAGS=-LC:/_32/msys_492/1.0/local/lib --prefix=C:/_32/msys_492/1.0/local

That seems to go ok, but 'make' fails early on with:

···

-----Original Message----- From: help@hdfgroup.org
Sent: Thursday, March 24, 2016 5:45 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] Release of HDF5-1.10.0-pre2

Release of HDF5-1.10.0-pre2

##################
  CC H5.lo
In file included from H5private.h:609:0,
                 from H5.c:24:
H5win32defs.h:70:8: error: redefinition of 'struct timezone'
struct timezone {
        ^
In file included from c:/_32/gcc-straw-492/i686-w64-mingw32/include/sys/time.h:10:0,
                 from H5private.h:106,
                 from H5.c:24:
c:/_32/gcc-straw-492/i686-w64-mingw32/include/time.h:250:8: note: originally defined here
struct timezone {
        ^
##################

I work around that by removing the redefinition of struct timezone from H5win32defs.h.
That allows 'make' to succeed until we get to the attempt to build test/twriteorder.exe:

##################
  CC twriteorder.o
  CCLD twriteorder.exe
twriteorder.o:twriteorder.c:(.text+0x8e8): undefined reference to `fork'
twriteorder.o:twriteorder.c:(.text+0xa0a): undefined reference to `waitpid'
twriteorder.o:twriteorder.c:(.text+0xa37): undefined reference to `WIFEXITED'
twriteorder.o:twriteorder.c:(.text+0xa47): undefined reference to `WEXITSTATUS'
collect2.exe: error: ld returned 1 exit status
make[1]: *** [twriteorder.exe] Error 1
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/test'
make: *** [all-recursive] Error 1
##################

This is the same as occurred in hdf5-1.10.0-pre1.
I don't know how to fix that, so I rewrote twriteorder.c to do nothing other than print "All skipped" and return 0.

That allows 'make' to proceed further, until we start hitting the test files that #include test/use.h (eg atomic_writer.c, use_append_chunk.c and use_common.c).
The problem with use.h is that it wants to #include the non-existent sys/wait.h.

Commenting out the inclusion of sys/wait.h does allow atomic_writer.exe to be built, but the attempt to build use_append_chunk.exe then fails with the same "undefined reference" errors that afflict twriteorder.

Cheers,
Rob

4

https://www.hdfgroup.org/HDF5/release/obtainsrc5110.html

···

-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of sisyphus1@optusnet.com.au
Sent: Thursday, March 24, 2016 6:35 AM
To: hdf-forum@lists.hdfgroup.org
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

-----Original Message-----
From: help@hdfgroup.org
Sent: Thursday, March 24, 2016 5:45 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] Release of HDF5-1.10.0-pre2

Release of HDF5-1.10.0-pre2

The HDF5-1.10.0-pre2 release is now available for anyone who would like to
try it.

It can be obtained from The HDF Group Downloads page:

  https://www.hdfgroup.org/downloads/

It can also be obtained directly from:

  https://www.hdfgroup.org/HDF5/release/obtain5110.html

Could you please provide a direct link to the actual source distro (either
bzipped or gzipped).

Cheers,
Rob

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

5

If anyone would like to try out a Docker image of this release (for Python users, h5py 2.6.0 is included as well), you can pull the image from Docker Hub with this command: $ docker run -it hdfgroup/hdf5lib:1.10.0-pre2 /bin/bash

See https://hub.docker.com/r/hdfgroup/hdf5lib for more information. If you don't have docker, see docs.docker.com for install instructions.

Cheers,
John

···

On 3/24/16, 5:20 AM, "Hdf-forum on behalf of Gerd Heber" <hdf-forum-bounces@lists.hdfgroup.org on behalf of gheber@hdfgroup.org> wrote:

https://www.hdfgroup.org/HDF5/release/obtainsrc5110.html

-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of sisyphus1@optusnet.com.au
Sent: Thursday, March 24, 2016 6:35 AM
To: hdf-forum@lists.hdfgroup.org
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

-----Original Message-----
From: help@hdfgroup.org
Sent: Thursday, March 24, 2016 5:45 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] Release of HDF5-1.10.0-pre2

Release of HDF5-1.10.0-pre2

The HDF5-1.10.0-pre2 release is now available for anyone who would like to
try it.

It can be obtained from The HDF Group Downloads page:

  https://www.hdfgroup.org/downloads/

It can also be obtained directly from:

  https://www.hdfgroup.org/HDF5/release/obtain5110.html

Could you please provide a direct link to the actual source distro (either
bzipped or gzipped).

Cheers,
Rob

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

6

Hi Rob,

- I'm not sure what to make of the timezone struct. Can you send me the src/H5pubconf.h that is generated by configure and your configure output? I'd like to see what MinGW thinks you have.

- Those problematic files in tests were designed for POSIX and assume the presence of fork(), pid_t, etc. Since they are only built by the autotools, our testing suite never flagged a problem since we only support Windows under CMake and don't support MinGW. In the grand scheme of things, they aren't important. The atomic writer and reader programs are for testing new file systems for SWMR and the others are programs that are invoked by a shell script that tests a few SWMR use cases. I'll try to have a MinGW bypass for the 1.10.0 release for all of them.

Cheers,

Dana

···

-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of sisyphus1@optusnet.com.au
Sent: Friday, March 25, 2016 8:09 AM
To: hdf-forum@lists.hdfgroup.org
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

-----Original Message-----
From: help@hdfgroup.org
Sent: Thursday, March 24, 2016 5:45 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] Release of HDF5-1.10.0-pre2

Release of HDF5-1.10.0-pre2

On Windows 7, (mingw-w64 port of) gcc-4.9.2, building in msys shell using
autotools.
I start with:

$ ./configure --disable-shared --enable-static CFLAGS=-DH5_HAVE_WIN32_API
CPPFLAGS=-IC:/_32/msys_492/1.0/local/include
LDFLAGS=-LC:/_32/msys_492/1.0/local/lib --prefix=C:/_32/msys_492/1.0/local

That seems to go ok, but 'make' fails early on with:

##################
  CC H5.lo
In file included from H5private.h:609:0,
                 from H5.c:24:
H5win32defs.h:70:8: error: redefinition of 'struct timezone'
struct timezone {
        ^
In file included from
c:/_32/gcc-straw-492/i686-w64-mingw32/include/sys/time.h:10:0,
                 from H5private.h:106,
                 from H5.c:24:
c:/_32/gcc-straw-492/i686-w64-mingw32/include/time.h:250:8: note: originally
defined here
struct timezone {
        ^
##################

I work around that by removing the redefinition of struct timezone from
H5win32defs.h.
That allows 'make' to succeed until we get to the attempt to build
test/twriteorder.exe:

##################
  CC twriteorder.o
  CCLD twriteorder.exe
twriteorder.o:twriteorder.c:(.text+0x8e8): undefined reference to `fork'
twriteorder.o:twriteorder.c:(.text+0xa0a): undefined reference to `waitpid'
twriteorder.o:twriteorder.c:(.text+0xa37): undefined reference to
`WIFEXITED'
twriteorder.o:twriteorder.c:(.text+0xa47): undefined reference to
`WEXITSTATUS'
collect2.exe: error: ld returned 1 exit status
make[1]: *** [twriteorder.exe] Error 1
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/test'
make: *** [all-recursive] Error 1
##################

This is the same as occurred in hdf5-1.10.0-pre1.
I don't know how to fix that, so I rewrote twriteorder.c to do nothing other
than print "All skipped" and return 0.

That allows 'make' to proceed further, until we start hitting the test files
that #include test/use.h (eg atomic_writer.c, use_append_chunk.c and
use_common.c).
The problem with use.h is that it wants to #include the non-existent
sys/wait.h.

Commenting out the inclusion of sys/wait.h does allow atomic_writer.exe to
be built, but the attempt to build use_append_chunk.exe then fails with the
same "undefined reference" errors that afflict twriteorder.

Cheers,
Rob

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

7

Hi Rob,

- I'm not sure what to make of the timezone struct. Can you send me the src/H5pubconf.h that is generated by configure and your configure output? I'd like to see what MinGW thinks you have.

Attached (in relation to the pre2 build).
I notice that from pre1 to pre2 , the line "#endif /* H5_HAVE_VISUAL_STUDIO */" in H5win32defs.h was raised a few lines higher, thereby exposing my build to the redefinition of "struct timezone".
(There was no issue with "struct timezone" in pre1.)
I'm also attaching a diff of the H5pubconf.h between pre1 and pre2. - as I'm not sure that all of those changes are correct. (Haven't yet detected any problems with them, however.)

The configure command (as copy'n'pasted from config.log) was:
$ ./configure --disable-shared --enable-static CFLAGS=-DH5_HAVE_WIN32_API CPPFLAGS=-IC:/_32/msys_492/1.0/local/include LDFLAGS=-LC:/_32/msys_492/1.0/local/lib --prefix=C:/_32/msys_492/1.0/local

- Those problematic files in tests were designed for POSIX and assume the presence of fork(), pid_t, etc. Since they are only built by the autotools, our testing suite never flagged a problem since we only support Windows under CMake and don't support MinGW. In the grand scheme of things, they aren't important. The atomic writer and reader programs are for testing new file systems for SWMR and the others are programs that are invoked by a shell script that tests a few SWMR use cases. I'll try to have a MinGW bypass for the 1.10.0 release for all of them.

I think that would be fine by me.

Thanks, Dana.

Cheers,
Rob

pubconf.diff (2.26 KB)

config.out (20 KB)

H5pubconf.h (18.4 KB)

···

-----Original Message----- From: Dana Robinson
Sent: Saturday, March 26, 2016 12:34 AM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

8

Does h5py 2.6.0 support all the new features? I ma particularly interested in the Virtual Dataset feature.

Thanks,

-Roy

···

On Mar 24, 2016, at 4:19 PM, John Readey <jreadey@hdfgroup.org> wrote:

If anyone would like to try out a Docker image of this release (for Python users, h5py 2.6.0 is included as well), you can pull the image from Docker Hub with this command: $ docker run -it hdfgroup/hdf5lib:1.10.0-pre2 /bin/bash

See https://hub.docker.com/r/hdfgroup/hdf5lib for more information. If you don't have docker, see docs.docker.com for install instructions.

Cheers,
John

On 3/24/16, 5:20 AM, "Hdf-forum on behalf of Gerd Heber" <hdf-forum-bounces@lists.hdfgroup.org on behalf of gheber@hdfgroup.org> wrote:

https://www.hdfgroup.org/HDF5/release/obtainsrc5110.html

-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of sisyphus1@optusnet.com.au
Sent: Thursday, March 24, 2016 6:35 AM
To: hdf-forum@lists.hdfgroup.org
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

-----Original Message-----
From: help@hdfgroup.org
Sent: Thursday, March 24, 2016 5:45 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] Release of HDF5-1.10.0-pre2

Release of HDF5-1.10.0-pre2

The HDF5-1.10.0-pre2 release is now available for anyone who would like to
try it.

It can be obtained from The HDF Group Downloads page:

https://www.hdfgroup.org/downloads/

It can also be obtained directly from:

https://www.hdfgroup.org/HDF5/release/obtain5110.html

Could you please provide a direct link to the actual source distro (either
bzipped or gzipped).

Cheers,
Rob

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new address and phone***
110 Shaffer Road
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn@noaa.gov www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

9

The Virtual Dataset feature is supported in the low-level h5py interface. See: https://github.com/h5py/h5py/pull/663.

John

···

On 3/24/16, 6:01 PM, "Hdf-forum on behalf of Roy Mendelssohn - NOAA Federal" <hdf-forum-bounces@lists.hdfgroup.org on behalf of roy.mendelssohn@noaa.gov> wrote:

Does h5py 2.6.0 support all the new features? I ma particularly interested in the Virtual Dataset feature.

Thanks,

-Roy

On Mar 24, 2016, at 4:19 PM, John Readey <jreadey@hdfgroup.org> wrote:

If anyone would like to try out a Docker image of this release (for Python users, h5py 2.6.0 is included as well), you can pull the image from Docker Hub with this command: $ docker run -it hdfgroup/hdf5lib:1.10.0-pre2 /bin/bash

See https://hub.docker.com/r/hdfgroup/hdf5lib for more information. If you don't have docker, see docs.docker.com for install instructions.

Cheers,
John

On 3/24/16, 5:20 AM, "Hdf-forum on behalf of Gerd Heber" <hdf-forum-bounces@lists.hdfgroup.org on behalf of gheber@hdfgroup.org> wrote:

https://www.hdfgroup.org/HDF5/release/obtainsrc5110.html

-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of sisyphus1@optusnet.com.au
Sent: Thursday, March 24, 2016 6:35 AM
To: hdf-forum@lists.hdfgroup.org
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

-----Original Message-----
From: help@hdfgroup.org
Sent: Thursday, March 24, 2016 5:45 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] Release of HDF5-1.10.0-pre2

Release of HDF5-1.10.0-pre2

The HDF5-1.10.0-pre2 release is now available for anyone who would like to
try it.

It can be obtained from The HDF Group Downloads page:

https://www.hdfgroup.org/downloads/

It can also be obtained directly from:

https://www.hdfgroup.org/HDF5/release/obtain5110.html

Could you please provide a direct link to the actual source distro (either
bzipped or gzipped).

Cheers,
Rob

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new address and phone***
110 Shaffer Road
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn@noaa.gov www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

10

Hi Rob,

Thanks! I'll try to get a look at this over the weekend so I can get it into 1.10.0. I changed the #ifdefs around so that MinGW would do better at picking up the Windows functions. I looks like I was off by a bit :confused:

The revise_chunks branch (a staging branch for 1.10.0 changes) has updated test files that are wrapped in #ifdefs.

https://svn.hdfgroup.uiuc.edu/hdf5/branches/revise_chunks

Can you copy the pertinent files from there into your 1.10.0 distribution and let me know if they build ok and don't interfere with the tests? test_usecases.sh should pass and the output should indicate that it was skipped.

The changed files are:

   M /branches/revise_chunks/test/atomic_reader.c
   M /branches/revise_chunks/test/atomic_writer.c
   M /branches/revise_chunks/test/test_usecases.sh.in
   M /branches/revise_chunks/test/twriteorder.c
   M /branches/revise_chunks/test/use.h
   M /branches/revise_chunks/test/use_append_chunk.c
   M /branches/revise_chunks/test/use_append_mchunks.c
   M /branches/revise_chunks/test/use_common.c
   M /branches/revise_chunks/test/use_disable_mdc_flushes.c

Cheers,

Dana

···

-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of sisyphus1@optusnet.com.au
Sent: Friday, March 25, 2016 7:45 PM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

-----Original Message-----
From: Dana Robinson
Sent: Saturday, March 26, 2016 12:34 AM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

Hi Rob,

- I'm not sure what to make of the timezone struct. Can you send me
the src/H5pubconf.h that is generated by configure and your configure output?
I'd like to see what MinGW thinks you have.

Attached (in relation to the pre2 build).
I notice that from pre1 to pre2 , the line "#endif /* H5_HAVE_VISUAL_STUDIO
*/" in H5win32defs.h was raised a few lines higher, thereby exposing my
build to the redefinition of "struct timezone".
(There was no issue with "struct timezone" in pre1.)
I'm also attaching a diff of the H5pubconf.h between pre1 and pre2. - as I'm
not sure that all of those changes are correct. (Haven't yet detected any
problems with them, however.)

The configure command (as copy'n'pasted from config.log) was:
$ ./configure --disable-shared --enable-static CFLAGS=-DH5_HAVE_WIN32_API
CPPFLAGS=-IC:/_32/msys_492/1.0/local/include
LDFLAGS=-LC:/_32/msys_492/1.0/local/lib --prefix=C:/_32/msys_492/1.0/local

- Those problematic files in tests were designed for POSIX and assume the
presence of fork(), pid_t, etc. Since they are only built by the
autotools, our testing suite never flagged a problem since we only support
Windows under CMake and don't support MinGW. In the grand scheme of
things, they aren't important. The atomic writer and reader programs are
for testing new file systems for SWMR and the others are programs that are
invoked by a shell script that tests a few SWMR use cases. I'll try to
have a MinGW bypass for the 1.10.0 release for all of them.

I think that would be fine by me.

Thanks, Dana.

Cheers,
Rob

11

Those changes look pretty good, Dana.

Running 'make' now gets as far as:

···

-----Original Message----- From: Dana Robinson
Sent: Saturday, March 26, 2016 12:33 PM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

Can you copy the pertinent files from there into your 1.10.0 distribution and let me know if they build ok and don't interfere with the tests? test_usecases.sh should pass and the output should indicate that it was skipped.

The changed files are:

  M /branches/revise_chunks/test/atomic_reader.c
  M /branches/revise_chunks/test/atomic_writer.c
  M /branches/revise_chunks/test/test_usecases.sh.in
  M /branches/revise_chunks/test/twriteorder.c
  M /branches/revise_chunks/test/use.h
  M /branches/revise_chunks/test/use_append_chunk.c
  M /branches/revise_chunks/test/use_append_mchunks.c
  M /branches/revise_chunks/test/use_common.c
  M /branches/revise_chunks/test/use_disable_mdc_flushes.c

###########################################
$ make
Making all in src
make[1]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/src'
make all-am
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/src'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/src'
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/src'
Making all in test
make[1]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/test'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/test'
Making all in tools
make[1]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools'
Making all in lib
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/lib'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/lib'
Making all in h5diff
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5diff'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5diff'
Making all in h5ls
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5ls'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5ls'
Making all in h5dump
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5dump'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5dump'
Making all in misc
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc'
Making all in vds
make[3]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc/vds'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc/vds'
make[3]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc'
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc'
Making all in h5import
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5import'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5import'
Making all in h5repack
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5repack'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5repack'
Making all in h5jam
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5jam'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5jam'
Making all in h5copy
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5copy'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5copy'
Making all in h5stat
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5stat'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5stat'
Making all in h5format_convert
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5format_convert
'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5format_convert'

Making all in perform
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/perform'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/perform'
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools'
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools'
Making all in .
make[1]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2'
Making all in hl
make[1]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl'
Making all in src
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/src'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/src'
Making all in test
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/test'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/test'
Making all in tools
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools'
Making all in gif2h5
make[3]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools/gif2h5'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools/gif2h5'
Making all in h5watch
make[3]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools/h5watch'
  CC h5watchgentest.o
h5watchgentest.c:22:26: fatal error: sys/resource.h: No such file or directory
#include <sys/resource.h>
                          ^
compilation terminated.
make[3]: *** [h5watchgentest.o] Error 1
make[3]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools/h5watch'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl'
make: *** [all-recursive] Error 1
###########################################

At that stage I ran 'make check', and that ran fine (for quite a while) until:

###########################################
.....
Finished testing swmr.exe

Testing testerror.sh

testerror.sh Test Log

Testing err_compat *FAILED*
    Expected result differs from actual result
    *** ./testfiles/err_compat_1 Wed Mar 23 06:01:06 2016
    --- ./err_compat.out Sat Mar 26 16:11:28 2016
    ***************
    *** 1,4 ****
    ! Testing error API H5Eset/get_auto
Testing error API based on data I/O All error API tests passed.
         This program tests the Error API compatible with HDF5 version (number).
  There're supposed to be some error messages
      ********* Print error stack in HDF5 default way *********
      HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
    --- 1,4 ----
    ! Testing error API H5Eset/get_auto Testing error API based on data I/O
                                   All error API tests passed.
         This program tests the Error API compatible with HDF5 version (number).
  There're supposed to be some error messages
      ********* Print error stack in HDF5 default way *********
      HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
Testing error_test PASSED
make[4]: *** [testerror.sh.chkexe_] Error 1

###########################################

I'm not *too* worried about failing tests. My interest in this library is that it works with the PDL::IO::HDF5 (perl) module on Windows - which has been the case to date (despite some failing tests in the past).

However, I do think it would be good to get 'make' to actually run to completion.
I was surprised to find that I can actually run 'make check' and 'make install' despite 'make' having terminated in error. That's a rather unusual behaviour in my experience.

Cheers,
Rob

12

Thanks!

-Roy

···

On Mar 24, 2016, at 11:51 PM, John Readey <jreadey@hdfgroup.org> wrote:

The Virtual Dataset feature is supported in the low-level h5py interface. See: https://github.com/h5py/h5py/pull/663.

John

On 3/24/16, 6:01 PM, "Hdf-forum on behalf of Roy Mendelssohn - NOAA Federal" <hdf-forum-bounces@lists.hdfgroup.org on behalf of roy.mendelssohn@noaa.gov> wrote:

Does h5py 2.6.0 support all the new features? I ma particularly interested in the Virtual Dataset feature.

Thanks,

-Roy

On Mar 24, 2016, at 4:19 PM, John Readey <jreadey@hdfgroup.org> wrote:

If anyone would like to try out a Docker image of this release (for Python users, h5py 2.6.0 is included as well), you can pull the image from Docker Hub with this command: $ docker run -it hdfgroup/hdf5lib:1.10.0-pre2 /bin/bash

See https://hub.docker.com/r/hdfgroup/hdf5lib for more information. If you don't have docker, see docs.docker.com for install instructions.

Cheers,
John

On 3/24/16, 5:20 AM, "Hdf-forum on behalf of Gerd Heber" <hdf-forum-bounces@lists.hdfgroup.org on behalf of gheber@hdfgroup.org> wrote:

https://www.hdfgroup.org/HDF5/release/obtainsrc5110.html

-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of sisyphus1@optusnet.com.au
Sent: Thursday, March 24, 2016 6:35 AM
To: hdf-forum@lists.hdfgroup.org
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

-----Original Message-----
From: help@hdfgroup.org
Sent: Thursday, March 24, 2016 5:45 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] Release of HDF5-1.10.0-pre2

Release of HDF5-1.10.0-pre2

The HDF5-1.10.0-pre2 release is now available for anyone who would like to
try it.

It can be obtained from The HDF Group Downloads page:

https://www.hdfgroup.org/downloads/

It can also be obtained directly from:

https://www.hdfgroup.org/HDF5/release/obtain5110.html

Could you please provide a direct link to the actual source distro (either
bzipped or gzipped).

Cheers,
Rob

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new address and phone***
110 Shaffer Road
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn@noaa.gov www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

**********************
"The contents of this message do not reflect any position of the U.S. Government or NOAA."
**********************
Roy Mendelssohn
Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new address and phone***
110 Shaffer Road
Santa Cruz, CA 95060
Phone: (831)-420-3666
Fax: (831) 420-3980
e-mail: Roy.Mendelssohn@noaa.gov www: http://www.pfeg.noaa.gov/

"Old age and treachery will overcome youth and skill."
"From those who have been given much, much will be expected"
"the arc of the moral universe is long, but it bends toward justice" -MLK Jr.

13

Hi Rob,

- I'll investigate and possibly enter a bug report for make install working after make check fails.

- I've updated the h5watch files in the revise_chunks branch.

- I'm not sure why err_compat is failing. I'd have to take a closer look into the output. I wonder if it's due to CR/LF differences? I'll see if I can get a basic MinGW system set up here to investigate, though that might not be possible before our code freeze on Monday. That issue might have to wait for 1.10.1.

- Still working on that timezone struct problem.

Cheers,

Dana

···

-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of sisyphus1@optusnet.com.au
Sent: Saturday, March 26, 2016 2:41 AM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

-----Original Message-----
From: Dana Robinson
Sent: Saturday, March 26, 2016 12:33 PM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

Can you copy the pertinent files from there into your 1.10.0
distribution and let me know if they build ok and don't interfere with the tests?
test_usecases.sh should pass and the output should indicate that it
was skipped.

The changed files are:

  M /branches/revise_chunks/test/atomic_reader.c
  M /branches/revise_chunks/test/atomic_writer.c
  M /branches/revise_chunks/test/test_usecases.sh.in
  M /branches/revise_chunks/test/twriteorder.c
  M /branches/revise_chunks/test/use.h
  M /branches/revise_chunks/test/use_append_chunk.c
  M /branches/revise_chunks/test/use_append_mchunks.c
  M /branches/revise_chunks/test/use_common.c
  M /branches/revise_chunks/test/use_disable_mdc_flushes.c

Those changes look pretty good, Dana.

Running 'make' now gets as far as:

###########################################
$ make
Making all in src
make[1]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/src'
make all-am
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/src'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/src'
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/src'
Making all in test
make[1]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/test'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/test'
Making all in tools
make[1]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools'
Making all in lib
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/lib'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/lib'
Making all in h5diff
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5diff'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5diff'
Making all in h5ls
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5ls'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5ls'
Making all in h5dump
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5dump'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5dump'
Making all in misc
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc'
Making all in vds
make[3]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc/vds'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc/vds'
make[3]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc'
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc'
Making all in h5import
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5import'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5import'
Making all in h5repack
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5repack'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5repack'
Making all in h5jam
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5jam'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5jam'
Making all in h5copy
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5copy'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5copy'
Making all in h5stat
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5stat'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5stat'
Making all in h5format_convert
make[2]: Entering directory
`/c/_32/comp/hdf5-1.10.0-pre2/tools/h5format_convert
'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory
`/c/_32/comp/hdf5-1.10.0-pre2/tools/h5format_convert'

Making all in perform
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/perform'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/perform'
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools'
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools'
Making all in .
make[1]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2'
Making all in hl
make[1]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl'
Making all in src
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/src'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/src'
Making all in test
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/test'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/test'
Making all in tools
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools'
Making all in gif2h5
make[3]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools/gif2h5'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools/gif2h5'
Making all in h5watch
make[3]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools/h5watch'
  CC h5watchgentest.o
h5watchgentest.c:22:26: fatal error: sys/resource.h: No such file or directory #include <sys/resource.h>
                          ^
compilation terminated.
make[3]: *** [h5watchgentest.o] Error 1
make[3]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools/h5watch'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl'
make: *** [all-recursive] Error 1
###########################################

At that stage I ran 'make check', and that ran fine (for quite a while)
until:

###########################################
.....
Finished testing swmr.exe

============================
Testing testerror.sh

testerror.sh Test Log

Testing err_compat
*FAILED*
    Expected result differs from actual result
    *** ./testfiles/err_compat_1 Wed Mar 23 06:01:06 2016
    --- ./err_compat.out Sat Mar 26 16:11:28 2016
    ***************
    *** 1,4 ****
    ! Testing error API H5Eset/get_auto
Testing error API based on data I/O All
error API tests passed.
         This program tests the Error API compatible with HDF5 version
(number).
  There're supposed to be some error messages
      ********* Print error stack in HDF5 default way *********
      HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
    --- 1,4 ----
    ! Testing error API H5Eset/get_auto
Testing error API based on data I/O
                                   All error API tests passed.
         This program tests the Error API compatible with HDF5 version
(number).
  There're supposed to be some error messages
      ********* Print error stack in HDF5 default way *********
      HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
Testing error_test
PASSED
make[4]: *** [testerror.sh.chkexe_] Error 1

###########################################

I'm not *too* worried about failing tests. My interest in this library is
that it works with the PDL::IO::HDF5 (perl) module on Windows - which has
been the case to date (despite some failing tests in the past).

However, I do think it would be good to get 'make' to actually run to
completion.
I was surprised to find that I can actually run 'make check' and 'make
install' despite 'make' having terminated in error. That's a rather unusual
behaviour in my experience.

Cheers,
Rob

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

14

Hi Rob,

Does moving the timezone struct in H5win32defs.h into the Visual Studio block just above it solve the problem?

In the very near future I hope that the struct will go away entirely. That feature has never worked properly across POSIX. It's probably too late for me to get that change into 1.10.0, though, so it'll have to wait another revision.

Cheers,

Dana

···

-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of Dana Robinson
Sent: Sunday, March 27, 2016 4:36 AM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

Hi Rob,

- I'll investigate and possibly enter a bug report for make install working after make check fails.

- I've updated the h5watch files in the revise_chunks branch.

- I'm not sure why err_compat is failing. I'd have to take a closer look into the output. I wonder if it's due to CR/LF differences? I'll see if I can get a basic MinGW system set up here to investigate, though that might not be possible before our code freeze on Monday. That issue might have to wait for 1.10.1.

- Still working on that timezone struct problem.

Cheers,

Dana

-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of sisyphus1@optusnet.com.au
Sent: Saturday, March 26, 2016 2:41 AM
To: HDF Users Discussion List <hdf-forum@lists.hdfgroup.org>
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

-----Original Message-----
From: Dana Robinson
Sent: Saturday, March 26, 2016 12:33 PM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

Can you copy the pertinent files from there into your 1.10.0
distribution and let me know if they build ok and don't interfere with the tests?
test_usecases.sh should pass and the output should indicate that it
was skipped.

The changed files are:

  M /branches/revise_chunks/test/atomic_reader.c
  M /branches/revise_chunks/test/atomic_writer.c
  M /branches/revise_chunks/test/test_usecases.sh.in
  M /branches/revise_chunks/test/twriteorder.c
  M /branches/revise_chunks/test/use.h
  M /branches/revise_chunks/test/use_append_chunk.c
  M /branches/revise_chunks/test/use_append_mchunks.c
  M /branches/revise_chunks/test/use_common.c
  M /branches/revise_chunks/test/use_disable_mdc_flushes.c

Those changes look pretty good, Dana.

Running 'make' now gets as far as:

###########################################
$ make
Making all in src
make[1]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/src'
make all-am
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/src'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/src'
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/src'
Making all in test
make[1]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/test'
make[1]: Nothing to be done for `all'.
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/test'
Making all in tools
make[1]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools'
Making all in lib
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/lib'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/lib'
Making all in h5diff
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5diff'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5diff'
Making all in h5ls
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5ls'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5ls'
Making all in h5dump
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5dump'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5dump'
Making all in misc
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc'
Making all in vds
make[3]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc/vds'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc/vds'
make[3]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc'
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/misc'
Making all in h5import
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5import'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5import'
Making all in h5repack
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5repack'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5repack'
Making all in h5jam
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5jam'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5jam'
Making all in h5copy
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5copy'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5copy'
Making all in h5stat
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5stat'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/h5stat'
Making all in h5format_convert
make[2]: Entering directory
`/c/_32/comp/hdf5-1.10.0-pre2/tools/h5format_convert
'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory
`/c/_32/comp/hdf5-1.10.0-pre2/tools/h5format_convert'

Making all in perform
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/perform'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools/perform'
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/tools'
make[2]: Nothing to be done for `all-am'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools'
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/tools'
Making all in .
make[1]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2'
make[1]: Nothing to be done for `all-am'.
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2'
Making all in hl
make[1]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl'
Making all in src
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/src'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/src'
Making all in test
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/test'
make[2]: Nothing to be done for `all'.
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/test'
Making all in tools
make[2]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools'
Making all in gif2h5
make[3]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools/gif2h5'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools/gif2h5'
Making all in h5watch
make[3]: Entering directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools/h5watch'
  CC h5watchgentest.o
h5watchgentest.c:22:26: fatal error: sys/resource.h: No such file or directory #include <sys/resource.h>
                          ^
compilation terminated.
make[3]: *** [h5watchgentest.o] Error 1
make[3]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools/h5watch'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl/tools'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/c/_32/comp/hdf5-1.10.0-pre2/hl'
make: *** [all-recursive] Error 1
###########################################

At that stage I ran 'make check', and that ran fine (for quite a while)
until:

###########################################
.....
Finished testing swmr.exe

============================
Testing testerror.sh

testerror.sh Test Log

Testing err_compat
*FAILED*
    Expected result differs from actual result
    *** ./testfiles/err_compat_1 Wed Mar 23 06:01:06 2016
    --- ./err_compat.out Sat Mar 26 16:11:28 2016
    ***************
    *** 1,4 ****
    ! Testing error API H5Eset/get_auto
Testing error API based on data I/O All
error API tests passed.
         This program tests the Error API compatible with HDF5 version (number).
  There're supposed to be some error messages
      ********* Print error stack in HDF5 default way *********
      HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
    --- 1,4 ----
    ! Testing error API H5Eset/get_auto Testing error API based on data I/O
                                   All error API tests passed.
         This program tests the Error API compatible with HDF5 version (number).
  There're supposed to be some error messages
      ********* Print error stack in HDF5 default way *********
      HDF5-DIAG: Error detected in HDF5 (version (number)) thread (IDs):
Testing error_test
PASSED
make[4]: *** [testerror.sh.chkexe_] Error 1

###########################################

I'm not *too* worried about failing tests. My interest in this library is that it works with the PDL::IO::HDF5 (perl) module on Windows - which has been the case to date (despite some failing tests in the past).

However, I do think it would be good to get 'make' to actually run to completion.
I was surprised to find that I can actually run 'make check' and 'make install' despite 'make' having terminated in error. That's a rather unusual behaviour in my experience.

Cheers,
Rob

_______________________________________________
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Hdf-forum@lists.hdfgroup.org
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Twitter: https://twitter.com/hdf5

_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
Twitter: https://twitter.com/hdf5

15

- I'll investigate and possibly enter a bug report for make install working after make check fails.

It's a normal thing for 'make install' to work even if 'make check' fails.
What struck me as odd was that I could run both 'make check' and 'make install' even though 'make' itself had failed. (I don't think that's normal - but it's *not* something I generally check on, so I could be wrong.)

- I've updated the h5watch files in the revise_chunks branch.

Yep - 'make' now runs successfully to completion !!

- I'm not sure why err_compat is failing. I'd have to take a closer look into the output. I wonder if it's due to CR/LF differences?

That's a distinct possibility.

I'll see if I can get a basic MinGW system set up here to investigate, though that might not be possible before our code freeze on Monday. That issue might have to wait for 1.10.1.

That would be ok by me - main thing is that 'make' now succeeds.
If we can get the rest fixed in svn, then all should be right to go when 1.10.1-pre1 comes along.

Cheers,
Rob

···

-----Original Message----- From: Dana Robinson
Sent: Sunday, March 27, 2016 7:35 PM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

16

Yes.

(I'm about to test the changes to the h5watch files.)

Cheers,
Rob

···

-----Original Message----- From: Dana Robinson
Sent: Sunday, March 27, 2016 7:55 PM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] Release of HDF5-1.10.0-pre2

Does moving the timezone struct in H5win32defs.h into the Visual Studio block just above it solve the problem?