HDF5 1.8.12 release candidate (pre2) is available for testing

epourmal · October 25, 2013, 3:22am

Dear HDF5 users,

New release candidate (with production mode on by default) is available from
ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.12/pre2/

If you have a spare minute please give it a try and report any problems found. We really appreciate your help.

Unfortunately we were not able to address the issues related to undefined compiler behavior, but we are working on them and hopefully will have a solution by the next release.

Thank you!

Elena

···

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

mike.jackson · October 28, 2013, 3:08pm

I found a "bug" that I am hoping is a quick fix.

If the following file:
config/cmake/H5pubconf.h.in

at line 750 is the following:

#define VERSION "@HDF5_PACKAGE_VERSION@"

The issue that I am having is a few other libraries that I am using also define the generic "VERSION" macro. I am wondering if we can change that to

#define H5_VERSION "@HDF5_PACKAGE_VERSION@"

There are 2 more
/* Number of bits in a file offset, on hosts where this is settable. */
#cmakedefine _FILE_OFFSET_BITS

/* Define for large files, on AIX-style hosts. */
#cmakedefine _LARGE_FILES

that are also a bit "generic" and should probably have the H5_ prefix applied to them also.

A quick compile on OS X seems to indicate it will compile. External libraries that may be looking for that #define might have issues.

Thoughts?

Thanks

···

On Oct 24, 2013, at 11:22 PM, Elena Pourmal <epourmal@hdfgroup.org> wrote:

Dear HDF5 users,

New release candidate (with production mode on by default) is available from
ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.12/pre2/

If you have a spare minute please give it a try and report any problems found. We really appreciate your help.

Unfortunately we were not able to address the issues related to undefined compiler behavior, but we are working on them and hopefully will have a solution by the next release.

Thank you!

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

_______________________________________________
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

epourmal · October 30, 2013, 10:44pm

Michael,

We did discuss the issue, and agreed that this should be addressed. I created JIRA issue HDFFV-8557 and we will see what we can do for this release; will not promise but will try.

Elena

···

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

On Oct 28, 2013, at 10:08 AM, Michael Jackson <mike.jackson@bluequartz.net> wrote:

I found a "bug" that I am hoping is a quick fix.

If the following file:
config/cmake/H5pubconf.h.in

at line 750 is the following:

#define VERSION "@HDF5_PACKAGE_VERSION@"

The issue that I am having is a few other libraries that I am using also define the generic "VERSION" macro. I am wondering if we can change that to

#define H5_VERSION "@HDF5_PACKAGE_VERSION@"

There are 2 more
/* Number of bits in a file offset, on hosts where this is settable. */
#cmakedefine _FILE_OFFSET_BITS

/* Define for large files, on AIX-style hosts. */
#cmakedefine _LARGE_FILES

that are also a bit "generic" and should probably have the H5_ prefix applied to them also.

A quick compile on OS X seems to indicate it will compile. External libraries that may be looking for that #define might have issues.

Thoughts?

Thanks

hyoklee · October 31, 2013, 4:58pm

$./configure && make check

failed on the latest Mac OS X Mavericks (10.9) with the following errors:

Running h5import out1.bin -c out3.h5import -o out1.h5
testh5dump.sh: line 887:
/Users/hyoklee/src/hdf5-1.8.12-pre2/tools/h5dump/../h5import/h5import:
No such file or directory

*FAILED*

Running h5diff tbinary.h5 out1.h5 /integer /integer
h5diff: <out1.h5>: unable to open file

*FAILED*

Running h5import out1.bin -c tbin1.ddl -o out1D.h5
testh5dump.sh: line 887:
/Users/hyoklee/src/hdf5-1.8.12-pre2/tools/h5dump/../h5import/h5import:
No such file or directory

*FAILED*

Running h5diff tbinary.h5 out1D.h5 /integer /integer
h5diff: <out1D.h5>: unable to open file

*FAILED*

Testing h5dump --enable-error-stack -b BE -d float -o out2.bin tbinary PASSED

Testing h5dump --enable-error-stack -d integer -o out3.bin -b NATIVE t PASSED

Running h5import out3.bin -c out3.h5import -o out3.h5
testh5dump.sh: line 887:
/Users/hyoklee/src/hdf5-1.8.12-pre2/tools/h5dump/../h5import/h5import:
No such file or directory

*FAILED*

Running h5diff tbinary.h5 out3.h5 /integer /integer
h5diff: <out3.h5>: unable to open file

*FAILED*

Running h5import out3.bin -c tbin3.ddl -o out3D.h5
testh5dump.sh: line 887:
/Users/hyoklee/src/hdf5-1.8.12-pre2/tools/h5dump/../h5import/h5import:
No such file or directory

*FAILED*

Running h5diff tbinary.h5 out3D.h5 /integer /integer
h5diff: <out3D.h5>: unable to open file

*FAILED*

Testing h5dump --enable-error-stack -d double -b FILE -o out4.bin tbin PASSED

Testing h5dump --enable-error-stack tdatareg.h5 PASSED

Testing h5dump --enable-error-stack -R tdatareg.h5 PASSED

Testing h5dump --enable-error-stack tattrreg.h5 PASSED

Testing h5dump --enable-error-stack -R tattrreg.h5 PASSED

Testing h5dump --enable-error-stack -d /Dataset1 -s 0 -R -y -o tbinreg PASSED

Testing h5dump --enable-error-stack --group=1 --sort_by=creation_order PASSED

Testing h5dump --enable-error-stack -g 2 -q name -z ascending tordergr PASSED

Testing h5dump --enable-error-stack -g 2 -q name -z descending torderg PASSED

Testing h5dump --enable-error-stack -q creation_order tordergr.h5 PASSED

Testing h5dump --enable-error-stack -H --sort_by=name --sort_order=asc PASSED

Testing h5dump --enable-error-stack -H --sort_by=name --sort_order=des PASSED

Testing h5dump --enable-error-stack -H --sort_by=creation_order --sort PASSED

Testing h5dump --enable-error-stack --sort_by=name --sort_order=ascend PASSED

Testing h5dump --enable-error-stack --sort_by=name --sort_order=descen PASSED

Testing h5dump --enable-error-stack -m %.7f tfpformat.h5 PASSED

Testing h5dump --enable-error-stack textlinksrc.h5 PASSED

Testing h5dump --enable-error-stack textlinkfar.h5 PASSED

Testing h5dump --enable-error-stack textlink.h5 PASSED

Testing h5dump --enable-error-stack filter_fail.h5 PASSED

Testing h5dump --enable-error-stack -y -o tall-6.txt -d /g1/g1.1/dset1 PASSED

h5dump tests failed with 8 errors.

15.77 real 7.63 user 7.33 sys

make[5]: *** [testh5dump.sh.chkexe_] Error 1

make[4]: *** [build-check-s] Error 2

make[3]: *** [test] Error 2

make[2]: *** [check-am] Error 2

make[1]: *** [check-recursive] Error 1

make: *** [check-recursive] Error 1

···

-----

All tests passed if I run

$./configure && make && make check

--
HDF: Software that Powers Science

On Wed, Oct 30, 2013 at 5:44 PM, Elena Pourmal <epourmal@hdfgroup.org> wrote:

Michael,

We did discuss the issue, and agreed that this should be addressed. I
created JIRA issue HDFFV-8557 and we will see what we can do for this
release; will not promise but will try.

Elena

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

On Oct 28, 2013, at 10:08 AM, Michael Jackson <mike.jackson@bluequartz.net> > wrote:

I found a "bug" that I am hoping is a quick fix.

If the following file:
config/cmake/H5pubconf.h.in

at line 750 is the following:

#define VERSION "@HDF5_PACKAGE_VERSION@"

The issue that I am having is a few other libraries that I am using also
define the generic "VERSION" macro. I am wondering if we can change that to

#define H5_VERSION "@HDF5_PACKAGE_VERSION@"

There are 2 more
/* Number of bits in a file offset, on hosts where this is settable. */
#cmakedefine _FILE_OFFSET_BITS

/* Define for large files, on AIX-style hosts. */
#cmakedefine _LARGE_FILES

that are also a bit "generic" and should probably have the H5_ prefix
applied to them also.

A quick compile on OS X seems to indicate it will compile. External
libraries that may be looking for that #define might have issues.

Thoughts?

Thanks

_______________________________________________
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

epourmal · October 31, 2013, 9:20pm

Joe,

This is a known dependency issue between the tools.

Please run three steps:

./configure
make --> after this step all tools will be build necessary to run make check
make check

Thank you!

Elena

···

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

On Oct 31, 2013, at 11:58 AM, H. Joe Lee <hyoklee@hdfgroup.org> wrote:

$./configure && make check

failed on the latest Mac OS X Mavericks (10.9) with the following errors:

Running h5import out1.bin -c out3.h5import -o out1.h5
testh5dump.sh: line 887:
/Users/hyoklee/src/hdf5-1.8.12-pre2/tools/h5dump/../h5import/h5import:
No such file or directory

*FAILED*

Running h5diff tbinary.h5 out1.h5 /integer /integer
h5diff: <out1.h5>: unable to open file

*FAILED*

Running h5import out1.bin -c tbin1.ddl -o out1D.h5
testh5dump.sh: line 887:
/Users/hyoklee/src/hdf5-1.8.12-pre2/tools/h5dump/../h5import/h5import:
No such file or directory

*FAILED*

Running h5diff tbinary.h5 out1D.h5 /integer /integer
h5diff: <out1D.h5>: unable to open file

*FAILED*

Testing h5dump --enable-error-stack -b BE -d float -o out2.bin tbinary PASSED

Testing h5dump --enable-error-stack -d integer -o out3.bin -b NATIVE t PASSED

Running h5import out3.bin -c out3.h5import -o out3.h5
testh5dump.sh: line 887:
/Users/hyoklee/src/hdf5-1.8.12-pre2/tools/h5dump/../h5import/h5import:
No such file or directory

*FAILED*

Running h5diff tbinary.h5 out3.h5 /integer /integer
h5diff: <out3.h5>: unable to open file

*FAILED*

Running h5import out3.bin -c tbin3.ddl -o out3D.h5
testh5dump.sh: line 887:
/Users/hyoklee/src/hdf5-1.8.12-pre2/tools/h5dump/../h5import/h5import:
No such file or directory

*FAILED*

Running h5diff tbinary.h5 out3D.h5 /integer /integer
h5diff: <out3D.h5>: unable to open file

*FAILED*

Testing h5dump --enable-error-stack -d double -b FILE -o out4.bin tbin PASSED

Testing h5dump --enable-error-stack tdatareg.h5 PASSED

Testing h5dump --enable-error-stack -R tdatareg.h5 PASSED

Testing h5dump --enable-error-stack tattrreg.h5 PASSED

Testing h5dump --enable-error-stack -R tattrreg.h5 PASSED

Testing h5dump --enable-error-stack -d /Dataset1 -s 0 -R -y -o tbinreg PASSED

Testing h5dump --enable-error-stack --group=1 --sort_by=creation_order PASSED

Testing h5dump --enable-error-stack --group=1 --sort_by=creation_order PASSED

Testing h5dump --enable-error-stack -g 2 -q name -z ascending tordergr PASSED

Testing h5dump --enable-error-stack -g 2 -q name -z descending torderg PASSED

Testing h5dump --enable-error-stack -q creation_order tordergr.h5 PASSED

Testing h5dump --enable-error-stack -H --sort_by=name --sort_order=asc PASSED

Testing h5dump --enable-error-stack -H --sort_by=name --sort_order=des PASSED

Testing h5dump --enable-error-stack -H --sort_by=creation_order --sort PASSED

Testing h5dump --enable-error-stack -H --sort_by=creation_order --sort PASSED

Testing h5dump --enable-error-stack --sort_by=name --sort_order=ascend PASSED

Testing h5dump --enable-error-stack --sort_by=name --sort_order=descen PASSED

Testing h5dump --enable-error-stack -m %.7f tfpformat.h5 PASSED

Testing h5dump --enable-error-stack textlinksrc.h5 PASSED

Testing h5dump --enable-error-stack textlinkfar.h5 PASSED

Testing h5dump --enable-error-stack textlink.h5 PASSED

Testing h5dump --enable-error-stack filter_fail.h5 PASSED

Testing h5dump --enable-error-stack -y -o tall-6.txt -d /g1/g1.1/dset1 PASSED

h5dump tests failed with 8 errors.

15.77 real 7.63 user 7.33 sys

make[5]: *** [testh5dump.sh.chkexe_] Error 1

make[4]: *** [build-check-s] Error 2

make[3]: *** [test] Error 2

make[2]: *** [check-am] Error 2

make[1]: *** [check-recursive] Error 1

make: *** [check-recursive] Error 1

-----

All tests passed if I run

$./configure && make && make check

--
HDF: Software that Powers Science

On Wed, Oct 30, 2013 at 5:44 PM, Elena Pourmal <epourmal@hdfgroup.org> wrote:

Michael,

We did discuss the issue, and agreed that this should be addressed. I
created JIRA issue HDFFV-8557 and we will see what we can do for this
release; will not promise but will try.

Elena

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

On Oct 28, 2013, at 10:08 AM, Michael Jackson <mike.jackson@bluequartz.net> >> wrote:

I found a "bug" that I am hoping is a quick fix.

If the following file:
config/cmake/H5pubconf.h.in

at line 750 is the following:

#define VERSION "@HDF5_PACKAGE_VERSION@"

The issue that I am having is a few other libraries that I am using also
define the generic "VERSION" macro. I am wondering if we can change that to

#define H5_VERSION "@HDF5_PACKAGE_VERSION@"

There are 2 more
/* Number of bits in a file offset, on hosts where this is settable. */
#cmakedefine _FILE_OFFSET_BITS

/* Define for large files, on AIX-style hosts. */
#cmakedefine _LARGE_FILES

that are also a bit "generic" and should probably have the H5_ prefix
applied to them also.

A quick compile on OS X seems to indicate it will compile. External
libraries that may be looking for that #define might have issues.

Thoughts?

Thanks

_______________________________________________
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

hyoklee · October 31, 2013, 10:05pm

Elena,

I know that the 3 steps will pass all tests as I wrote at the last line of the previous message.

By the way, 'make distclean' doesn't seem to clean all test files.

hdf-idap-[5:01pm]~/src>diff -r hdf5-1.8.12-pre2 hdf5-1.8.12-pre2.joe/
Only in hdf5-1.8.12-pre2: Makefile
Only in hdf5-1.8.12-pre2.joe/test: dtypes10
Only in hdf5-1.8.12-pre2.joe/test: testdir1
Only in hdf5-1.8.12-pre2.joe/test: th5o_file
Only in hdf5-1.8.12-pre2.joe/test: tsohm.h5
Only in hdf5-1.8.12-pre2.joe/test: tsohm_dst.h5
Only in hdf5-1.8.12-pre2.joe/test: tsohm_src.h5
Only in hdf5-1.8.12-pre2.joe/tools/h5dump: testfiles
Only in hdf5-1.8.12-pre2.joe/tools/h5jam/testfiles: h5jam-help.txt.err-sav
Only in hdf5-1.8.12-pre2.joe/tools/h5jam/testfiles: h5jam-help.txt.out-sav
Only in hdf5-1.8.12-pre2.joe/tools/h5jam/testfiles: h5jam-ub-nohdf5.txt.err-sav
Only in hdf5-1.8.12-pre2.joe/tools/h5jam/testfiles: h5jam-ub-nohdf5.txt.out-sav
Only in hdf5-1.8.12-pre2.joe/tools/h5jam/testfiles: h5unjam-help.txt.err-sav
Only in hdf5-1.8.12-pre2.joe/tools/h5jam/testfiles: h5unjam-help.txt.out-sav
Only in hdf5-1.8.12-pre2.joe/tools/h5ls: testfiles
Only in hdf5-1.8.12-pre2.joe/tools/h5repack/testfiles: h5diff_attr1.h5
Only in hdf5-1.8.12-pre2.joe/tools/h5repack/testfiles: tfamily00000.h5
Only in hdf5-1.8.12-pre2.joe/tools/h5repack/testfiles: tfamily00001.h5
Only in hdf5-1.8.12-pre2.joe/tools/h5repack/testfiles: tfamily00002.h5
Only in hdf5-1.8.12-pre2.joe/tools/h5repack/testfiles: tfamily00003.h5
Only in hdf5-1.8.12-pre2.joe/tools/h5repack/testfiles: tfamily00004.h5
Only in hdf5-1.8.12-pre2.joe/tools/h5repack/testfiles: tfamily00005.h5
Only in hdf5-1.8.12-pre2.joe/tools/h5repack/testfiles: tfamily00006.h5
Only in hdf5-1.8.12-pre2.joe/tools/h5repack/testfiles: tfamily00007.h5
Only in hdf5-1.8.12-pre2.joe/tools/h5repack/testfiles: tfamily00008.h5
Only in hdf5-1.8.12-pre2.joe/tools/h5repack/testfiles: tfamily00009.h5
Only in hdf5-1.8.12-pre2.joe/tools/h5repack/testfiles: tfamily00010.h5
Only in hdf5-1.8.12-pre2.joe/tools/misc/testfiles: h5mkgrp_nested_lp.ls
Only in hdf5-1.8.12-pre2.joe/tools/misc/testfiles: h5mkgrp_nested_mult_lp.ls
Only in hdf5-1.8.12-pre2.joe/tools/misc/testfiles: h5mkgrp_nested_mult_p.ls
Only in hdf5-1.8.12-pre2.joe/tools/misc/testfiles: h5mkgrp_nested_p.ls
Only in hdf5-1.8.12-pre2.joe/tools/misc/testfiles: h5mkgrp_several.ls
Only in hdf5-1.8.12-pre2.joe/tools/misc/testfiles: h5mkgrp_several_l.ls
Only in hdf5-1.8.12-pre2.joe/tools/misc/testfiles: h5mkgrp_several_p.ls
Only in hdf5-1.8.12-pre2.joe/tools/misc/testfiles: h5mkgrp_several_v.ls
Only in hdf5-1.8.12-pre2.joe/tools/misc/testfiles: h5mkgrp_single.ls
Only in hdf5-1.8.12-pre2.joe/tools/misc/testfiles: h5mkgrp_single_l.ls
Only in hdf5-1.8.12-pre2.joe/tools/misc/testfiles: h5mkgrp_single_p.ls
Only in hdf5-1.8.12-pre2.joe/tools/misc/testfiles: h5mkgrp_single_v.ls

···

From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of Elena Pourmal
Sent: Thursday, October 31, 2013 4:20 PM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] HDF5 1.8.12 release candidate (pre2) is available for testing

Joe,

This is a known dependency issue between the tools.

Please run three steps:

./configure
make --> after this step all tools will be build necessary to run make check
make check

Thank you!

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

On Oct 31, 2013, at 11:58 AM, H. Joe Lee <hyoklee@hdfgroup.org<mailto:hyoklee@hdfgroup.org>> wrote: