Pre-release of HDF5 1.8.5 is available for testing

Hdf-forum archives
1

Hi all,

A pre-release version of HDF5 1.8.5 is available for testing, and can be downloaded at the following link:

ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/

If you have a few moments to test this, we would greatly appreciate it. While we have tested it on the platforms that we have access to, there are many others that we are unable to test on ourselves. Please report any errors to help@hdfgroup.org, preferably within the next week or so. We are planning to create and distribute the official release by mid-June if no critical errors are reported beforehand.

Thank you!

The HDF Team

2

--- Ven 28/5/10, Mike McGreevy ha scritto:

Hi all,

A pre-release version of HDF5 1.8.5 is available for
testing, and can be downloaded at the following link:

ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/

If you have a few moments to test this, we would greatly
appreciate it. While we have tested it on the platforms that
we have access to, there are many others that we are unable
to test on ourselves. Please report any errors to help@hdfgroup.org,
preferably within the next week or so. We are planning to
create and distribute the official release by mid-June if no
critical errors are reported beforehand.

Thank you!

The HDF Team

May I suggest that the testing continues also when any test
fails ? It will help to have a general view.

currently on cygwin-1.7 , "make check" stop here:

Testing -- Low-Level File I/O (file)
*** UNEXPECTED VALUE from H5Fcreate should be -1, but is 16777217 at line 149 i n /pub/cygports/hdf5/hdf5-1.8.5-pre2-1/src/hdf5-1.8.5-pre2/test/tfile.c
*** UNEXPECTED VALUE from H5Fclose should be -1, but is 0 at line 158 in /pub/c ygports/hdf5/hdf5-1.8.5-pre2-1/src/hdf5-1.8.5-pre2/test/tfile.c
Testing -- Generic Object Functions (objects)
Testing -- Dataspaces (h5s)
Testing -- Dataspace coordinates (coords)
Testing -- Shared Object Header Messages (sohm)
*** UNEXPECTED RETURN from H5Dopen2 is -1 line 3153 in /pub/cygports/hdf5/hdf5-1 .8.5-pre2-1/src/hdf5-1.8.5-pre2/test/tsohm.c
HDF5-DIAG: Error detected in HDF5 (1.8.5-pre2) thread 10223720:
  #000: /pub/cygports/hdf5/hdf5-1.8.5-pre2-1/src/hdf5-1.8.5-pre2/src/H5D.c line 320 in H5Dopen2(): not found
    major: Dataset
    minor: Object not found
  #001: /pub/cygports/hdf5/hdf5-1.8.5-pre2-1/src/hdf5-1.8.5-pre2/src/H5Gloc.c li ne 480 in H5G_loc_find(): can't find object
    major: Symbol table
    minor: Object not found
  #002: /pub/cygports/hdf5/hdf5-1.8.5-pre2-1/src/hdf5-1.8.5-pre2/src/H5Gtraverse .c line 952 in H5G_traverse(): internal path traversal failed
    major: Symbol table
    minor: Object not found
  #003: /pub/cygports/hdf5/hdf5-1.8.5-pre2-1/src/hdf5-1.8.5-pre2/src/H5Gtraverse .c line 759 in H5G_traverse_real(): traversal operator failed
    major: Symbol table
    minor: Callback failed
  #004: /pub/cygports/hdf5/hdf5-1.8.5-pre2-1/src/hdf5-1.8.5-pre2/src/H5Gloc.c li ne 435 in H5G_loc_find_cb(): object 'dataset' doesn't exist
    major: Symbol table
    minor: Object not found
*** UNEXPECTED RETURN from H5Dclose is -1 line 3157 in /pub/cygports/hdf5/hdf5-1 .8.5-pre2-1/src/hdf5-1.8.5-pre2/test/tsohm.c
HDF5-DIAG: Error detected in HDF5 (1.8.5-pre2) thread 10223720:
  #000: /pub/cygports/hdf5/hdf5-1.8.5-pre2-1/src/hdf5-1.8.5-pre2/src/H5D.c line 377 in H5Dclose(): not a dataset
    major: Invalid arguments to routine
    minor: Inappropriate type
Testing -- Attributes (attr)
Testing -- Selections (select)
Testing -- Time Datatypes (time)
Testing -- References (reference)
Testing -- Variable-Length Datatypes (vltypes)
Testing -- Variable-Length Strings (vlstrings)
Testing -- Group & Attribute Iteration (iterate)
Testing -- Array Datatypes (array)
Testing -- Generic Properties (genprop)
Testing -- UTF-8 Encoding (unicode)
Testing -- User-Created Identifiers (id)
Testing -- Miscellaneous (misc)

!!! 4 Error(s) were detected !!!

Regards
Marco

3

A Friday 28 May 2010 22:54:24 Mike McGreevy escrigué:

Hi all,

A pre-release version of HDF5 1.8.5 is available for testing, and can be
downloaded at the following link:

ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/

If you have a few moments to test this, we would greatly appreciate it.
While we have tested it on the platforms that we have access to, there
are many others that we are unable to test on ourselves. Please report
any errors to help@hdfgroup.org, preferably within the next week or so.
We are planning to create and distribute the official release by
mid-June if no critical errors are reported beforehand.

Looks good here on Linux platform (openSUSE 64-bit). My measured performance
in critical places seems okay too. By the way, I like the new performance
excerpts during test time. In particular, I'm curious about this one:

···

============================
iopipe Test Log

[clip]
I/O request size is 1000000.0MB
Before getrusage() call
fill raw 0.00user 0.00system 0.01elapsed 8509.83MB/s
fill hdf5 0.00user 0.00system 0.01elapsed 6306.27MB/s
out raw 0.00user 0.03system 0.03elapsed 1425.14MB/s
out hdf5 0.00user 0.03system 0.03elapsed 1350.30MB/s
in raw 0.00user 0.02system 0.02elapsed 1778.29MB/s
in hdf5 0.00user 0.02system 0.02elapsed 2098.98MB/s
in hdf5 partial 0.01user 0.02system 0.03elapsed 1410.44MB/s
0.05user 0.28system 0:01.71elapsed 20%CPU (0avgtext+0avgdata 0maxresident)k
184inputs+3984outputs (2major+15920minor)pagefaults 0swaps

where HDF5 seems to behave well compared with pure POSIX, except for the fill
test where POSIX is significantly faster. Is this expected?

--
Francesc Alted

4

Hello,

I 've compiled HDF5 1.8.5 pre-release under windows with :

CMake 2.8.1
Microsoft Visual C++ 2008 Express Edition

CMake generates a mingw Makefile (on request)
make / make install ok for C/C++/HL/tools generation.

However when I request the fortran (Intel ifort 11.1 with Visual Studio 2008) binding, CMake stopped with the message reported hereafter.

Best regards,

Cyril.

""""
Configure Checks that still need to be implemented

GetConsoleScreenBufferInfo function for Windows

CMake Warning (dev) at C:/Program Files/CMake 2.8/share/cmake-2.8/Modules/FortranCInterface.cmake:207 (message):

No FortranCInterface mangling known for mysub

Call Stack (most recent call first):

fortran/CMakeLists.txt:8 (FortranCInterface_HEADER)

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake 2.8/share/cmake-2.8/Modules/FortranCInterface.cmake:193 (message):

No FortranCInterface mangling known for mymod:my_sub

Call Stack (most recent call first):

fortran/CMakeLists.txt:8 (FortranCInterface_HEADER)

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Error at fortran/CMakeLists.txt:16 (STRING):

string sub-command REGEX, mode MATCH needs at least 5 arguments total to

command.

CMake Error at fortran/CMakeLists.txt:20 (STRING):

string sub-command REGEX, mode MATCH needs at least 5 arguments total to

command.

SKIP h5repack_layout.h5 -f;dset1:GZIP=1;-l;dset1:CHUNK=20x10

SKIP h5repack_layout.h5 -f;GZIP=1

SKIP h5repack_layout.h5 -f;dset2:SZIP=8,EC;-l;dset2:CHUNK=20x10

SKIP h5repack_layout.h5 -f;SZIP=8,NN

SKIP h5repack_layout.h5 -f;dset2:SHUF;-f;dset2:FLET;-f;dset2:SZIP=8,NN;-f;dset2:GZIP=1;-l;dset2:CHUNK=20x10

SKIP h5repack_szip.h5

SKIP h5repack_szip.h5 --filter=dset_szip:NONE

SKIP h5repack_deflate.h5

SKIP h5repack_deflate.h5 -f;dset_deflate:NONE

SKIP h5repack_filters.h5 -f;NONE

SKIP h5repack_deflate.h5 -f;dset_deflate:SZIP=8,NN

SKIP h5repack_szip.h5 -f;dset_szip:GZIP=1

SKIP h5repack_layout.h5 -f;GZIP=1;-m;1024

SKIP h5repack_layout.h5 -e;testfiles/h5repack.info

SKIP h5repack_layout.h5 --layout;CHUNK=20x10;--filter;GZIP=1;--minimum=10;--native;--latest;--compact=8;--indexed=6;--ssize=8[:dtype]

SKIP h5repack_layout.h5 -l;CHUNK=20x10;-f;GZIP=1;-m;10;-n;-L;-c;8;-d;6;-s;8[:dtype]

SKIP h5repack_layout.h5 --filter;GZIP=1;--filter;SHUF

Configuring incomplete, errors occurred!

"""

Le 28/05/2010 22:54, Mike McGreevy a �crit :

···

Hi all,

A pre-release version of HDF5 1.8.5 is available for testing, and can be downloaded at the following link:

ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/

If you have a few moments to test this, we would greatly appreciate it. While we have tested it on the platforms that we have access to, there are many others that we are unable to test on ourselves. Please report any errors to help@hdfgroup.org, preferably within the next week or so. We are planning to create and distribute the official release by mid-June if no critical errors are reported beforehand.

Thank you!

The HDF Team

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

5

Ok, I've compiled 1.8.5 with CFLAGS=-g and ran my battery of Silo tests
on it. I am hitting three assertion failures. Two of these I have
reported in the past on 1.8.2 and 1.8.4. The third one is a new one. The
are described below. Part of the difficulty in providing information is
that I think these occur in the I/O pipeline and so the stack trace is a
bit meaningless to me. Any hints on what I could do to help get better
stack traces?

Also, be aware that I use HDF5-1.8 series libs using the
#define H5_USE_16_API mode of compilation.

Assertion failure #1...

This is occuring in a test where I am using my own compression filters.
My 'can_apply' method has been set to always return 1 as I have had
difficulty if 'can_apply' returns '0'. So, I rely solely on the op
method returning '0' if it cannot compress and do not rely on the
can_apply method. In the specific test that triggers this assertion, my
compression filter attempts to compress by 1000:1 ratio and fails
because it cannot achieve it. So, it returns a value of 0 and DOES NOT
TOUCH buf_size of buf arguments of the op caller.

#0 0x00163cef in raise () from /lib/tls/libc.so.6
#1 0x001654f5 in abort () from /lib/tls/libc.so.6
#2 0x0015d619 in __assert_fail () from /lib/tls/libc.so.6
#3 0x00852d93 in H5D_close (dataset=0x9eb2118) at H5Dint.c:1419
#4 0x00c13ee1 in FUNC.11 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#5 0x00c13bd7 in FUNC.11 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#6 0x00000551 in ?? ()
#7 0x00c13eac in FUNC.11 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#8 0x09eb2d28 in ?? ()
#9 0x00000000 in ?? ()

Assertion failure #2...
This is failing in an H5Aread call. That same call, with identical
arguments, succeeds a few times prior to this failure.

#0 0x00138cef in raise () from /lib/tls/libc.so.6
#1 0x0013a4f5 in abort () from /lib/tls/libc.so.6
#2 0x00132619 in __assert_fail () from /lib/tls/libc.so.6
#3 0x00de6e4f in H5T_conv_s_s (src_id=27984512, dst_id=156518872, cdata=0x9544d4f, nelmts=14515311, buf_stride=50332219,
    bkg_stride=50332220, buf=0x9544a34, bkg=0x1, dxpl_id=0) at H5Tconv.c:4451
#4 0x019382e4 in FUNC.339 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#5 0x0192c233 in FUNC.17 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#6 0x00001163 in ?? ()
#7 0x0192c4f7 in FUNC.17 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#8 0x094ed848 in ?? ()
#9 0xa040f5a8 in ?? ()
#10 0x09518b68 in ?? ()
#11 0x09540ad8 in ?? ()
#12 0x00000000 in ?? ()

This is a new failure that does NOT occur in 1.8.4. It is happening in a
test where many files are being opened and closed. I have yet to
investigate further to find out where it is precisely failing.

#0 0x088d3cef in raise () from /lib/tls/libc.so.6
#1 0x088d54f5 in abort () from /lib/tls/libc.so.6
#2 0x088cd619 in __assert_fail () from /lib/tls/libc.so.6
#3 0x00356e1d in H5C_load_entry (f=0x5827be4, dxpl_id=0, type=0xb22ab008, addr=29234605433298983, udata=0xa000008,
    skip_file_checks=18464604) at H5C.c:8250
#4 0x0068fdd4 in FUNC.88 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#5 0x0067cef9 in FUNC.13 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#6 0x00002027 in ?? ()
#7 0x0067dcb8 in FUNC.13 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#8 0xfffffcdb in ?? ()
#9 0xffffffff in ?? ()
#10 0x06e27be4 in ?? ()
#11 0x00000000 in ?? ()

···

On Fri, 2010-05-28 at 13:54, Mike McGreevy wrote:

Hi all,

A pre-release version of HDF5 1.8.5 is available for testing, and can be
downloaded at the following link:

ftp://*ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/

If you have a few moments to test this, we would greatly appreciate it.
While we have tested it on the platforms that we have access to, there
are many others that we are unable to test on ourselves. Please report
any errors to help@hdfgroup.org, preferably within the next week or so.
We are planning to create and distribute the official release by
mid-June if no critical errors are reported beforehand.

Thank you!

The HDF Team

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

--
Mark C. Miller, Lawrence Livermore National Laboratory
================!!LLNL BUSINESS ONLY!!================
miller86@llnl.gov urgent: miller86@pager.llnl.gov
T:8-6 (925)-423-5901 M/W/Th:7-12,2-7 (530)-753-851

6

Marco,

Thank you for reporting the problem. Could you please specify the system you ran on (Windows XP 32/ Vista/64....)?

You may also use -i with "make" to continue after some tests fail.

Elena

···

On May 29, 2010, at 4:32 PM, Marco Atzeri wrote:

--- Ven 28/5/10, Mike McGreevy ha scritto:

Hi all,

A pre-release version of HDF5 1.8.5 is available for
testing, and can be downloaded at the following link:

ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/

If you have a few moments to test this, we would greatly
appreciate it. While we have tested it on the platforms that
we have access to, there are many others that we are unable
to test on ourselves. Please report any errors to help@hdfgroup.org,
preferably within the next week or so. We are planning to
create and distribute the official release by mid-June if no
critical errors are reported beforehand.

Thank you!

The HDF Team

May I suggest that the testing continues also when any test
fails ? It will help to have a general view.

currently on cygwin-1.7 , "make check" stop here:

Testing -- Low-Level File I/O (file)
*** UNEXPECTED VALUE from H5Fcreate should be -1, but is 16777217 at line 149 i n /pub/cygports/hdf5/hdf5-1.8.5-pre2-1/src/hdf5-1.8.5-pre2/test/tfile.c
*** UNEXPECTED VALUE from H5Fclose should be -1, but is 0 at line 158 in /pub/c ygports/hdf5/hdf5-1.8.5-pre2-1/src/hdf5-1.8.5-pre2/test/tfile.c
Testing -- Generic Object Functions (objects)
Testing -- Dataspaces (h5s)
Testing -- Dataspace coordinates (coords)
Testing -- Shared Object Header Messages (sohm)
*** UNEXPECTED RETURN from H5Dopen2 is -1 line 3153 in /pub/cygports/hdf5/hdf5-1 .8.5-pre2-1/src/hdf5-1.8.5-pre2/test/tsohm.c
HDF5-DIAG: Error detected in HDF5 (1.8.5-pre2) thread 10223720:
#000: /pub/cygports/hdf5/hdf5-1.8.5-pre2-1/src/hdf5-1.8.5-pre2/src/H5D.c line 320 in H5Dopen2(): not found
   major: Dataset
   minor: Object not found
#001: /pub/cygports/hdf5/hdf5-1.8.5-pre2-1/src/hdf5-1.8.5-pre2/src/H5Gloc.c li ne 480 in H5G_loc_find(): can't find object
   major: Symbol table
   minor: Object not found
#002: /pub/cygports/hdf5/hdf5-1.8.5-pre2-1/src/hdf5-1.8.5-pre2/src/H5Gtraverse .c line 952 in H5G_traverse(): internal path traversal failed
   major: Symbol table
   minor: Object not found
#003: /pub/cygports/hdf5/hdf5-1.8.5-pre2-1/src/hdf5-1.8.5-pre2/src/H5Gtraverse .c line 759 in H5G_traverse_real(): traversal operator failed
   major: Symbol table
   minor: Callback failed
#004: /pub/cygports/hdf5/hdf5-1.8.5-pre2-1/src/hdf5-1.8.5-pre2/src/H5Gloc.c li ne 435 in H5G_loc_find_cb(): object 'dataset' doesn't exist
   major: Symbol table
   minor: Object not found
*** UNEXPECTED RETURN from H5Dclose is -1 line 3157 in /pub/cygports/hdf5/hdf5-1 .8.5-pre2-1/src/hdf5-1.8.5-pre2/test/tsohm.c
HDF5-DIAG: Error detected in HDF5 (1.8.5-pre2) thread 10223720:
#000: /pub/cygports/hdf5/hdf5-1.8.5-pre2-1/src/hdf5-1.8.5-pre2/src/H5D.c line 377 in H5Dclose(): not a dataset
   major: Invalid arguments to routine
   minor: Inappropriate type
Testing -- Attributes (attr)
Testing -- Selections (select)
Testing -- Time Datatypes (time)
Testing -- References (reference)
Testing -- Variable-Length Datatypes (vltypes)
Testing -- Variable-Length Strings (vlstrings)
Testing -- Group & Attribute Iteration (iterate)
Testing -- Array Datatypes (array)
Testing -- Generic Properties (genprop)
Testing -- UTF-8 Encoding (unicode)
Testing -- User-Created Identifiers (id)
Testing -- Miscellaneous (misc)

!!! 4 Error(s) were detected !!!

Regards
Marco

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

7

Make sure when you enable fortran that you run cmake from inside a command prompt where you've run the fortran batch files which setup paths.
Specifically, the error

No FortranCInterface mangling known for mysub

is caused by the generated file that is trying to detect the mangling being empty. Most like caused by a compilation failure. All the other errors stem from this.

Does it detect ifort correctly? If yers, then ignore previous comment . I've had the error above, but can't remember what was the trouble. Something simple.

Away after clicking send, so unable to help for a few days.

JB

···

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org]
On Behalf Of Giraudon Cyril
Sent: 01 June 2010 11:26
To: hdf-forum@hdfgroup.org
Subject: Re: [Hdf-forum] Pre-release of HDF5 1.8.5 is available for testing

Hello,

I 've compiled HDF5 1.8.5 pre-release under windows with :

CMake 2.8.1
Microsoft Visual C++ 2008 Express Edition

CMake generates a mingw Makefile (on request) make / make install ok for
C/C++/HL/tools generation.

However when I request the fortran (Intel ifort 11.1 with Visual Studio
2008) binding, CMake stopped with the message reported hereafter.

Best regards,

Cyril.

""""
Configure Checks that still need to be implemented

GetConsoleScreenBufferInfo function for Windows

CMake Warning (dev) at C:/Program Files/CMake 2.8/share/cmake-
2.8/Modules/FortranCInterface.cmake:207 (message):

No FortranCInterface mangling known for mysub

Call Stack (most recent call first):

fortran/CMakeLists.txt:8 (FortranCInterface_HEADER)

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake 2.8/share/cmake-
2.8/Modules/FortranCInterface.cmake:193 (message):

No FortranCInterface mangling known for mymod:my_sub

Call Stack (most recent call first):

fortran/CMakeLists.txt:8 (FortranCInterface_HEADER)

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Error at fortran/CMakeLists.txt:16 (STRING):

string sub-command REGEX, mode MATCH needs at least 5 arguments total to

command.

CMake Error at fortran/CMakeLists.txt:20 (STRING):

string sub-command REGEX, mode MATCH needs at least 5 arguments total to

command.

SKIP h5repack_layout.h5 -f;dset1:GZIP=1;-l;dset1:CHUNK=20x10

SKIP h5repack_layout.h5 -f;GZIP=1

SKIP h5repack_layout.h5 -f;dset2:SZIP=8,EC;-l;dset2:CHUNK=20x10

SKIP h5repack_layout.h5 -f;SZIP=8,NN

SKIP h5repack_layout.h5 -f;dset2:SHUF;-f;dset2:FLET;-f;dset2:SZIP=8,NN;-
f;dset2:GZIP=1;-l;dset2:CHUNK=20x10

SKIP h5repack_szip.h5

SKIP h5repack_szip.h5 --filter=dset_szip:NONE

SKIP h5repack_deflate.h5

SKIP h5repack_deflate.h5 -f;dset_deflate:NONE

SKIP h5repack_filters.h5 -f;NONE

SKIP h5repack_deflate.h5 -f;dset_deflate:SZIP=8,NN

SKIP h5repack_szip.h5 -f;dset_szip:GZIP=1

SKIP h5repack_layout.h5 -f;GZIP=1;-m;1024

SKIP h5repack_layout.h5 -e;testfiles/h5repack.info

SKIP h5repack_layout.h5 --layout;CHUNK=20x10;--filter;GZIP=1;--minimum=10;--
native;--latest;--compact=8;--indexed=6;--ssize=8[:dtype]

SKIP h5repack_layout.h5 -l;CHUNK=20x10;-f;GZIP=1;-m;10;-n;-L;-c;8;-d;6;-
s;8[:dtype]

SKIP h5repack_layout.h5 --filter;GZIP=1;--filter;SHUF

Configuring incomplete, errors occurred!

"""

Le 28/05/2010 22:54, Mike McGreevy a écrit :

  Hi all,

  A pre-release version of HDF5 1.8.5 is available for testing, and can
be downloaded at the following link:

  ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/

  If you have a few moments to test this, we would greatly appreciate
it. While we have tested it on the platforms that we have access to, there
are many others that we are unable to test on ourselves. Please report any
errors to help@hdfgroup.org, preferably within the next week or so. We are
planning to create and distribute the official release by mid-June if no
critical errors are reported beforehand.

  Thank you!

  The HDF Team

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

8

Mark,

Thank you very much for trying the source and reporting the problems. It will be very helpful if you could provide us with the example program for the new failure.

Two bugs you reported are in our database awaiting their extermination.

Elena

···

On Jun 2, 2010, at 11:27 AM, Mark Miller wrote:

Ok, I've compiled 1.8.5 with CFLAGS=-g and ran my battery of Silo tests
on it. I am hitting three assertion failures. Two of these I have
reported in the past on 1.8.2 and 1.8.4. The third one is a new one. The
are described below. Part of the difficulty in providing information is
that I think these occur in the I/O pipeline and so the stack trace is a
bit meaningless to me. Any hints on what I could do to help get better
stack traces?

Also, be aware that I use HDF5-1.8 series libs using the
#define H5_USE_16_API mode of compilation.

Assertion failure #1...

This is occuring in a test where I am using my own compression filters.
My 'can_apply' method has been set to always return 1 as I have had
difficulty if 'can_apply' returns '0'. So, I rely solely on the op
method returning '0' if it cannot compress and do not rely on the
can_apply method. In the specific test that triggers this assertion, my
compression filter attempts to compress by 1000:1 ratio and fails
because it cannot achieve it. So, it returns a value of 0 and DOES NOT
TOUCH buf_size of buf arguments of the op caller.

#0 0x00163cef in raise () from /lib/tls/libc.so.6
#1 0x001654f5 in abort () from /lib/tls/libc.so.6
#2 0x0015d619 in __assert_fail () from /lib/tls/libc.so.6
#3 0x00852d93 in H5D_close (dataset=0x9eb2118) at H5Dint.c:1419
#4 0x00c13ee1 in FUNC.11 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#5 0x00c13bd7 in FUNC.11 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#6 0x00000551 in ?? ()
#7 0x00c13eac in FUNC.11 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#8 0x09eb2d28 in ?? ()
#9 0x00000000 in ?? ()

Assertion failure #2...
This is failing in an H5Aread call. That same call, with identical
arguments, succeeds a few times prior to this failure.

#0 0x00138cef in raise () from /lib/tls/libc.so.6
#1 0x0013a4f5 in abort () from /lib/tls/libc.so.6
#2 0x00132619 in __assert_fail () from /lib/tls/libc.so.6
#3 0x00de6e4f in H5T_conv_s_s (src_id=27984512, dst_id=156518872, cdata=0x9544d4f, nelmts=14515311, buf_stride=50332219,
   bkg_stride=50332220, buf=0x9544a34, bkg=0x1, dxpl_id=0) at H5Tconv.c:4451
#4 0x019382e4 in FUNC.339 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#5 0x0192c233 in FUNC.17 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#6 0x00001163 in ?? ()
#7 0x0192c4f7 in FUNC.17 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#8 0x094ed848 in ?? ()
#9 0xa040f5a8 in ?? ()
#10 0x09518b68 in ?? ()
#11 0x09540ad8 in ?? ()
#12 0x00000000 in ?? ()

This is a new failure that does NOT occur in 1.8.4. It is happening in a
test where many files are being opened and closed. I have yet to
investigate further to find out where it is precisely failing.

#0 0x088d3cef in raise () from /lib/tls/libc.so.6
#1 0x088d54f5 in abort () from /lib/tls/libc.so.6
#2 0x088cd619 in __assert_fail () from /lib/tls/libc.so.6
#3 0x00356e1d in H5C_load_entry (f=0x5827be4, dxpl_id=0, type=0xb22ab008, addr=29234605433298983, udata=0xa000008,
   skip_file_checks=18464604) at H5C.c:8250
#4 0x0068fdd4 in FUNC.88 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#5 0x0067cef9 in FUNC.13 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#6 0x00002027 in ?? ()
#7 0x0067dcb8 in FUNC.13 () from /home/miller86/tmp/hdf5-1.8.5-pre2/install/lib/libhdf5.so.6
#8 0xfffffcdb in ?? ()
#9 0xffffffff in ?? ()
#10 0x06e27be4 in ?? ()
#11 0x00000000 in ?? ()

On Fri, 2010-05-28 at 13:54, Mike McGreevy wrote:

Hi all,

A pre-release version of HDF5 1.8.5 is available for testing, and can be
downloaded at the following link:

ftp://*ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/

If you have a few moments to test this, we would greatly appreciate it.
While we have tested it on the platforms that we have access to, there
are many others that we are unable to test on ourselves. Please report
any errors to help@hdfgroup.org, preferably within the next week or so.
We are planning to create and distribute the official release by
mid-June if no critical errors are reported beforehand.

Thank you!

The HDF Team

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

--
Mark C. Miller, Lawrence Livermore National Laboratory
================!!LLNL BUSINESS ONLY!!================
miller86@llnl.gov urgent: miller86@pager.llnl.gov
T:8-6 (925)-423-5901 M/W/Th:7-12,2-7 (530)-753-851

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

9

--- Lun 31/5/10, Elena Pourmal ha scritto:

Marco,

Thank you for reporting the problem. Could you please
specify the system you ran on (Windows XP 32/
Vista/64....)?

Hi Elena,
Windows XP SP2 32 bit
latest cygwin snapshot 2010-05-26 (so future 1.7.6)

built with

···

---------------------------------------------------------------
configure --with-zlib \
          --with-gnu-ld \
          --enable-shared \
          --enable-threadsafe \
          --with-pthread \
          CC=gcc-4 FC=gfortran-4 \
          CXX=g++-4 CPP=cpp-4 \
          LDFLAGS=-no-undefined

# hack to bypass wrong libtool detection
sed -e "1,100s/^build_libtool_libs=no/build_libtool_libs=yes/" -i libtool
make

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

Plus some patches on Makefile.am's to allow the building of
the dynamic library.

You may also use -i with "make" to continue after some
tests fail.

thanks for the hint.
Most of the tests are PASSED.
Few are clearly broken like
Check file ../src/.libs/libhdf5.so

I need to skip fpheap test as it never ends.

Do you want a copy of the test log and/or the patch and
cygport build system ?

Marco

10

Hello,

I succeed in building my own project so I suppose CMake/Ifort is OK.
I don't understand the problem.

Does somebody compile hdf5_fortran with ifort 11.1 under windows ?

Regards,

Cyril.

Le 01/06/2010 11:51, Biddiscombe, John A. a �crit :

···

Make sure when you enable fortran that you run cmake from inside a command prompt where you've run the fortran batch files which setup paths.
Specifically, the error
  

No FortranCInterface mangling known for mysub
    

is caused by the generated file that is trying to detect the mangling being empty. Most like caused by a compilation failure. All the other errors stem from this.

Does it detect ifort correctly? If yers, then ignore previous comment . I've had the error above, but can't remember what was the trouble. Something simple.

Away after clicking send, so unable to help for a few days.

JB

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org]
On Behalf Of Giraudon Cyril
Sent: 01 June 2010 11:26
To: hdf-forum@hdfgroup.org
Subject: Re: [Hdf-forum] Pre-release of HDF5 1.8.5 is available for testing

Hello,

I 've compiled HDF5 1.8.5 pre-release under windows with :

CMake 2.8.1
Microsoft Visual C++ 2008 Express Edition

CMake generates a mingw Makefile (on request) make / make install ok for
C/C++/HL/tools generation.

However when I request the fortran (Intel ifort 11.1 with Visual Studio
2008) binding, CMake stopped with the message reported hereafter.

Best regards,

Cyril.

""""
Configure Checks that still need to be implemented

GetConsoleScreenBufferInfo function for Windows

CMake Warning (dev) at C:/Program Files/CMake 2.8/share/cmake-
2.8/Modules/FortranCInterface.cmake:207 (message):

No FortranCInterface mangling known for mysub

Call Stack (most recent call first):

fortran/CMakeLists.txt:8 (FortranCInterface_HEADER)

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake 2.8/share/cmake-
2.8/Modules/FortranCInterface.cmake:193 (message):

No FortranCInterface mangling known for mymod:my_sub

Call Stack (most recent call first):

fortran/CMakeLists.txt:8 (FortranCInterface_HEADER)

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Error at fortran/CMakeLists.txt:16 (STRING):

string sub-command REGEX, mode MATCH needs at least 5 arguments total to

command.

CMake Error at fortran/CMakeLists.txt:20 (STRING):

string sub-command REGEX, mode MATCH needs at least 5 arguments total to

command.

SKIP h5repack_layout.h5 -f;dset1:GZIP=1;-l;dset1:CHUNK=20x10

SKIP h5repack_layout.h5 -f;GZIP=1

SKIP h5repack_layout.h5 -f;dset2:SZIP=8,EC;-l;dset2:CHUNK=20x10

SKIP h5repack_layout.h5 -f;SZIP=8,NN

SKIP h5repack_layout.h5 -f;dset2:SHUF;-f;dset2:FLET;-f;dset2:SZIP=8,NN;-
f;dset2:GZIP=1;-l;dset2:CHUNK=20x10

SKIP h5repack_szip.h5

SKIP h5repack_szip.h5 --filter=dset_szip:NONE

SKIP h5repack_deflate.h5

SKIP h5repack_deflate.h5 -f;dset_deflate:NONE

SKIP h5repack_filters.h5 -f;NONE

SKIP h5repack_deflate.h5 -f;dset_deflate:SZIP=8,NN

SKIP h5repack_szip.h5 -f;dset_szip:GZIP=1

SKIP h5repack_layout.h5 -f;GZIP=1;-m;1024

SKIP h5repack_layout.h5 -e;testfiles/h5repack.info

SKIP h5repack_layout.h5 --layout;CHUNK=20x10;--filter;GZIP=1;--minimum=10;--
native;--latest;--compact=8;--indexed=6;--ssize=8[:dtype]

SKIP h5repack_layout.h5 -l;CHUNK=20x10;-f;GZIP=1;-m;10;-n;-L;-c;8;-d;6;-
s;8[:dtype]

SKIP h5repack_layout.h5 --filter;GZIP=1;--filter;SHUF

Configuring incomplete, errors occurred!

"""

Le 28/05/2010 22:54, Mike McGreevy a �crit :

  Hi all,

  A pre-release version of HDF5 1.8.5 is available for testing, and can
be downloaded at the following link:

  ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/

  If you have a few moments to test this, we would greatly appreciate
it. While we have tested it on the platforms that we have access to, there
are many others that we are unable to test on ourselves. Please report any
errors to help@hdfgroup.org, preferably within the next week or so. We are
planning to create and distribute the official release by mid-June if no
critical errors are reported beforehand.

  Thank you!

  The HDF Team

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

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

11

Marco,

Thank you for your report. Treadsafe and shared libraries features are not supported on Windows. (We will make sure before the release that our docs are up-to-date; we are very sorry that we missed it when provided the tar ball for testing).

Could you please, when you have time, reconfigure without threadsafe and check if your patches for shared libraries work? If so, we will be happy to accept the patches and make them available in the future releases.

fheap test does take a lot of time, but it should also pass (it does for us when we build static libraries).

Elena

···

On Jun 1, 2010, at 4:23 AM, Marco Atzeri wrote:

--- Lun 31/5/10, Elena Pourmal ha scritto:

Marco,

Thank you for reporting the problem. Could you please
specify the system you ran on (Windows XP 32/
Vista/64....)?

Hi Elena,
Windows XP SP2 32 bit
latest cygwin snapshot 2010-05-26 (so future 1.7.6)

built with
---------------------------------------------------------------
configure --with-zlib \
         --with-gnu-ld \
         --enable-shared \
         --enable-threadsafe \
         --with-pthread \
         CC=gcc-4 FC=gfortran-4 \
         CXX=g++-4 CPP=cpp-4 \
         LDFLAGS=-no-undefined

# hack to bypass wrong libtool detection
sed -e "1,100s/^build_libtool_libs=no/build_libtool_libs=yes/" -i libtool
make

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

Plus some patches on Makefile.am's to allow the building of
the dynamic library.

You may also use -i with "make" to continue after some
tests fail.

thanks for the hint.
Most of the tests are PASSED.
Few are clearly broken like
Check file ../src/.libs/libhdf5.so

I need to skip fpheap test as it never ends.

Do you want a copy of the test log and/or the patch and
cygport build system ?

Marco

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

12

Cyril,
   AFAIK the express edition does not integrate with Intel Fortran. I use the the professional version of VS2008 with Intel Fortran 10 and 11 in testing the HDF library. If you can identify where and what I can add to the CMake files to use the express edition with Intel Fortran, we would appreciate your help.

Allen

···

Hello,

I succeed in building my own project so I suppose CMake/Ifort is OK.
I don't understand the problem.

Does somebody compile hdf5_fortran with ifort 11.1 under windows ?

Regards,

Cyril.

Le 01/06/2010 11:51, Biddiscombe, John A. a écrit :
> Make sure when you enable fortran that you run cmake from inside a command prompt where you've run the fortran batch files which setup paths.
> Specifically, the error
>
>> No FortranCInterface mangling known for mysub
>>
> is caused by the generated file that is trying to detect the mangling being empty. Most like caused by a compilation failure. All the other errors stem from this.
>
> Does it detect ifort correctly? If yers, then ignore previous comment . I've had the error above, but can't remember what was the trouble. Something simple.
>
> Away after clicking send, so unable to help for a few days.
>
> JB
>
>
>
>> -----Original Message-----
>> From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org]
>> On Behalf Of Giraudon Cyril
>> Sent: 01 June 2010 11:26
>> To: hdf-forum@hdfgroup.org
>> Subject: Re: [Hdf-forum] Pre-release of HDF5 1.8.5 is available for testing
>>
>> Hello,
>>
>> I 've compiled HDF5 1.8.5 pre-release under windows with :
>>
>> CMake 2.8.1
>> Microsoft Visual C++ 2008 Express Edition
>>
>> CMake generates a mingw Makefile (on request) make / make install ok for
>> C/C++/HL/tools generation.
>>
>> However when I request the fortran (Intel ifort 11.1 with Visual Studio
>> 2008) binding, CMake stopped with the message reported hereafter.
>>
>> Best regards,
>>
>> Cyril.
>>
>>
>> """"
>> Configure Checks that still need to be implemented
>>
>> GetConsoleScreenBufferInfo function for Windows
>>
>> CMake Warning (dev) at C:/Program Files/CMake 2.8/share/cmake-
>> 2.8/Modules/FortranCInterface.cmake:207 (message):
>>
>> No FortranCInterface mangling known for mysub
>>
>> Call Stack (most recent call first):
>>
>> fortran/CMakeLists.txt:8 (FortranCInterface_HEADER)
>>
>> This warning is for project developers. Use -Wno-dev to suppress it.
>>
>> CMake Warning (dev) at C:/Program Files/CMake 2.8/share/cmake-
>> 2.8/Modules/FortranCInterface.cmake:193 (message):
>>
>> No FortranCInterface mangling known for mymod:my_sub
>>
>> Call Stack (most recent call first):
>>
>> fortran/CMakeLists.txt:8 (FortranCInterface_HEADER)
>>
>> This warning is for project developers. Use -Wno-dev to suppress it.
>>
>> CMake Error at fortran/CMakeLists.txt:16 (STRING):
>>
>> string sub-command REGEX, mode MATCH needs at least 5 arguments total to
>>
>> command.
>>
>> CMake Error at fortran/CMakeLists.txt:20 (STRING):
>>
>> string sub-command REGEX, mode MATCH needs at least 5 arguments total to
>>
>> command.
>>
>> SKIP h5repack_layout.h5 -f;dset1:GZIP=1;-l;dset1:CHUNK=20x10
>>
>> SKIP h5repack_layout.h5 -f;GZIP=1
>>
>> SKIP h5repack_layout.h5 -f;dset2:SZIP=8,EC;-l;dset2:CHUNK=20x10
>>
>> SKIP h5repack_layout.h5 -f;SZIP=8,NN
>>
>> SKIP h5repack_layout.h5 -f;dset2:SHUF;-f;dset2:FLET;-f;dset2:SZIP=8,NN;-
>> f;dset2:GZIP=1;-l;dset2:CHUNK=20x10
>>
>> SKIP h5repack_szip.h5
>>
>> SKIP h5repack_szip.h5 --filter=dset_szip:NONE
>>
>> SKIP h5repack_deflate.h5
>>
>> SKIP h5repack_deflate.h5 -f;dset_deflate:NONE
>>
>> SKIP h5repack_filters.h5 -f;NONE
>>
>> SKIP h5repack_deflate.h5 -f;dset_deflate:SZIP=8,NN
>>
>> SKIP h5repack_szip.h5 -f;dset_szip:GZIP=1
>>
>> SKIP h5repack_layout.h5 -f;GZIP=1;-m;1024
>>
>> SKIP h5repack_layout.h5 -e;testfiles/h5repack.info
>>
>> SKIP h5repack_layout.h5 --layout;CHUNK=20x10;--filter;GZIP=1;--minimum=10;--
>> native;--latest;--compact=8;--indexed=6;--ssize=8[:dtype]
>>
>> SKIP h5repack_layout.h5 -l;CHUNK=20x10;-f;GZIP=1;-m;10;-n;-L;-c;8;-d;6;-
>> s;8[:dtype]
>>
>> SKIP h5repack_layout.h5 --filter;GZIP=1;--filter;SHUF
>>
>> Configuring incomplete, errors occurred!
>>
>> """
>>
>> Le 28/05/2010 22:54, Mike McGreevy a écrit :
>>
>> Hi all,
>>
>> A pre-release version of HDF5 1.8.5 is available for testing, and can
>> be downloaded at the following link:
>>
>> ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/
>>
>> If you have a few moments to test this, we would greatly appreciate
>> it. While we have tested it on the platforms that we have access to, there
>> are many others that we are unable to test on ourselves. Please report any
>> errors to help@hdfgroup.org, preferably within the next week or so. We are
>> planning to create and distribute the official release by mid-June if no
>> critical errors are reported beforehand.
>>
>> Thank you!
>>
>> The HDF Team
>>
>> _______________________________________________
>> Hdf-forum is for HDF software users discussion.
>> Hdf-forum@hdfgroup.org
>> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>>
>>
>>
>
> _______________________________________________
> Hdf-forum is for HDF software users discussion.
> Hdf-forum@hdfgroup.org
> http://mail.hdfgroup.org/mailman/listinfo/hdf-forum_hdfgroup.org
>

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

13

I'm afraid it is not an HDF5 CMakeList problem but a CMake module problem.

I believe CMake doesn't recognize the couple (VCExpress, Ifort), seems I
have to obtain a Visual Studio 2008 licence.

In addition, do you test CMake project with Mingw/gcc/gfortran under
windows ?

In fact I would to compile HDF5 to check if the issue reported in this
http://www.mail-archive.com/hdf-forum@hdfgroup.org/msg00865.html is fixed.

Were there really a problem ... ?

Thanks a lot,

Cyril.

Le 07/06/2010 17:12, Allen D Byrne a �crit :

···

Cyril,
   AFAIK the express edition does not integrate with Intel Fortran. I use the the professional version of VS2008 with Intel Fortran 10 and 11 in testing the HDF library. If you can identify where and what I can add to the CMake files to use the express edition with Intel Fortran, we would appreciate your help.

Allen

Hello,

I succeed in building my own project so I suppose CMake/Ifort is OK.
I don't understand the problem.

Does somebody compile hdf5_fortran with ifort 11.1 under windows ?

Regards,

Cyril.

Le 01/06/2010 11:51, Biddiscombe, John A. a �crit :
    

Make sure when you enable fortran that you run cmake from inside a command prompt where you've run the fortran batch files which setup paths.
Specifically, the error
  

No FortranCInterface mangling known for mysub
    

is caused by the generated file that is trying to detect the mangling being empty. Most like caused by a compilation failure. All the other errors stem from this.

Does it detect ifort correctly? If yers, then ignore previous comment . I've had the error above, but can't remember what was the trouble. Something simple.

Away after clicking send, so unable to help for a few days.

JB

-----Original Message-----
From: hdf-forum-bounces@hdfgroup.org [mailto:hdf-forum-bounces@hdfgroup.org]
On Behalf Of Giraudon Cyril
Sent: 01 June 2010 11:26
To: hdf-forum@hdfgroup.org
Subject: Re: [Hdf-forum] Pre-release of HDF5 1.8.5 is available for testing

Hello,

I 've compiled HDF5 1.8.5 pre-release under windows with :

CMake 2.8.1
Microsoft Visual C++ 2008 Express Edition

CMake generates a mingw Makefile (on request) make / make install ok for
C/C++/HL/tools generation.

However when I request the fortran (Intel ifort 11.1 with Visual Studio
2008) binding, CMake stopped with the message reported hereafter.

Best regards,

Cyril.

""""
Configure Checks that still need to be implemented

GetConsoleScreenBufferInfo function for Windows

CMake Warning (dev) at C:/Program Files/CMake 2.8/share/cmake-
2.8/Modules/FortranCInterface.cmake:207 (message):

No FortranCInterface mangling known for mysub

Call Stack (most recent call first):

fortran/CMakeLists.txt:8 (FortranCInterface_HEADER)

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Warning (dev) at C:/Program Files/CMake 2.8/share/cmake-
2.8/Modules/FortranCInterface.cmake:193 (message):

No FortranCInterface mangling known for mymod:my_sub

Call Stack (most recent call first):

fortran/CMakeLists.txt:8 (FortranCInterface_HEADER)

This warning is for project developers. Use -Wno-dev to suppress it.

CMake Error at fortran/CMakeLists.txt:16 (STRING):

string sub-command REGEX, mode MATCH needs at least 5 arguments total to

command.

CMake Error at fortran/CMakeLists.txt:20 (STRING):

string sub-command REGEX, mode MATCH needs at least 5 arguments total to

command.

SKIP h5repack_layout.h5 -f;dset1:GZIP=1;-l;dset1:CHUNK=20x10

SKIP h5repack_layout.h5 -f;GZIP=1

SKIP h5repack_layout.h5 -f;dset2:SZIP=8,EC;-l;dset2:CHUNK=20x10

SKIP h5repack_layout.h5 -f;SZIP=8,NN

SKIP h5repack_layout.h5 -f;dset2:SHUF;-f;dset2:FLET;-f;dset2:SZIP=8,NN;-
f;dset2:GZIP=1;-l;dset2:CHUNK=20x10

SKIP h5repack_szip.h5

SKIP h5repack_szip.h5 --filter=dset_szip:NONE

SKIP h5repack_deflate.h5

SKIP h5repack_deflate.h5 -f;dset_deflate:NONE

SKIP h5repack_filters.h5 -f;NONE

SKIP h5repack_deflate.h5 -f;dset_deflate:SZIP=8,NN

SKIP h5repack_szip.h5 -f;dset_szip:GZIP=1

SKIP h5repack_layout.h5 -f;GZIP=1;-m;1024

SKIP h5repack_layout.h5 -e;testfiles/h5repack.info

SKIP h5repack_layout.h5 --layout;CHUNK=20x10;--filter;GZIP=1;--minimum=10;--
native;--latest;--compact=8;--indexed=6;--ssize=8[:dtype]

SKIP h5repack_layout.h5 -l;CHUNK=20x10;-f;GZIP=1;-m;10;-n;-L;-c;8;-d;6;-
s;8[:dtype]

SKIP h5repack_layout.h5 --filter;GZIP=1;--filter;SHUF

Configuring incomplete, errors occurred!

"""

Le 28/05/2010 22:54, Mike McGreevy a �crit :

  Hi all,

  A pre-release version of HDF5 1.8.5 is available for testing, and can
be downloaded at the following link:

  ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/hdf5-1.8.5-pre2/

  If you have a few moments to test this, we would greatly appreciate
it. While we have tested it on the platforms that we have access to, there
are many others that we are unable to test on ourselves. Please report any
errors to help@hdfgroup.org, preferably within the next week or so. We are
planning to create and distribute the official release by mid-June if no
critical errors are reported beforehand.

  Thank you!

  The HDF Team

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

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

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

14

--- Mar 1/6/10, Elena Pourmal ha scritto:

Marco,

Thank you for your report. Treadsafe and shared libraries
features are not supported on Windows. (We will make sure
before the release that our docs are up-to-date; we are very
sorry that we missed it when provided the tar ball for
testing).

Could you please, when you have time, reconfigure without
threadsafe and check if your patches for shared libraries
work? If so, we will be happy to accept the patches and make
them available in the future releases.

rebuilt with
      configure --with-zlib \
                --with-gnu-ld \
                --enable-shared \
                --with-pthread \
                CC=gcc-4 FC=gfortran-4 \
                CXX=g++-4 CPP=cpp-4 \
                LDFLAGS=-no-undefined

and I don't see major change.

Without "--enable-threadsafe"
$ grep PASSED hdf5-1.8.5-pre2-1-check.log | wc -l
3588
$ grep SKIP hdf5-1.8.5-pre2-1-check.log | wc -l
37
$ grep FAIL hdf5-1.8.5-pre2-1-check.log | wc -l
8

With "--enable-threadsafe"
$ grep PASSED hdf5-1.8.5-pre2-1-check.log | wc -l
3930
$ grep SKIP hdf5-1.8.5-pre2-1-check.log | wc -l
37
$ grep FAIL hdf5-1.8.5-pre2-1-check.log | wc -l
8

fheap test does take a lot of time, but it should also pass
(it does for us when we build static libraries).

How much ? Much more than all the other tests together ?
I have the strong feeling that it is going in some
never ending loop.

Another issue, on installation I found that examples
are put in

EXAMPLETOPDIR=${DESTDIR}$(exec_prefix)/share/hdf5_examples

but I think it is better to have them on something like

${docdir}/hdf5_examples
as they are documentation and not shared data.

Elena

Regards
Marco

15

Marco,

We tested Cygwin 1.7.5 on Windows XP 32-bit (worked fine). We used default C, C++ and Fortran compilers that come with the system.

Could you please try to configure and test just HDF5 C library
./configure
....

and if this works, try your shared library patches. If this works, then let's try gcc-4 compiler (what is an exact version?)

Thank you!

Elena

···

On Jun 1, 2010, at 4:40 PM, Marco Atzeri wrote:

--- Mar 1/6/10, Elena Pourmal ha scritto:

Marco,

Thank you for your report. Treadsafe and shared libraries
features are not supported on Windows. (We will make sure
before the release that our docs are up-to-date; we are very
sorry that we missed it when provided the tar ball for
testing).

Could you please, when you have time, reconfigure without
threadsafe and check if your patches for shared libraries
work? If so, we will be happy to accept the patches and make
them available in the future releases.

rebuilt with
     configure --with-zlib \
               --with-gnu-ld \
               --enable-shared \
               --with-pthread \
               CC=gcc-4 FC=gfortran-4 \
               CXX=g++-4 CPP=cpp-4 \
               LDFLAGS=-no-undefined

and I don't see major change.

Without "--enable-threadsafe"
$ grep PASSED hdf5-1.8.5-pre2-1-check.log | wc -l
3588
$ grep SKIP hdf5-1.8.5-pre2-1-check.log | wc -l
37
$ grep FAIL hdf5-1.8.5-pre2-1-check.log | wc -l
8

With "--enable-threadsafe"
$ grep PASSED hdf5-1.8.5-pre2-1-check.log | wc -l
3930
$ grep SKIP hdf5-1.8.5-pre2-1-check.log | wc -l
37
$ grep FAIL hdf5-1.8.5-pre2-1-check.log | wc -l
8

fheap test does take a lot of time, but it should also pass
(it does for us when we build static libraries).

How much ? Much more than all the other tests together ?
I have the strong feeling that it is going in some
never ending loop.

Another issue, on installation I found that examples
are put in

EXAMPLETOPDIR=${DESTDIR}$(exec_prefix)/share/hdf5_examples

but I think it is better to have them on something like

${docdir}/hdf5_examples
as they are documentation and not shared data.

Elena

Regards
Marco

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

16

--- Mer 2/6/10, Elena Pourmal ha scritto:

Marco,

We tested Cygwin 1.7.5 on Windows XP 32-bit (worked fine).
We used default C, C++ and Fortran compilers that come with
the system.

Could you please try to configure and test just HDF5 C
library
./configure
....

and if this works, try your shared library patches. If this
works, then let's try gcc-4 compiler (what is an exact
version?)

Elena,
currently gcc-4 is the default compiler for cygwin-1.7,
so we are likely using the same compiler
gcc (GCC) 4.3.4 20090804 (release) 1

The default is built as
gcc -> alternatives -> gcc-4

gcc-3 (gcc 3.4.4) is still available; it was the
compiler used on cygwin-1.5.

This portion is likely superfluous

                CC=gcc-4 FC=gfortran-4 \
                CXX=g++-4 CPP=cpp-4 \

as it is more a remaining of the transition to gcc-4 when
it was not yet the default compiler.
I used it for building the cygwin hdf5 1.6 packages,
so it is still around in my building scripts.

Sometime it is useful to avoid that configure choose
as C compiler gcc that now means gcc-4 and as fortran compiler
g77 that is gcc-3.

On cywin, we already have hdf5-1.6 as shared library
from june 2008

http://article.gmane.org/gmane.os.cygwin.announce/2293/match=hdf5

$ cygcheck -c -d |grep hdf5
hdf5 1.6.9-2
libhdf5-devel 1.6.9-2
libhdf5_0 1.6.9-2

Thank you!

Elena

Regards
Marco