Just for your information, the h5diff that comes from the EPEL distribution, 1.8.5-patch1 does not behave the same way, it responds like this:
jtemple@monch01:Sat Dec 07-08:44:/mnt/lnec/jtemple > h5diff -cp 1.e-2 SingleSiteBethe.output.h5 SingleSiteBethe.reference.h5
Not comparable: </G/__BlockIndicesList> has sign H5T_SGN_NONE and </G/__BlockIndicesList> has sign H5T_SGN_ERROR
Not comparable: </G/__Name> has sign H5T_SGN_NONE and </G/__Name> has sign H5T_SGN_ERROR
Not comparable: </G/__Note> has sign H5T_SGN_NONE and </G/__Note> has sign H5T_SGN_ERROR
Not comparable: </G/down/IndicesL> has sign H5T_SGN_NONE and </G/down/IndicesL> has sign H5T_SGN_ERROR
Not comparable: </G/down/IndicesR> has sign H5T_SGN_NONE and </G/down/IndicesR> has sign H5T_SGN_ERROR
Not comparable: </G/down/Mesh/Statistic> has sign H5T_SGN_NONE and </G/down/Mesh/Statistic> has sign H5T_SGN_ERROR
Not comparable: </G/down/Mesh/TypeGF> has sign H5T_SGN_NONE and </G/down/Mesh/TypeGF> has sign H5T_SGN_ERROR
Not comparable: </G/down/Name> has sign H5T_SGN_NONE and </G/down/Name> has sign H5T_SGN_ERROR
Not comparable: </G/down/Note> has sign H5T_SGN_NONE and </G/down/Note> has sign H5T_SGN_ERROR
Not comparable: </G/down/Tail/IndicesL> has sign H5T_SGN_NONE and </G/down/Tail/IndicesL> has sign H5T_SGN_ERROR
Not comparable: </G/down/Tail/IndicesR> has sign H5T_SGN_NONE and </G/down/Tail/IndicesR> has sign H5T_SGN_ERROR
Not comparable: </G/up/IndicesL> has sign H5T_SGN_NONE and </G/up/IndicesL> has sign H5T_SGN_ERROR
Not comparable: </G/up/IndicesR> has sign H5T_SGN_NONE and </G/up/IndicesR> has sign H5T_SGN_ERROR
Not comparable: </G/up/Mesh/Statistic> has sign H5T_SGN_NONE and </G/up/Mesh/Statistic> has sign H5T_SGN_ERROR
Not comparable: </G/up/Mesh/TypeGF> has sign H5T_SGN_NONE and </G/up/Mesh/TypeGF> has sign H5T_SGN_ERROR
Not comparable: </G/up/Name> has sign H5T_SGN_NONE and </G/up/Name> has sign H5T_SGN_ERROR
Not comparable: </G/up/Note> has sign H5T_SGN_NONE and </G/up/Note> has sign H5T_SGN_ERROR
Not comparable: </G/up/Tail/IndicesL> has sign H5T_SGN_NONE and </G/up/Tail/IndicesL> has sign H5T_SGN_ERROR
Not comparable: </G/up/Tail/IndicesR> has sign H5T_SGN_NONE and </G/up/Tail/IndicesR> has sign H5T_SGN_ERROR
Not comparable: </Gtau/__BlockIndicesList> has sign H5T_SGN_NONE and </Gtau/__BlockIndicesList> has sign H5T_SGN_ERROR
Not comparable: </Gtau/__Name> has sign H5T_SGN_NONE and </Gtau/__Name> has sign H5T_SGN_ERROR
Not comparable: </Gtau/__Note> has sign H5T_SGN_NONE and </Gtau/__Note> has sign H5T_SGN_ERROR
Not comparable: </Gtau/down/IndicesL> has sign H5T_SGN_NONE and </Gtau/down/IndicesL> has sign H5T_SGN_ERROR
Not comparable: </Gtau/down/IndicesR> has sign H5T_SGN_NONE and </Gtau/down/IndicesR> has sign H5T_SGN_ERROR
Not comparable: </Gtau/down/Mesh/Statistic> has sign H5T_SGN_NONE and </Gtau/down/Mesh/Statistic> has sign H5T_SGN_ERROR
Not comparable: </Gtau/down/Mesh/TypeGF> has sign H5T_SGN_NONE and </Gtau/down/Mesh/TypeGF> has sign H5T_SGN_ERROR
Not comparable: </Gtau/down/Name> has sign H5T_SGN_NONE and </Gtau/down/Name> has sign H5T_SGN_ERROR
Not comparable: </Gtau/down/Note> has sign H5T_SGN_NONE and </Gtau/down/Note> has sign H5T_SGN_ERROR
Not comparable: </Gtau/down/Tail/IndicesL> has sign H5T_SGN_NONE and </Gtau/down/Tail/IndicesL> has sign H5T_SGN_ERROR
Not comparable: </Gtau/down/Tail/IndicesR> has sign H5T_SGN_NONE and </Gtau/down/Tail/IndicesR> has sign H5T_SGN_ERROR
Not comparable: </Gtau/up/IndicesL> has sign H5T_SGN_NONE and </Gtau/up/IndicesL> has sign H5T_SGN_ERROR
Not comparable: </Gtau/up/IndicesR> has sign H5T_SGN_NONE and </Gtau/up/IndicesR> has sign H5T_SGN_ERROR
Not comparable: </Gtau/up/Mesh/Statistic> has sign H5T_SGN_NONE and </Gtau/up/Mesh/Statistic> has sign H5T_SGN_ERROR
Not comparable: </Gtau/up/Mesh/TypeGF> has sign H5T_SGN_NONE and </Gtau/up/Mesh/TypeGF> has sign H5T_SGN_ERROR
Not comparable: </Gtau/up/Name> has sign H5T_SGN_NONE and </Gtau/up/Name> has sign H5T_SGN_ERROR
Not comparable: </Gtau/up/Note> has sign H5T_SGN_NONE and </Gtau/up/Note> has sign H5T_SGN_ERROR
Not comparable: </Gtau/up/Tail/IndicesL> has sign H5T_SGN_NONE and </Gtau/up/Tail/IndicesL> has sign H5T_SGN_ERROR
Not comparable: </Gtau/up/Tail/IndicesR> has sign H5T_SGN_NONE and </Gtau/up/Tail/IndicesR> has sign H5T_SGN_ERROR
···
________________________________________
From: Hdf-forum [hdf-forum-bounces@lists.hdfgroup.org] on behalf of Barbara Jones [bljones@hdfgroup.org]
Sent: Friday, December 06, 2013 8:23 PM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] h5diff crash and core dump
Hi Jason,
Thank you for the files!
I can reproduce the problem, and it does not look like a known issue, so I entered a bug report for it.
For your reference it is bug HDFFV-8639. (Though our bug database is not open to the public, you can
just send a message to the Helpdesk, if you want to check on the status.)
Thanks, again!
-Barbara
HDF Helpdesk
help@hdfgroup.org
-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On Behalf Of Jason Temple
Sent: Friday, December 06, 2013 7:46 AM
To: HDF Users Discussion List
Subject: Re: [Hdf-forum] h5diff crash and core dump
Hi,
Sorry for my slow response.
I placed the files in the put/incoming/help directory - both of them are called SingleSiteBethe.reference.h5 and SingleSiteBethe.output.h5.
I am using hdf5 version 1.8.11, compiled with the following flags:
./configure --prefix=/apps/hdf5/1.8.11-parallel --enable-fortran --enable-shared --enable-fast-install --enable-cxx --enable-production --enable-unsupported --enable-threadsafe --enable-clear-file-buffers --enable-filters=all --enable-direct-vfd --enable-dconv-exception --enable-dconv-accuracy --enable-hl --enable-deprecated-symbols --enable-embedded-libinfo --with-pthread=/usr/include --enable-parallel --with-szlib=/apps/monch/szip/intel CFLAGS=-fPIC LDFLAGS=-L/apps/monch/intel/impi/4.1.1.036/lib64/
CPPFLAGS=-DMPICH_IGNORE_CXX_SEEK CC=mpicc FC=mpifc F90=mpif90 F77=mpif77 CXX=mpicxx
Thanks,
Jason Temple
On 12/05/2013 05:06 PM, Barbara Jones wrote:
Hello Jason,
There is a bug report in our system for a similar error with h5diff with a dataset containing an attribute that is an object reference.
Is the 'problem' attribute an object reference?
Would you be able to give us your file to look at?
Below are instructions for placing a file on our local ftp server, if you can.
Thanks!
-Barbara
help@hdfgroup.org
---
PLACING FILE ON THE HDF GROUP FTP SERVER:
From a command line, you can access The HDF Group (local) ftp server by typing:
ftp ftp.hdfgroup.uiuc.edu
Login as "anonymous"
Go to the pub/incoming/help/ directory:
cd pub/incoming/help
Type 'pwd' to see if you are in that location. (You will not be able
to see the contents of the directory.):
pwd
Type 'bin' to put in binary mode:
bin
Place file in directory after you are in binary mode:
put xxx
Get out of ftp:
quit
Please let me know if you have placed the file there.
-----Original Message-----
From: Hdf-forum [mailto:hdf-forum-bounces@lists.hdfgroup.org] On
Behalf Of Jason Temple
Sent: Thursday, December 05, 2013 7:02 AM
To: hdf-forum@lists.hdfgroup.org
Subject: [Hdf-forum] h5diff crash and core dump
Hello,
When using h5diff, my users are seeing crash and core dumps.
Any ideas?
h5diff -cp 1.e-2 SingleSiteBethe.output.h5
SingleSiteBethe.reference.h5
HDF5-DIAG: Error detected in HDF5 (1.8.11) thread 0:
#000: H5A.c line 1092 in H5Aread(): unable to read attribute
major: Attribute
minor: Read failed
#001: H5A.c line 1152 in H5A_read(): unable to convert between src and dst datatypes
major: Attribute
minor: Feature is unsupported
#002: H5T.c line 4525 in H5T_path_find(): no appropriate function for conversion path
major: Datatype
minor: Unable to initialize object Not comparable:
</G/__BlockIndicesList> has sign H5T_SGN_NONE and
</G/__BlockIndicesList> has sign H5T_SGN_ERROR Not comparable:
</G/__Name> has sign H5T_SGN_NONE and </G/__Name> has sign
H5T_SGN_ERROR Not comparable: </G/__Note> has sign H5T_SGN_NONE and
</G/__Note> has sign H5T_SGN_ERROR
HDF5-DIAG: Error detected in HDF5 (1.8.11) thread 0:
#000: H5A.c line 1092 in H5Aread(): unable to read attribute
major: Attribute
minor: Read failed
#001: H5A.c line 1152 in H5A_read(): unable to convert between src and dst datatypes
major: Attribute
minor: Feature is unsupported
#002: H5T.c line 4525 in H5T_path_find(): no appropriate function for conversion path
major: Datatype
minor: Unable to initialize object Not comparable:
</G/down/IndicesL> has sign H5T_SGN_NONE and </G/down/IndicesL> has
sign H5T_SGN_ERROR Not comparable: </G/down/IndicesR> has sign
H5T_SGN_NONE and </G/down/IndicesR> has sign H5T_SGN_ERROR
HDF5-DIAG: Error detected in HDF5 (1.8.11) thread 0:
#000: H5A.c line 1092 in H5Aread(): unable to read attribute
major: Attribute
minor: Read failed
#001: H5A.c line 1152 in H5A_read(): unable to convert between src and dst datatypes
major: Attribute
minor: Feature is unsupported
#002: H5T.c line 4525 in H5T_path_find(): no appropriate function for conversion path
major: Datatype
minor: Unable to initialize object
*** glibc detected *** h5diff: free(): invalid pointer:
0x000000335eb8eed8 ***
======= Backtrace: =========
/lib64/libc.so.6[0x335e8760e6]
/apps/monch/hdf5/1.8.11-parallel/intel/14.0.1-impi/lib/libhdf5.so.8(H5
MM_xfree+0xb)[0x2b76c5db401b]
/apps/monch/hdf5/1.8.11-parallel/intel/14.0.1-impi/lib/libhdf5.so.8(+0
x29b097)[0x2b76c5ee6097]
/apps/monch/hdf5/1.8.11-parallel/intel/14.0.1-impi/lib/libhdf5.so.8(H5
T_vlen_reclaim+0x44)[0x2b76c5ee5c34]
/apps/monch/hdf5/1.8.11-parallel/intel/14.0.1-impi/lib/libhdf5.so.8(H5
S_select_iterate+0x28a)[0x2b76c5e3640a]
/apps/monch/hdf5/1.8.11-parallel/intel/14.0.1-impi/lib/libhdf5.so.8(H5
D_vlen_reclaim+0x59)[0x2b76c5cf8c19]
/apps/monch/hdf5/1.8.11-parallel/intel/14.0.1-impi/lib/libhdf5.so.8(H5
Dvlen_reclaim+0x123)[0x2b76c5cdcaf3]
h5diff[0x41d68a]
h5diff[0x41c79c]
h5diff[0x41badf]
h5diff[0x41a535]
h5diff[0x40606f]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x335e81ecdd]
h5diff[0x405ed9]
Thanks,
Jason
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgro
up.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgro
up.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
_______________________________________________
Hdf-forum is for HDF software users discussion.
Hdf-forum@lists.hdfgroup.org
http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org
