Hi Jason, I am working on it. Chances are good that it will be fixed in the coming release.
-Albert On Apr 2, 2014, at 9:50 AM, Jason Temple <[email protected]> wrote: > Hi, > > Is this bug fix still landing in the next release? > > Thanks, > > Jason > > On 01/08/2014 03:49 PM, Barbara Jones wrote: >> Hi Jason, >> >> This issue will be fixed in the HDF5-1.8.13 release, due out in May. It >> does not look like the >> developer has begun work on this yet, but if I find out differently, I'll >> let you know. >> >> -Barbara >> [email protected] >> >> -----Original Message----- >> From: Hdf-forum [mailto:[email protected]] On Behalf Of >> Jason Temple >> Sent: Wednesday, January 08, 2014 8:31 AM >> To: HDF Users Discussion List >> Subject: Re: [Hdf-forum] h5diff crash and core dump >> >> Hello, >> >> Has there been any resolution for this problem? Any patches that were made >> (if at all) would be handy. >> >> Thanks, >> >> Jason >> >> On 12/06/2013 08:23 PM, Barbara Jones wrote: >>> 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 >>> [email protected] >>> >>> -----Original Message----- >>> From: Hdf-forum [mailto:[email protected]] 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 >>>> [email protected] >>>> >>>> --- >>>> 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:[email protected]] On >>>> Behalf Of Jason Temple >>>> Sent: Thursday, December 05, 2013 7:02 AM >>>> To: [email protected] >>>> 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(H >>>> 5 >>>> 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(H >>>> 5 >>>> T_vlen_reclaim+0x44)[0x2b76c5ee5c34] >>>> /apps/monch/hdf5/1.8.11-parallel/intel/14.0.1-impi/lib/libhdf5.so.8(H >>>> 5 S_select_iterate+0x28a)[0x2b76c5e3640a] >>>> /apps/monch/hdf5/1.8.11-parallel/intel/14.0.1-impi/lib/libhdf5.so.8(H >>>> 5 >>>> D_vlen_reclaim+0x59)[0x2b76c5cf8c19] >>>> /apps/monch/hdf5/1.8.11-parallel/intel/14.0.1-impi/lib/libhdf5.so.8(H >>>> 5 >>>> 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. >>>> [email protected] >>>> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgr >>>> o >>>> up.org >>>> >>>> _______________________________________________ >>>> Hdf-forum is for HDF software users discussion. >>>> [email protected] >>>> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgr >>>> o >>>> up.org >>> _______________________________________________ >>> Hdf-forum is for HDF software users discussion. >>> [email protected] >>> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgro >>> up.org >>> >>> _______________________________________________ >>> Hdf-forum is for HDF software users discussion. >>> [email protected] >>> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgro >>> up.org >> >> _______________________________________________ >> Hdf-forum is for HDF software users discussion. >> [email protected] >> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org >> >> _______________________________________________ >> Hdf-forum is for HDF software users discussion. >> [email protected] >> http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://mail.lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org _______________________________________________ Hdf-forum is for HDF software users discussion. 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