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. 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