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(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. >> [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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