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(H5MM_xfree+0xb)[0x2b76c5db401b] > /apps/monch/hdf5/1.8.11-parallel/intel/14.0.1-impi/lib/libhdf5.so.8(+0x29b097)[0x2b76c5ee6097] > /apps/monch/hdf5/1.8.11-parallel/intel/14.0.1-impi/lib/libhdf5.so.8(H5T_vlen_reclaim+0x44)[0x2b76c5ee5c34] > /apps/monch/hdf5/1.8.11-parallel/intel/14.0.1-impi/lib/libhdf5.so.8(H5S_select_iterate+0x28a)[0x2b76c5e3640a] > /apps/monch/hdf5/1.8.11-parallel/intel/14.0.1-impi/lib/libhdf5.so.8(H5D_vlen_reclaim+0x59)[0x2b76c5cf8c19] > /apps/monch/hdf5/1.8.11-parallel/intel/14.0.1-impi/lib/libhdf5.so.8(H5Dvlen_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.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
