Hi,
It seems the error was caused by the same reasons as Erik explained. It happens while checkpointing. It could be by-passed without checkpointing or with "unchunked=no".
However, what I don't understand is - Why did it not happen for the other case of the same computational size, not exactly same because of different eos, though. - Why did it not happen on the other machines of Lustre filesystem, even with "unchunked=yes"
Cheers,
Hee Il
2010/11/8 Erik Schnetter schnetter@cct.lsu.edu
Hee Il
HDF5 errors can have two likely kinds of sources: You may be running out of disk space, or the HDF5 file may be corrupt. The latter happens if you copy a file while it is being written, or if you interrupt a program that is writing to a file, or if two processes are writing to the same file at the same time.
-erik
On Mon, Nov 8, 2010 at 8:00 AM, Hee Il Kim heeilkim@gmail.com wrote:
Hi,
Recently I've encountered the hdf error. It didn't happen on all my machines but at least I saw this on QueenBee. I'm using the latest development version of EinsteinToolkit.
I attached below my hdf5 parameter setup, stderr, and stdout.
Thanks in advance,
Hee Il
# IOHDF5 IOHDF5::out_every = 128 iohdf5::out_dir = "h5" iohdf5::compression_level = 9 IOHDF5::output_symmetry_points = no IOHDF5::out3D_ghosts = no IOHDF5::out_vars = " hydrobase::rho{ downsample={4 4 4} } weylscal4::psi4r{ downsample={4 4 4} } weylscal4::psi4i{ downsample={4 4 4} } "
IO::out_unchunked = "yes" IO::out_mode = "onefile"
### stderr ### ... HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5Dio.c line 266 in H5Dwrite(): can't write data major: Dataset minor: Write failed #001: H5Dio.c line 578 in H5D_write(): can't write data major: Dataset minor: Write failed #002: H5Dcontig.c line 557 in H5D_contig_write(): contiguous write failed major: Dataset minor: Write failed
### stdout ###
WARNING[L1,P0] (CarpetIOHDF5): HDF5 call 'H5Dwrite (memdataset, memdatatype, overlap_dataspace, dataspace, H5P_DEFAULT, data)' returned error code -1 WARNING[L1,P0] (CarpetIOHDF5): HDF5 call 'H5Dwrite (memdataset, memdatatype, overlap_dataspace, dataspace, H5P_DEFAULT, data)' returned error code -1 WARNING[L1,P0] (CarpetIOHDF5): HDF5 call 'H5Dwrite (memdataset, memdatatype, overlap_dataspace, dataspace, H5P_DEFAULT, data)' returned error code -1