Hi,
SphericalHarmonicDecomp should not be writing output at the same time as a checkpoint. Are you using an NFS mount? I noticed issues with NFS servers becoming unresponsive (due to a large number of blocking io operations) during a checkpoint. Perhaps right after a checkpoint, the server is still too busy.
This certainly sounds like an issue that needs to be fixed, although I am not sure how. Perhaps a failed IO operation should be a fatal error that kills the run.
Could you try setting the output for metric_obs_0_Decomp.h5 so that it doesn't correspond to a the iteration immediately before or after a checkpoint?
On 07/27/2012 03:59 AM, Jakob Hansen wrote:
Hi,
I'm experimenting a bit with using the PittNull / SphericalHarmonicDecomp thorn but I've been experiencing a few errors in writing to its output metric_obs_0_Decomp.h5 file.
On some occations it seems that this output file cannot be opened and hence leaving gaps in the data file. This always occurs when carpet is doing checkpoininting. Everything else runs well, though, and the simulations finishes fine. However, when trying to fftwfilter the metric_obs_0_Decomp.h5 file, I notice the missing data points.
I've checked system logs and there seem to be no hardware failure. Also, as far as I can see, I'm not overusing memory allocation either.
Anyone else experienced similar issues?
Here follows output from error file :
HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5F.c line 1509 in H5Fopen(): unable to open file major: File accessability minor: Unable to open file #001: H5F.c line 1300 in H5F_open(): unable to read superblock major: File accessability minor: Read failed #002: H5Fsuper.c line 324 in H5F_super_read(): unable to load superblock major: Object cache minor: Unable to protect metadata #003: H5AC.c line 1597 in H5AC_protect(): H5C_protect() failed. major: Object cache minor: Unable to protect metadata #004: H5C.c line 3333 in H5C_protect(): can't load entry major: Object cache minor: Unable to load metadata into cache #005: H5C.c line 8177 in H5C_load_entry(): unable to load entry major: Object cache minor: Unable to load metadata into cache #006: H5Fsuper_cache.c line 469 in H5F_sblock_load(): truncated file major: File accessability minor: File has been truncated HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5Gdeprec.c line 214 in H5Gcreate1(): not a location major: Invalid arguments to routine minor: Inappropriate type #001: H5Gloc.c line 253 in H5G_loc(): invalid object ID major: Invalid arguments to routine minor: Bad value HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5Adeprec.c line 153 in H5Acreate1(): not a location major: Invalid arguments to routine minor: Inappropriate type #001: H5Gloc.c line 253 in H5G_loc(): invalid object ID major: Invalid arguments to routine minor: Bad value [etc. etc. etc. ...... ]
Cheers, Jakob
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