On 1 Oct 2015, at 15:49, Erik Schnetter <schnet...@cct.lsu.edu> wrote:
> Geraint > > Some very fundamental HDF5 operations fail. This could be due to a file > system problem; maybe you don't have write access to the file, or your disk > is full. It could also be that there exists a corrupted HDF5 file, and you > are trying to write to it (extend it). > > HDF5 files can get corrupted if you have opened it for writing, and then the > application is interrupted or crashes, or you run out of disk space. Even if > you make free space later, a corrupted file remains corrupted. Hi Geraint, Are you trying to run a simulation with output in the same directory as one that was run before? > > -erik > > > On Thu, Oct 1, 2015 at 9:30 AM, Geraint Pratten <g.prat...@sussex.ac.uk> > wrote: > Hi all, > > I recently built the latest release (Hilbert) on the local cluster and I've > been getting a HDF5 error. I've tried building Cactus with both the local > HDF5 package on the cluster as well as letting Cactus build HDF5 from > scratch. Does anyone have any insight into the error I've attached below > (extract of a long chain of errors of the same form)? > > I can dump the output to file or give configuration files if needed. > > Thanks in advance! > Geraint > > ---------- > > HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 0: > #000: H5Ddeprec.c line 193 in H5Dcreate1(): unable to create dataset > major: Dataset > minor: Unable to initialize object > #001: H5Dint.c line 453 in H5D__create_named(): unable to create and link > to dataset > major: Dataset > minor: Unable to initialize object > #002: H5L.c line 1638 in H5L_link_object(): unable to create new link to > object > major: Links > minor: Unable to initialize object > #003: H5L.c line 1882 in H5L_create_real(): can't insert link > major: Symbol table > minor: Unable to insert object > #004: H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal > failed > major: Symbol table > minor: Object not found > #005: H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator > failed > major: Symbol table > minor: Callback failed > #006: H5L.c line 1674 in H5L_link_cb(): name already exists > major: Symbol table > minor: Object already exists > WARNING level 1 from host node207.cm.cluster process 0 > while executing schedule bin (none), routine (no thorn)::(no routine) > in thorn CarpetIOHDF5, file > /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc:677: > -> HDF5 call 'dataset = H5Dcreate (outfile, datasetname.str().c_str(), > filedatatype, dataspace, plist)' returned error code -1 > WARNING level 1 from host node207.cm.cluster process 0 > while executing schedule bin (none), routine (no thorn)::(no routine) > in thorn CarpetIOHDF5, file > /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc:689: > -> HDF5 call 'H5Dwrite (dataset, memdatatype, H5S_ALL, H5S_ALL, > H5P_DEFAULT, data)' returned error code -1 > WARNING level 1 from host node207.cm.cluster process 0 > while executing schedule bin (none), routine (no thorn)::(no routine) > in thorn CarpetIOHDF5, file > /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc:725: > -> HDF5 call 'attr = H5Acreate (dataset, "level", H5T_NATIVE_INT, > dataspace, H5P_DEFAULT)' returned error code -1 > WARNING level 1 from host node207.cm.cluster process 0 > while executing schedule bin (none), routine (no thorn)::(no routine) > in thorn CarpetIOHDF5, file > /mnt/pact/gp234/NR/Cactus/arrangements/Carpet/CarpetIOHDF5/src/Output.cc:726: > -> HDF5 call 'H5Awrite (attr, H5T_NATIVE_INT, &refinementlevel)' returned > error code -1 > WARNING level 1 from host node207.cm.cluster process 0 > > -- > Geraint Pratten > Postdoctoral Research Associate > > Mobile: +44(0) 7581709282 > E-mail: g.prat...@sussex.ac.uk > Skype: geraint.pratten > > School of Mathematical and Physical Sciences > Pevensey 3 Building > University of Sussex > Falmer Campus > Brighton > BN1 9QH > United Kingdom > > _______________________________________________ > Users mailing list > Users@einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users > > > > > -- > Erik Schnetter <schnet...@cct.lsu.edu> > http://www.perimeterinstitute.ca/personal/eschnetter/ > _______________________________________________ > Users mailing list > Users@einsteintoolkit.org > http://lists.einsteintoolkit.org/mailman/listinfo/users -- Ian Hinder http://members.aei.mpg.de/ianhin
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