Hi, I am trying to run a simulation with the same output directory - though I've been removing the simulations after each run while trying to fix the above issue. I should have write access to the file and there should be sufficient storage.
Geraint On 5 October 2015 at 11:34, Ian Hinder <[email protected]> wrote: > > On 1 Oct 2015, at 15:49, Erik Schnetter <[email protected]> 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 <[email protected]> > 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: [email protected] >> 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 >> [email protected] >> http://lists.einsteintoolkit.org/mailman/listinfo/users >> >> > > > -- > Erik Schnetter <[email protected]> > http://www.perimeterinstitute.ca/personal/eschnetter/ > _______________________________________________ > Users mailing list > [email protected] > http://lists.einsteintoolkit.org/mailman/listinfo/users > > > -- > Ian Hinder > http://members.aei.mpg.de/ianhin > > -- Geraint Pratten Postdoctoral Research Associate Mobile: +44(0) 7581709282 E-mail: [email protected] Skype: geraint.pratten School of Mathematical and Physical Sciences Pevensey 3 Building University of Sussex Falmer Campus Brighton BN1 9QH United Kingdom
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