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.

-erik

On Thu, Oct 1, 2015 at 9:30 AM, Geraint Pratten <g.pratten@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.Pratten@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

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--

Erik Schnetter <schnetter@cct.lsu.edu>
http://www.perimeterinstitute.ca/personal/eschnetter/

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