[Users] HDF5 Error, Hilbert

[Geraint Pratten]

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 <ian.hinder at aei.mpg.de> wrote:

>
> On 1 Oct 2015, at 15:49, Erik Schnetter <schnetter at 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.pratten at 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 at 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 at cct.lsu.edu>
> http://www.perimeterinstitute.ca/personal/eschnetter/
> _______________________________________________
> Users mailing list
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>
>
> --
> Ian Hinder
> http://members.aei.mpg.de/ianhin
>
>


-- 
Geraint Pratten
Postdoctoral Research Associate

Mobile: +44(0) 7581709282
E-mail: G.Pratten at 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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