[aspect-devel] Troubles with opening vtk files in Paraview

Thu Jul 27 11:22:43 PDT 2017

Lev,

that is a weird situation. To make sure I understand:
1. if you set it to a value greater than one, you randomly get invalid
.vtu files? Is it always file -0000 or are other files affected?
2. If you set it to 1, it works correctly?
3. Can you check what happens if you set "number of grouped files" to 0?

As this seems to be related to MPI I/O, can you tell us what MPI
library you are using?

On Thu, Jul 27, 2017 at 2:08 PM, Lev Karatun <lev.karatun at gmail.com> wrote:
> Hi,
>
> after updating Aspect (not sure if it played any role) I only have troubles
> with vtu files if I don't set "number of grouped files" to 1 (so far, at
> least). The same input files produces NULL symbols in different files during
> different runs.
> I can, of course, run models with "number of grouped files" set to 1, so I
> don't need immediate help, but I thought it's worth noting (and maybe
> registering as a bug) anyway.
>
> Best regards,
> Lev Karatun.
>
> 2017-07-24 17:08 GMT-04:00 Lev Karatun <lev.karatun at gmail.com>:
>>
>> Hi Juliane, Wolfgang,
>>
>> it happenned in several different models, but I can't run them 1 more time
>> and compare the output because when I encountered the problem I started
>> updating Aspect and now I'm having trouble compiling it with Intel compilers
>> (trying to work it out with the guys from cluster support). I can't use gcc
>> because everything on the cluster is compiled with icc, there is not even an
>> MPI wrapper for gcc.
>> I appreciate your help and I'll let you know once I can check if the error
>> is reproducible.
>>
>>
>>
>> Best regards,
>> Lev Karatun.
>>
>> 2017-07-21 16:47 GMT-04:00 Juliane Dannberg <dannberg at gfz-potsdam.de>:
>>>
>>> Hi Lev,
>>>
>>> if I open your file in a browser, I get the same error (which is exactly
>>> where the weird zero characters you mentioned are):
>>>
>>> XML Parsing Error: not well-formed
>>> Location:
>>> file:///home/dannberg/old_home_arbeit/test/solution-00000.0000.vtu
>>> Line Number 434, Column 20:    <DataArray type
>>>
>>> So it is definitely a problem with the file (not with Paraview). In
>>> principle, this line should contain the type of the data array (something
>>> like <DataArray type="Float64" Name="viscosity" format="binary">)
>>>
>>> Is this a reproducible error, or did it happen only once?
>>>
>>> Best,
>>> Juliane
>>>
>>>
>>> On 07/21/2017 01:43 PM, Lev Karatun wrote:
>>>
>>> Hi Wolfgang,
>>>
>>> in the file there is a bunch of null symbols, not sure where they came
>>> from. I definitely didn't hit ctrl+c and Aspect wasn't killed because this
>>> is the output for 0th timestep, there are others. For the same reason, I
>>> don't think I ran out of space. I attached the file just in case.
>>>
>>> Best regards,
>>> Lev Karatun.
>>>
>>> 2017-07-21 15:23 GMT-04:00 Wolfgang Bangerth <bangerth at tamu.edu>:
>>>>
>>>>
>>>> Lev,
>>>>
>>>>> I'm getting an error when trying to open a solution file in Paraview.
>>>>> It's strange because I don't even have a C:\DBD folder. I tried new and old
>>>>> versions of Paraview, enabling and disabling "set Number of grouped files =
>>>>> 1", but it didn't help.
>>>>
>>>>
>>>> C:\DBD is the folder in which Paraview was compiled. If you installed a
>>>> binary file you downloaded, then this is not a path on your system.
>>>>
>>>>
>>>>> Did anyone see something like this before?
>>>>>
>>>>> ERROR: In
>>>>> C:\DBD\pvs-x64\paraview\src\paraview\VTK\IO\XMLParser\vtkXMLParser.cxx, line
>>>>> 483
>>>>>
>>>>> vtkXMLDataParser (0000000016127230): Error parsing XML in stream at
>>>>> line 434, column 19, byte index 233472: not well-formed (invalid token)
>>>>
>>>>
>>>> It's a pity that paraview doesn't say which file this is in. What
>>>> typically happens with errors such as this is that the file you're trying to
>>>> read is corrupted. This could be because you hit Ctrl-C while ASPECT
>>>> happened to be writing that file (or because your cluster's scheduler
>>>> happened to kill ASPECT just in that moment). It could also be because you
>>>> ran out of file space while ASPECT was running.
>>>>
>>>> If you can guess which file is being read right now, take a look at line
>>>> 434 and see how the context around it looks like.
>>>>
>>>> Best
>>>>  W.
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Wolfgang Bangerth          email:                 bangerth at colostate.edu
>>>>                            www: https://urldefense.proofpoint.com/v2/url?u=http-3A__www.math.colostate.edu_-7Ebangerth_&d=DwIFaQ&c=Ngd-ta5yRYsqeUsEDgxhcqsYYY1Xs5ogLxWPA_2Wlc4&r=c08Btfq4m9QEScXN3ZQwLZzzWQE7S8CYq1IYuzKV_Zk&m=ZI_xyF0SVGrQ5tAYjg9qFVIEBfzOsFqNOWWY4n7Oj8s&s=afuGZlrZZTPbKphYVPYO02pzcVjaWhg4HOUFgjlDNPg&e= 
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-- 
Timo Heister
http://www.math.clemson.edu/~heister/