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

[Max Rudolph]

Lev,
Usually it is possible to use whichever compilers you want by setting
environment variables. For instance on my cluster we have the Intel MPI
library but by adding to my .bashrc:

export I_MPI_CC=gcc
export I_MPI_CXX=g++

I can use the gnu compilers with the vendor-supplied mpi. There are similar
environment variables for openmpi (OMPI_CC and OMPI_CXX if memory serves).

Hope that this helps.
Max

On Mon, Jul 24, 2017 at 2:08 PM, Lev Karatun <lev.karatun at gmail.com> wrote:

> 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: http://www.math.colostate.edu/~bangerth/
>>> _______________________________________________
>>> Aspect-devel mailing list
>>> Aspect-devel at geodynamics.org
>>> http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
>>
>>
>>
>>
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-- 
---------------------------------
Max Rudolph
Assistant Professor, Earth and Planetary Sciences, UC Davis
webpage <http://www.maxrudolph.org>
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