subject:"\[Paraview\] Error reading timeseries with spatial grid collection with XDMF"

Re: [Paraview] Error reading timeseries with spatial grid collection with XDMF

2017-11-20 Thread Nikolaos Beratlis

I tried reading them with XDMF 3 reader and it works fine.

Thank you for the suggestions.

Nikos

On Mon, Nov 20, 2017 at 2:14 PM, David E DeMarle 
wrote:

> It might be that the reader doesn't like or want that both of your times
> are 0.0.
> ...
> 
> ...
> 
> ...
> but your third case doesn't fit that hypothesis.
>
> Otherwise your file looks ok at first glance. I'ld have to debug the
> reader on your data to figure out what is going wrong.
>
> David E DeMarle
> Kitware, Inc.
> Principal Engineer
> 21 Corporate Drive
> 
> Clifton Park, NY 12065
> 
> -8662
> Phone: 518-881-4909 <(518)%20881-4909>
>
> On Sun, Nov 12, 2017 at 11:15 PM, Joachim Pouderoux <
> joachim.pouder...@kitware.com> wrote:
>
>> Nikos,
>>
>> It looks like you are using the Xdmf2 based reader.
>> Did you give a chance to the one based on Xdmf3?
>> What version of ParaView are you using?
>> Can you provide a full dataset we could use to reproduce the issue?
>>
>> Best,
>>
>>
>> *Joachim Pouderoux*, PhD
>>
>> *Technical Expert - Scientific Computing Team*
>> *Kitware SAS *
>>
>>
>> 2017-11-11 19:31 GMT+01:00 Nikolaos Beratlis :
>>
>>> Hi,
>>>
>>> I have a cartesian structured grid made of two sub-domains and a two
>>> snap shots in a time that I would like to read in Paraview. The data and
>>> grid files are stored in HDF5 file and I use a XDMF file to read them in a
>>> Paraview. The XDMF files looks like this:
>>>
>>> 
>>> 
>>> 
>>> 
>>> 
>>>
>>> 
>>> 
>>>
>>> 
>>> 
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/YC
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>>> 
>>> 
>>> 
>>> >> Format="HDF">
>>> ../Q_VPreg.h5sp.0001:/zone0001
>>> 
>>> 
>>> 
>>>
>>> 
>>> 
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/YC
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
>>> 
>>> 
>>> 
>>> >> Format="HDF">
>>> ../Q_VPreg.h5sp.0001:/zone0002
>>> 
>>> 
>>> 
>>> 
>>>
>>> 
>>> 
>>>
>>> 
>>> 
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/YC
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>>> 
>>> 
>>> 
>>> >> Format="HDF">
>>> ../Q_VPreg.h5sp.0001:/zone0001
>>> 
>>> 
>>> 
>>>
>>> 
>>> 
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/YC
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
>>> 
>>> 
>>> 
>>> >> Format="HDF">
>>> ../Q_VPreg.h5sp.0002:/zone0002
>>> 
>>> 
>>> 
>>>
>>> 
>>>
>>> 
>>> 
>>> 
>>>
>>> The file is read in Paraview. When I advance in to the second instant in
>>> time I get the following error:
>>>
>>> Failed to read attribute data.
>>>
>>> Paraview shows data from the first subset (zone0001), it can't read the
>>> data from the second subset (zone0002).
>>>
>>>
>>> When I read only on instant in time like this:
>>>
>>> 
>>> 
>>> 
>>> 
>>> 
>>>
>>> 
>>> 
>>>
>>> 
>>> 
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/YC
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>>> 
>>> 
>>> 
>>> >> Format="HDF">
>>> ../Q_VPreg.h5sp.0001:/zone0001
>>> 
>>> 
>>> 
>>>
>>> 
>>> 
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/YC
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
>>> 
>>> 
>>> 
>>> >> Format="HDF">
>>> ../Q_VPreg.h5sp.0001:/zone0002
>>> 
>>> 
>>> 
>>> 
>>>
>>> 
>>> 
>>> 
>>>
>>> the file is read successfully and no errors show up.
>>>
>>> Also when I read two time instants but with only one subset (zone0001)
>>> Paraview doesn't throw any errors.
>>>
>>> 
>>> 
>>> 
>>> 
>>> 
>>>
>>> 
>>> 
>>>
>>> 
>>> 
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/YC
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>>> 
>>> 
>>> 
>>> >> Format="HDF">
>>> ../Q_VPreg.h5sp.0001:/zone0001
>>> 
>>> 
>>> 
>>>
>>> 
>>> 
>>>
>>> 
>>> 
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/YC
>>> 
>>> >> Format="HDF">
>>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>>> 
>>> 
>>> 
>>> >> Format="HDF">
>>> ../Q_VPreg.h5sp.0001:/zone0001
>>> 
>>> 
>>> 
>>>
>>> 
>>>
>>> 
>>> 
>>> 
>>>
>>>
>>> Does anyone see the problem in the code?
>>>
>>> Kind regards,
>>>
>>> Nikos
>>>
>>>
>>> ___
>>> Powered by www.kitware.com
>>>
>>> Visit other Kitware open-source projects at
>>> http://www.

Re: [Paraview] Error reading timeseries with spatial grid collection with XDMF

2017-11-20 Thread David E DeMarle

It might be that the reader doesn't like or want that both of your times
are 0.0.
...

...

...
but your third case doesn't fit that hypothesis.

Otherwise your file looks ok at first glance. I'ld have to debug the reader
on your data to figure out what is going wrong.

David E DeMarle
Kitware, Inc.
Principal Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4909

On Sun, Nov 12, 2017 at 11:15 PM, Joachim Pouderoux <
joachim.pouder...@kitware.com> wrote:

> Nikos,
>
> It looks like you are using the Xdmf2 based reader.
> Did you give a chance to the one based on Xdmf3?
> What version of ParaView are you using?
> Can you provide a full dataset we could use to reproduce the issue?
>
> Best,
>
>
> *Joachim Pouderoux*, PhD
>
> *Technical Expert - Scientific Computing Team*
> *Kitware SAS *
>
>
> 2017-11-11 19:31 GMT+01:00 Nikolaos Beratlis :
>
>> Hi,
>>
>> I have a cartesian structured grid made of two sub-domains and a two snap
>> shots in a time that I would like to read in Paraview. The data and grid
>> files are stored in HDF5 file and I use a XDMF file to read them in a
>> Paraview. The XDMF files looks like this:
>>
>> 
>> 
>> 
>> 
>> 
>>
>> 
>> 
>>
>> 
>> 
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/YC
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>> 
>> 
>> 
>> > Format="HDF">
>> ../Q_VPreg.h5sp.0001:/zone0001
>> 
>> 
>> 
>>
>> 
>> 
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/YC
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
>> 
>> 
>> 
>> > Format="HDF">
>> ../Q_VPreg.h5sp.0001:/zone0002
>> 
>> 
>> 
>> 
>>
>> 
>> 
>>
>> 
>> 
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/YC
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>> 
>> 
>> 
>> > Format="HDF">
>> ../Q_VPreg.h5sp.0001:/zone0001
>> 
>> 
>> 
>>
>> 
>> 
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/YC
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
>> 
>> 
>> 
>> > Format="HDF">
>> ../Q_VPreg.h5sp.0002:/zone0002
>> 
>> 
>> 
>>
>> 
>>
>> 
>> 
>> 
>>
>> The file is read in Paraview. When I advance in to the second instant in
>> time I get the following error:
>>
>> Failed to read attribute data.
>>
>> Paraview shows data from the first subset (zone0001), it can't read the
>> data from the second subset (zone0002).
>>
>>
>> When I read only on instant in time like this:
>>
>> 
>> 
>> 
>> 
>> 
>>
>> 
>> 
>>
>> 
>> 
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/YC
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>> 
>> 
>> 
>> > Format="HDF">
>> ../Q_VPreg.h5sp.0001:/zone0001
>> 
>> 
>> 
>>
>> 
>> 
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/YC
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
>> 
>> 
>> 
>> > Format="HDF">
>> ../Q_VPreg.h5sp.0001:/zone0002
>> 
>> 
>> 
>> 
>>
>> 
>> 
>> 
>>
>> the file is read successfully and no errors show up.
>>
>> Also when I read two time instants but with only one subset (zone0001)
>> Paraview doesn't throw any errors.
>>
>> 
>> 
>> 
>> 
>> 
>>
>> 
>> 
>>
>> 
>> 
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/YC
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>> 
>> 
>> 
>> > Format="HDF">
>> ../Q_VPreg.h5sp.0001:/zone0001
>> 
>> 
>> 
>>
>> 
>> 
>>
>> 
>> 
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/YC
>> 
>> > Format="HDF">
>> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
>> 
>> 
>> 
>> > Format="HDF">
>> ../Q_VPreg.h5sp.0001:/zone0001
>> 
>> 
>> 
>>
>> 
>>
>> 
>> 
>> 
>>
>>
>> Does anyone see the problem in the code?
>>
>> Kind regards,
>>
>> Nikos
>>
>>
>> ___
>> Powered by www.kitware.com
>>
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>>
>> Please keep messages on-topic and check the ParaView Wiki at:
>> http://paraview.org/Wiki/ParaView
>>
>> Search the list archives at: http://markmail.org/search/?q=ParaView
>>
>> Follow this link to subscribe/unsubscribe:
>> http://public.kitware.com/mailman/listinfo/paraview
>>
>>
>
> ___
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/
> opensource/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link

Re: [Paraview] Error reading timeseries with spatial grid collection with XDMF

2017-11-12 Thread Joachim Pouderoux

Nikos,

It looks like you are using the Xdmf2 based reader.
Did you give a chance to the one based on Xdmf3?
What version of ParaView are you using?
Can you provide a full dataset we could use to reproduce the issue?

Best,


*Joachim Pouderoux*, PhD

*Technical Expert - Scientific Computing Team*
*Kitware SAS *


2017-11-11 19:31 GMT+01:00 Nikolaos Beratlis :

> Hi,
>
> I have a cartesian structured grid made of two sub-domains and a two snap
> shots in a time that I would like to read in Paraview. The data and grid
> files are stored in HDF5 file and I use a XDMF file to read them in a
> Paraview. The XDMF files looks like this:
>
> 
> 
> 
> 
> 
>
> 
> 
>
> 
> 
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/YC
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
> 
> 
> 
>  Format="HDF">
> ../Q_VPreg.h5sp.0001:/zone0001
> 
> 
> 
>
> 
> 
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/YC
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
> 
> 
> 
>  Format="HDF">
> ../Q_VPreg.h5sp.0001:/zone0002
> 
> 
> 
> 
>
> 
> 
>
> 
> 
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/YC
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
> 
> 
> 
>  Format="HDF">
> ../Q_VPreg.h5sp.0001:/zone0001
> 
> 
> 
>
> 
> 
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/YC
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
> 
> 
> 
>  Format="HDF">
> ../Q_VPreg.h5sp.0002:/zone0002
> 
> 
> 
>
> 
>
> 
> 
> 
>
> The file is read in Paraview. When I advance in to the second instant in
> time I get the following error:
>
> Failed to read attribute data.
>
> Paraview shows data from the first subset (zone0001), it can't read the
> data from the second subset (zone0002).
>
>
> When I read only on instant in time like this:
>
> 
> 
> 
> 
> 
>
> 
> 
>
> 
> 
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/YC
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
> 
> 
> 
>  Format="HDF">
> ../Q_VPreg.h5sp.0001:/zone0001
> 
> 
> 
>
> 
> 
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0002
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/YC
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002
> 
> 
> 
>  Format="HDF">
> ../Q_VPreg.h5sp.0001:/zone0002
> 
> 
> 
> 
>
> 
> 
> 
>
> the file is read successfully and no errors show up.
>
> Also when I read two time instants but with only one subset (zone0001)
> Paraview doesn't throw any errors.
>
> 
> 
> 
> 
> 
>
> 
> 
>
> 
> 
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/YC
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
> 
> 
> 
>  Format="HDF">
> ../Q_VPreg.h5sp.0001:/zone0001
> 
> 
> 
>
> 
> 
>
> 
> 
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/XC-zone0001
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/YC
> 
> 
> ../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001
> 
> 
> 
>  Format="HDF">
> ../Q_VPreg.h5sp.0001:/zone0001
> 
> 
> 
>
> 
>
> 
> 
> 
>
>
> Does anyone see the problem in the code?
>
> Kind regards,
>
> Nikos
>
>
> ___
> Powered by www.kitware.com
>
> Visit other Kitware open-source projects at http://www.kitware.com/opensou
> rce/opensource.html
>
> Please keep messages on-topic and check the ParaView Wiki at:
> http://paraview.org/Wiki/ParaView
>
> Search the list archives at: http://markmail.org/search/?q=ParaView
>
> Follow this link to subscribe/unsubscribe:
> http://public.kitware.com/mailman/listinfo/paraview
>
>
___
Powered by www.kitware.com

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[Paraview] Error reading timeseries with spatial grid collection with XDMF

2017-11-11 Thread Nikolaos Beratlis

Hi,

I have a cartesian structured grid made of two sub-domains and a two snap
shots in a time that I would like to read in Paraview. The data and grid
files are stored in HDF5 file and I use a XDMF file to read them in a
Paraview. The XDMF files looks like this:














../grid_VPreg_vxvyvz.h5sp:/XC-zone0001


../grid_VPreg_vxvyvz.h5sp:/YC


../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001




../Q_VPreg.h5sp.0001:/zone0001








../grid_VPreg_vxvyvz.h5sp:/XC-zone0002


../grid_VPreg_vxvyvz.h5sp:/YC


../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002




../Q_VPreg.h5sp.0001:/zone0002












../grid_VPreg_vxvyvz.h5sp:/XC-zone0001


../grid_VPreg_vxvyvz.h5sp:/YC


../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001




../Q_VPreg.h5sp.0001:/zone0001








../grid_VPreg_vxvyvz.h5sp:/XC-zone0002


../grid_VPreg_vxvyvz.h5sp:/YC


../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002




../Q_VPreg.h5sp.0002:/zone0002










The file is read in Paraview. When I advance in to the second instant in
time I get the following error:

Failed to read attribute data.

Paraview shows data from the first subset (zone0001), it can't read the
data from the second subset (zone0002).


When I read only on instant in time like this:














../grid_VPreg_vxvyvz.h5sp:/XC-zone0001


../grid_VPreg_vxvyvz.h5sp:/YC


../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001




../Q_VPreg.h5sp.0001:/zone0001








../grid_VPreg_vxvyvz.h5sp:/XC-zone0002


../grid_VPreg_vxvyvz.h5sp:/YC


../grid_VPreg_vxvyvz.h5sp:/ZC-zone0002




../Q_VPreg.h5sp.0001:/zone0002









the file is read successfully and no errors show up.

Also when I read two time instants but with only one subset (zone0001)
Paraview doesn't throw any errors.














../grid_VPreg_vxvyvz.h5sp:/XC-zone0001


../grid_VPreg_vxvyvz.h5sp:/YC


../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001




../Q_VPreg.h5sp.0001:/zone0001











../grid_VPreg_vxvyvz.h5sp:/XC-zone0001


../grid_VPreg_vxvyvz.h5sp:/YC


../grid_VPreg_vxvyvz.h5sp:/ZC-zone0001




../Q_VPreg.h5sp.0001:/zone0001











Does anyone see the problem in the code?

Kind regards,

Nikos
___
Powered by www.kitware.com

Visit other Kitware open-source projects at 
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Search the list archives at: http://markmail.org/search/?q=ParaView

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Re: [Paraview] Error reading timeseries with spatial grid collection with XDMF

Re: [Paraview] Error reading timeseries with spatial grid collection with XDMF

Re: [Paraview] Error reading timeseries with spatial grid collection with XDMF

[Paraview] Error reading timeseries with spatial grid collection with XDMF

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