Hi Suzon,
the files contain duplicate entries for temperature (T), if I remove one
it can be loaded into Paraview.
Best,
Mathis
------------------------------------------------------------------------
From: Suzon Jammes <[email protected]>
To: Christoph Grüninger <[email protected]>, DuMux User Mailing List
<[email protected]>
Reply-To: DuMux User Mailing List <[email protected]>
Date: Mon, 5 Aug, 2024 12:18:25 +0200
Subject: [DuMux] Problem with fluidsystems
Hi Timo and Christoph,
I still can't solve the problem, I installed the latest version of
Paraview but it doesn't help. Below you will see the error message I
got from paraview.
Attached you ll also find one vtp file for the fractures and one vtu
file for the matrix. they look fine to me.
I tried to use the binary output as Timo suggested but it didn't help
Do you see anything wrong in the vtp/vtu file ?
Thank you for your help,
Suzon
[suzon-Precision-7920:94675] Signal: Segmentation fault (11)
[suzon-Precision-7920:94675] Signal code: Address not mapped (1)
[suzon-Precision-7920:94675] Failing at address: 0x60
[suzon-Precision-7920:94675] [ 0]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x14420)[0x7fd6c69d7420]
[suzon-Precision-7920:94675] [ 1]
/home/suzon/paraview_build/bin/../lib/libvtkIOXML-pv5.12.so.1(_ZN28vtkXMLUnstructuredGridReader17ReadArrayForCellsEP17vtkXMLDataElementP16vtkAbstractArray+0x19)[0x7fd6cb6e2d69]
[suzon-Precision-7920:94675] [ 2]
/home/suzon/paraview_build/bin/../lib/libvtkIOXML-pv5.12.so.1(_ZN16vtkXMLDataReader13ReadPieceDataEv+0x45c)[0x7fd6cb68993c]
[suzon-Precision-7920:94675] [ 3]
/home/suzon/paraview_build/bin/../lib/libvtkIOXML-pv5.12.so.1(_ZN28vtkXMLUnstructuredDataReader13ReadPieceDataEv+0x118)[0x7fd6cb6dcda8]
[suzon-Precision-7920:94675] [ 4]
/home/suzon/paraview_build/bin/../lib/libvtkIOXML-pv5.12.so.1(_ZN28vtkXMLUnstructuredGridReader13ReadPieceDataEv+0x18a)[0x7fd6cb6e391a]
[suzon-Precision-7920:94675] [ 5]
/home/suzon/paraview_build/bin/../lib/libvtkIOXML-pv5.12.so.1(_ZN28vtkXMLUnstructuredDataReader11ReadXMLDataEv+0x357)[0x7fd6cb6d67a7]
[suzon-Precision-7920:94675] [ 6]
/home/suzon/paraview_build/bin/../lib/libvtkIOXML-pv5.12.so.1(_ZN12vtkXMLReader11RequestDataEP14vtkInformationPP20vtkInformationVectorS3_+0x60d)[0x7fd6cb6bdd5d]
[suzon-Precision-7920:94675] [ 7]
/home/suzon/paraview_build/bin/../lib/libvtkIOXML-pv5.12.so.1(_ZN12vtkXMLReader14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x76)[0x7fd6cb6c3af6]
[suzon-Precision-7920:94675] [ 8]
/home/suzon/paraview_build/bin/../lib/libvtkPVVTKExtensionsIOCore-pv5.12.so.1(_ZN19vtkFileSeriesReader11RequestDataEP14vtkInformationPP20vtkInformationVectorS3_+0x6f)[0x7fd6c1ee9dbf]
[suzon-Precision-7920:94675] [ 9]
/home/suzon/paraview_build/bin/../lib/libvtkPVVTKExtensionsIOCore-pv5.12.so.1(_ZN19vtkFileSeriesReader14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x1f2)[0x7fd6c1eea042]
[suzon-Precision-7920:94675] [10]
/home/suzon/paraview_build/bin/../lib/libvtkCommonExecutionModel-pv5.12.so.1(_ZN12vtkExecutive13CallAlgorithmEP14vtkInformationiPP20vtkInformationVectorS3_+0x5d)[0x7fd6ca6696cd]
[suzon-Precision-7920:94675] [11]
/home/suzon/paraview_build/bin/../lib/libvtkCommonExecutionModel-pv5.12.so.1(_ZN23vtkDemandDrivenPipeline11ExecuteDataEP14vtkInformationPP20vtkInformationVectorS3_+0x3d)[0x7fd6ca65f62d]
[suzon-Precision-7920:94675] [12]
/home/suzon/paraview_build/bin/../lib/libvtkCommonExecutionModel-pv5.12.so.1(_ZN24vtkCompositeDataPipeline11ExecuteDataEP14vtkInformationPP20vtkInformationVectorS3_+0x81)[0x7fd6ca65bec1]
[suzon-Precision-7920:94675] [13]
/home/suzon/paraview_build/bin/../lib/libvtkCommonExecutionModel-pv5.12.so.1(_ZN23vtkDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x54f)[0x7fd6ca662ccf]
[suzon-Precision-7920:94675] [14]
/home/suzon/paraview_build/bin/../lib/libvtkCommonExecutionModel-pv5.12.so.1(_ZN32vtkStreamingDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x381)[0x7fd6ca6cd1c1]
[suzon-Precision-7920:94675] [15]
/home/suzon/paraview_build/bin/../lib/libvtkCommonExecutionModel-pv5.12.so.1(_ZN24vtkCompositeDataPipeline15ForwardUpstreamEP14vtkInformation+0x182)[0x7fd6ca65aca2]
[suzon-Precision-7920:94675] [16]
/home/suzon/paraview_build/bin/../lib/libvtkCommonExecutionModel-pv5.12.so.1(_ZN23vtkDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x13a)[0x7fd6ca6628ba]
[suzon-Precision-7920:94675] [17]
/home/suzon/paraview_build/bin/../lib/libvtkCommonExecutionModel-pv5.12.so.1(_ZN32vtkStreamingDemandDrivenPipeline14ProcessRequestEP14vtkInformationPP20vtkInformationVectorS3_+0x381)[0x7fd6ca6cd1c1]
[suzon-Precision-7920:94675] [18]
/home/suzon/paraview_build/bin/../lib/libvtkCommonExecutionModel-pv5.12.so.1(_ZN23vtkDemandDrivenPipeline10UpdateDataEi+0xa3)[0x7fd6ca660ff3]
[suzon-Precision-7920:94675] [19]
/home/suzon/paraview_build/bin/../lib/libvtkCommonExecutionModel-pv5.12.so.1(_ZN32vtkStreamingDemandDrivenPipeline6UpdateEiP20vtkInformationVector+0x117)[0x7fd6ca6ce917]
[suzon-Precision-7920:94675] [20]
/home/suzon/paraview_build/bin/../lib/libvtkRemotingServerManager-pv5.12.so.1(_ZN16vtkSISourceProxy14UpdatePipelineEidb+0x202)[0x7fd6cd67be12]
[suzon-Precision-7920:94675] [21]
/home/suzon/paraview_build/bin/../lib/libvtkRemotingApplication-pv5.12.so.1(_Z23vtkSISourceProxyCommandP26vtkClientServerInterpreterP13vtkObjectBasePKcRK21vtkClientServerStreamRS5_Pv+0x8c3)[0x7fd6c4f18433]
[suzon-Precision-7920:94675] [22]
/home/suzon/paraview_build/bin/../lib/libvtkRemotingClientServerStream-pv5.12.so.1(_ZN26vtkClientServerInterpreter19CallCommandFunctionEPKcP13vtkObjectBaseS1_RK21vtkClientServerStreamRS4_+0x20d)[0x7fd6cc595dbd]
[suzon-Precision-7920:94675] [23]
/home/suzon/paraview_build/bin/../lib/libvtkRemotingApplication-pv5.12.so.1(_Z27vtkSIMetaReaderProxyCommandP26vtkClientServerInterpreterP13vtkObjectBasePKcRK21vtkClientServerStreamRS5_Pv+0x164)[0x7fd6c4f12a44]
[suzon-Precision-7920:94675] [24]
/home/suzon/paraview_build/bin/../lib/libvtkRemotingClientServerStream-pv5.12.so.1(_ZN26vtkClientServerInterpreter19CallCommandFunctionEPKcP13vtkObjectBaseS1_RK21vtkClientServerStreamRS4_+0x20d)[0x7fd6cc595dbd]
[suzon-Precision-7920:94675] [25]
/home/suzon/paraview_build/bin/../lib/libvtkRemotingClientServerStream-pv5.12.so.1(_ZN26vtkClientServerInterpreter20ProcessCommandInvokeERK21vtkClientServerStreami+0x495)[0x7fd6cc5964e5]
[suzon-Precision-7920:94675] [26]
/home/suzon/paraview_build/bin/../lib/libvtkRemotingClientServerStream-pv5.12.so.1(_ZN26vtkClientServerInterpreter17ProcessOneMessageERK21vtkClientServerStreami+0xc2)[0x7fd6cc596622]
[suzon-Precision-7920:94675] [27]
/home/suzon/paraview_build/bin/../lib/libvtkRemotingClientServerStream-pv5.12.so.1(_ZN26vtkClientServerInterpreter13ProcessStreamERK21vtkClientServerStream+0x25)[0x7fd6cc596ae5]
[suzon-Precision-7920:94675] [28]
/home/suzon/paraview_build/bin/../lib/libvtkRemotingServerManager-pv5.12.so.1(_ZN16vtkPVSessionCore21ExecuteStreamInternalERK21vtkClientServerStreamb+0xf9)[0x7fd6cd640559]
[suzon-Precision-7920:94675] [29]
/home/suzon/paraview_build/bin/../lib/libvtkRemotingServerManager-pv5.12.so.1(_ZN16vtkPVSessionCore13ExecuteStreamEjRK21vtkClientServerStreamb+0x54)[0x7fd6cd640384]
[suzon-Precision-7920:94675] *** End of error message ***
Segmentation fault (core dumped)
On 04/08/2024 10:30, Christoph Grüninger wrote:
Hi Suzon,
have you tried the lastest version of ParaView, too? Does it still
crash?
It would be good to open an issue for ParaView. They might be
interested in fixing the crash and add proper error handling. If you
need assistance with reporting the bug, reach out to me in a private
email and I assist you.
Kind regards,
Christoph
Am 02.08.24 um 17:51 schrieb Timo Koch:
Hi Suzon,
I’m answering to the mailing list so others can see the answers too.
I hope this is ok.
If the vtu file is not too big maybe you can attach it?
Paraview might crash if there is NaNs in the file.
I’ve also seen issue with locale settings (numbers written
German/French style with commas as floating point separators instead
of points can also mess up things). Then setting locale to English
settings in the terminal should help.
Maybe in this case it also helps switching to binary output (not
sure). Ascii is the default.
Where you have something like
|vtkWriter.write(timeLoop->time());|
|
|
You could try
|
|
|vtkWriter.write(timeLoop->time(),
Dune::VTK::OutputType::appendedraw);|
|
|
Finally, there can be crashes, if the file is otherwise corrupt,
e.g. less numbers written out for cell data than elements,
But that would usually only occur if you modified something
significant in the way output is written and did something wrong there.
Best,
Timo
———————————————————
Timo Koch,
Postdoctoral MSC fellow (Scientia II fellows)
Mechanics section, Department of Mathematics,
University of Oslo, Norway
https://www.mn.uio.no/math/personer/vit/timokoch/index.html
https://timokoch.github.io/
On 2 Aug 2024, at 17:37, Suzon Jammes <[email protected]> wrote:
Hi Timo,
Thank you for your help.
I changed my properties.hh file (see below) and now the code
compiles. It also runs correctly but I can’t open the results file
in paraview. So there is still a problem somewhere. Paraview crashs
when I try to load the results file. Do you know what can create
this type of problem ?
—————————————————————————————
Suzon Jammes
Researcher & Consultant
M&U sas, Geology by Research
www.mandu-geology.fr <http://www.mandu-geology.fr/>
[email protected]
<mailto:[email protected]> / +33(0)768692934
Ce message est confidentiel. Son contenu ne représente en aucun cas
un engagement de la part de M&U SAS sous reserve de tout accord
conclu par écrit avec la société. Toute publication, utilisation
ou diffusion, meme partielle, doit être autorisée préalablement.
Si vous n'êtes pas destinataire de ce message, merci d'en
avertir immédiatement l'expéditeur ou par email
:[email protected] <mailto:[email protected]>.
This message is confidential. Its contents do not constitute
a commitment by M&U SAS except
where provided for in a written agreement with the company.
Any unauthorised disclosure, use
or dissemination, either whole or partial, is prohibited. If you
are not the intended recipient, please notify the sender
immediately or with the following email: [email protected]
<mailto:[email protected]>
On 2 Aug 2024, at 13:15, Timo Koch <[email protected]> wrote:
Hi Suzon,
the error looks like the program is confusing the Policy and the
CO2Tables.
Your class “H2ON2O2CO2CH4H2” has three template arguments: Scalar,
CO2Tables, Policy.
I’m suspecting that when you set the type via the property system
you might have forgotten the second argument?
How does your FluidSystem property setter look like? That is, what
template arguments do you use for the template type H2ON2O2CO2CH4H2?
Best wishes
Timo
———————————————————
Timo Koch,
Postdoctoral MSC fellow (Scientia II fellows)
Mechanics section, Department of Mathematics,
University of Oslo, Norway
https://www.mn.uio.no/math/personer/vit/timokoch/index.html
https://timokoch.github.io/
On 2 Aug 2024, at 13:00, Suzon Jammes <[email protected]>
wrote:
Hi all,
I am still working on the exercices with fractures. I made lot of
progress since the course and I was able to run 2PNCNI models
with 3 components (H20 H2,CH4).
I would like to add more components so I used the fluids systems
presented in the Ahmadi et al 2021 paper (see below) and
available on the dumux repository. I just added H2 in the gas
mix. The fluid systems that I am using is attached to this email.
When I try to compile I get the following error.
In file included from
/Users/suzon/Desktop/Numerical_Model/dumux/dumux/dumux/material/fluidsystems/h2on2o2co2ch4h2.hh:41:
*/Users/suzon/Desktop/Numerical_Model/dumux/dumux/dumux/material/components/co2.hh:160:24:**error:**no
member named 'tabulatedEnthalpy' in
'Dumux::FluidSystems::H2ON2O2CO2CH4H2DefaultPolicy<true>'*
CO2Tables::tabulatedEnthalpy.at(temperature, pressure);
* ~~~~~~~~~~~^*
*/Users/suzon/Desktop/Numerical_Model/dumux/dumux/dumux/material/fluidsystems/h2on2o2co2ch4h2.hh:839:24:
note:*in instantiation of member function
'Dumux::Components::CO2<double,
Dumux::FluidSystems::H2ON2O2CO2CH4H2DefaultPolicy<true>>::gasEnthalpy'
requested here
* CO2::gasEnthalpy(T,p);
* ^*
*/Users/suzon/Desktop/Numerical_Model/dumux/dumux/dumux/material/fluidsystems/base.hh:377:32:
note:*in instantiation of function template specialization
'Dumux::FluidSystems::H2ON2O2CO2CH4H2<double,
Dumux::FluidSystems::H2ON2O2CO2CH4H2DefaultPolicy<true>>::enthalpy<Dumux::CompositionalFluidState<double,
Dumux::FluidSystems::H2ON2O2CO2CH4H2<double,
Dumux::FluidSystems::H2ON2O2CO2CH4H2DefaultPolicy<true>>>>'
requested here
return Implementation::enthalpy(fluidState, phaseIdx);
* ^*
*/Users/suzon/Desktop/Numerical_Model/dumux/dumux/dumux/porousmediumflow/nonisothermal/volumevariables.hh:355:29:
note:*in instantiation of function template specialization
'Dumux::FluidSystems::Base<double,
Dumux::FluidSystems::H2ON2O2CO2CH4H2<double,
Dumux::FluidSystems::H2ON2O2CO2CH4H2DefaultPolicy<true>>>::enthalpy<Dumux::CompositionalFluidState<double,
Dumux::FluidSystems::H2ON2O2CO2CH4H2<double,
Dumux::FluidSystems::H2ON2O2CO2CH4H2DefaultPolicy<true>>>>'
requested here
return FluidSystem::enthalpy(fluidState, paramCache,
phaseIdx);
Do you know, how I can correct this error ?
Thank you for your help,
Suzon
Ahmadi, N., Heck, K., Rolle, M., Helmig, R., & Mosthaf, K.
(2021). On multicomponent gas diffusion and coupling
concepts for porous media and free flow: a benchmark study.
Computational Geosciences, 25, 1493–1507.
https://doi.org/10.1007/s10596-021-10057-y—————————————————————————————
—————————————————————————————
Suzon Jammes
Researcher & Consultant
M&U sas, Geology by Research
www.mandu-geology.fr
[email protected] / +33(0)768692934
Ce message est confidentiel. Son contenu ne représente en aucun
cas un engagement de la part de M&U SAS sous reserve de tout
accord conclu par écrit avec la société. Toute
publication, utilisation
ou diffusion, meme partielle, doit être autorisée préalablement.
Si vous n'êtes pas destinataire de ce message, merci d'en
avertir immédiatement l'expéditeur ou par email
:[email protected].
This message is confidential. Its contents do not constitute
a commitment by M&U SAS except
where provided for in a written agreement with the company.
Any unauthorised disclosure, use
or dissemination, either whole or partial, is prohibited. If you
are not the intended recipient, please notify the sender
immediately or with the following email: [email protected]
<h2on2o2co2ch4h2.hh><M&U LOGO-25.tif>
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--
********************************************************
Mathis Kelm
Universitaet Stuttgart
Institut fuer Wasser- und Umweltsystemmodellierung
Lehrstuhl fuer Hydromechanik und Hydrosystemmodellierung
Pfaffenwaldring 61, 70569 Stuttgart
Tel.: 0711/685-60146
[email protected]
https://www.iws.uni-stuttgart.de/lh2/
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