Hello Dennis, Yes, I have in installed. libsuitesparse-dev is already the newest version (1:5.7.1+dfsg-2).
I can run some test examples using BlockDiagAMGBiCGSTABSolver when the discretization scheme is either tpfa or mpfa, so far these crashes have happened when using the Box. I wonder why. Best wishes Ana Em seg., 22 de nov. de 2021 às 17:48, Dennis Gläser < [email protected]> escreveu: > Hi Ana, > > do you have UMFPack (a direct solver) installed on your system? As far as > I know, that is used under the hood to do the coarse grid solve in the > AMGSolver, but has an iterative fallback in case it is not found. > > On ubuntu, you can install it with 'apt install libsuitesparse-dev'. > > After installing, you may need to remove your cmake caches and rerun > dunecontrol. > > Let me know if this helps! > > Best wishes, > Dennis > On 22.11.21 17:30, Ana Carolina Loyola wrote: > > Following up on my question on the precision error of my boundary fluxes, > I am trying to introduce the quad precision for my multidomain problem with > facets. For that, I have to use another Linear Solver. Following the test > case in dumux/test/multidomain/facet/1p_1p/analytical, I tried to > use BlockDiagAMGBiCGSTABSolver, but the following error occurs: > > Solve: M deltax^k = rNewton: Caught exception: "NumericalProblem > [solveLinearSystem:/home/analoyola/dumux/dumux/dumux/nonlinear/newtonsolver.hh:383]: > Linear solver did not converge" > Dune reported error: NumericalProblem > [.../dumux/dumux/dumux/nonlinear/newtonsolver.hh:260]: Newton solver didn't > converge after 0 iterations. > ---> Abort! > > When I try to run the test in > dumux/test/multidomain/facet/1p_1p/analytical for the box method, a crash > also occurs: > > Solve: M deltax^k = rNewton: Caught exception: "SolverAbort > [apply:/home/analoyola/dumux3.4/dune-istl/dune/istl/solvers.hh:494]: > breakdown in BiCGSTAB - rho 0 <= EPSILON 1e-80 after 93.5 iterations" > terminate called after throwing an instance of 'Dumux::NumericalProblem' > what(): NumericalProblem > [.../dumux/dumux/nonlinear/newtonsolver.hh:397]: Newton solver didn't > converge after 0 iterations. > > The same does not occur for the cell-centered schemes. > > Any idea on what may be causing the crash and how to solve this ? > > Thanks a lot > > Ana > > Em sex., 19 de nov. de 2021 às 00:02, < > [email protected]> escreveu: > >> Send DuMux mailing list submissions to >> [email protected] >> >> To subscribe or unsubscribe via the World Wide Web, visit >> https://listserv.uni-stuttgart.de/mailman/listinfo/dumux >> or, via email, send a message with subject or body 'help' to >> [email protected] >> >> You can reach the person managing the list at >> [email protected] >> >> When replying, please edit your Subject line so it is more specific >> than "Re: Contents of DuMux digest..." >> >> >> Today's Topics: >> >> 1. Re: Integration of boundary flux for upscaling: "errors" >> (Christoph Gr?ninger) >> 2. Re: (no subject) (Pham, Vuong Van) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Thu, 18 Nov 2021 23:07:15 +0100 >> From: Christoph Gr?ninger <[email protected]> >> To: [email protected] >> Subject: Re: [DuMux] Integration of boundary flux for upscaling: >> "errors" >> Message-ID: <[email protected]> >> Content-Type: text/plain; charset=utf-8; format=flowed >> >> Hi Ana, >> I am not sure whether you are right that 1e-14 to 1e-16 should not be >> considered as zero. It is the expected precision of a double. In >> general, you cannot expect it to be better, just because in the regular >> case it by luck is actually better. >> >> Maybe you can run your simulation with quad precision. That might help >> to get more knowledge regarding the limits of double precision. >> >> Bye >> Christoph >> >> >> Am 17.11.21 um 11:31 schrieb Ana Carolina Loyola: >> > Hello, >> > >> > I have been working on the?upscaling of the 2D permeability tensor of >> > fractured media with the Box Method using the multidomain module of >> > Dumux 3.2. The code attached has worked well when compared to the >> > analytical solutions of perpendicular and equally spaced fractures. >> > I apply linear pressure boundary conditions and integrate flow at the >> > boundaries using the following equation* >> > image.png >> > And for that, I created a "boundary flux" function (at main.cc), which >> > calls the computeFlux function for all the faces that are located at >> the >> > boundary of the domain. >> > >> > The reason I send this message is that I have noticed some precision >> > errors that concern me when running another simple test case (one >> > horizontal?and non-persistent fracture, meshes are attached).? It is >> > expected that I have kxy and kyx equal to 0, which seems to work fine >> > when I use a symmetric mesh (signalized with -sym in the .msh files), >> > since I get kxy and kyx in the order of < 1e-30 and net flux balances >> in >> > the order of <1e-28. >> > >> > But when I use non-symmetric meshes I get kxy in the order of 1e-17, >> > which can not be considered to be 0, considering the matrix >> > permeability, and boundary fluxes summation as high as 1e-14 when I >> > apply the x gradient. The "error" does not seem to improve when >> > refining?the mesh. >> > >> > So what I would like to ask here is if I am using the appropriate >> > functions to integrate flow and if you would have any >> > implementation-related suggestions to get past this issue. >> > >> > I am sorry for the long text; this may be more of a theoretical issue >> > than a code-related one, but I thought it was worth the shot just?to >> see >> > if I am missing something. >> > >> > *Equation used by Pouya and Fouch? (2009) >> > Pouya, Amade & Fouch?, Olivier. (2009). Permeability of 3D >> discontinuity >> > networks: New tensors from boundary-conditioned homogenization. >> Advances >> > in Water Resources. 32. 303-314. 10.1016/j.advwatres.2008.08.004. >> > >> > Thanks >> > >> > Ana Loyola >> > >> > _______________________________________________ >> > DuMux mailing list >> > [email protected] >> > https://listserv.uni-stuttgart.de/mailman/listinfo/dumux >> > >> >> -- >> Als w?r es nix, leb'?ich von [IT] und mach' nur, was ich lieb' >> Lebe wie?im?Paradies,?womit hab' ich?das verdient? >> Die Wahrheit?ist: Hab' ich nicht, ich bin nur reicher beschenkt >> Als jemand in einem armen Land mit dem gleichen Talent >> [frei nach Tua von Die Orsons - Oioioiropa] >> >> >> ------------------------------ >> >> Message: 2 >> Date: Thu, 18 Nov 2021 23:01:44 +0000 >> From: "Pham, Vuong Van" <[email protected]> >> To: Timo Koch <[email protected]>, DuMux User Mailing List >> <[email protected]> >> Subject: Re: [DuMux] (no subject) >> Message-ID: >> < >> sn6pr01mb47029cf9172df257c3e86d95b6...@sn6pr01mb4702.prod.exchangelabs.com >> > >> >> Content-Type: text/plain; charset="utf-8" >> >> Dear all, >> Thanks for pointing that out, and so that is the issue I want to address. >> My point is, I read the DuMuX course tutorial and came up with this >> procedure, as follows (in order to use DuMuX): >> >> Install DUNE and DuMuX -> build the source files (i.e., >> CMakeLists.txt; problem.hh, params.input, etc) -> cmake CMakeLists.txt -> >> execute DuMuX as ./?. params.input >> >> Therefore, please assist me on the mistakes in my understanding above >> (especially the meaning, use, and how-to-create such the _build_ directory, >> or build-cmake) >> >> I really appreciate your support. I am a beginner in DuMuX so I hope that >> my questions are not that dumb. >> Best regards, >> Vuong Van Pham >> Graduate Research Assistant (GRA) >> Department of Chemical and Petroleum Engineering (CPE), University of >> Kansas >> Email: [email protected]<mailto:[email protected]> >> Phone: +1-(785)-979-2664 >> >> >> >> From: Timo Koch <[email protected]> >> Sent: Thursday, November 18, 2021 4:30 AM >> To: DuMux User Mailing List <[email protected]> >> Cc: Pham, Vuong Van <[email protected]> >> Subject: Re: [DuMux] (no subject) >> >> Dear Vuong, >> >> it looks like you ran cmake in the source directory. You have to run >> ?make executable? in the _build_ directory. Per default dumux/build-cmake/? >> Timo >> >> >> 18. nov. 2021 kl. 08:19 skrev Kilian Weishaupt < >> [email protected]<mailto: >> [email protected]>>: >> ? >> >> Dear Vuong Van, >> >> did you modify anything in your CMakeLists.txt file? You said the test >> ran successfully so the executable in >> dumux/dumux/build-cmake/test/porousmediumflow/1p" was build successfully? >> >> Best wishes >> Kilian >> On 18.11.21 07:53, Pham, Vuong Van wrote: >> Dear Kilian, >> Still following the Cmake command (i.e., make name_of_executable), I >> attempted to do so in the Ubuntu command window, however I received this >> error as attached: >> <image001.png> >> The picture indicated that for some reasons the command >> ?dune_symlink_to_source_files? is unknown to Cmake. Besides, what I >> observed was that, the commands that are relevant to DUNE, somehow are >> unknown by Cmake and cause incomplete configuration. Please assist me on >> this error. >> >> Best regards, >> Vuong Van Pham >> Graduate Research Assistant (GRA) >> Department of Chemical and Petroleum Engineering (CPE), University of >> Kansas >> Email: [email protected]<mailto:[email protected]> >> Phone: +1-(785)-979-2664 >> >> >> >> >> From: Kilian Weishaupt <[email protected]><mailto: >> [email protected]> >> Sent: Thursday, November 18, 2021 12:42 AM >> To: Pham, Vuong Van <[email protected]><mailto:[email protected]> >> Cc: DuMux User Mailing List <[email protected]><mailto: >> [email protected]> >> Subject: Re: [DuMux] (no subject) >> >> >> Dear Vuong Van, >> >> I'm glad the installation worked now. >> >> 1.) >> >> CMakeLists.txt is a configuration file read by CMake, a build system >> generator. If configured correctly, >> you compile your source code just by calling >> >> make name_of_the_executable >> >> If you make any changes to CMakeLists.txt, a simple >> >> make >> >> will update the build configuration. >> >> Have a look at the tests or at our course exercises here >> https://git.iws.uni-stuttgart.de/dumux-repositories/dumux-course/-/tree/master/exercises/exercise-basic >> < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.iws.uni-stuttgart.de%2Fdumux-repositories%2Fdumux-course%2F-%2Ftree%2Fmaster%2Fexercises%2Fexercise-basic&data=04%7C01%7Cvuongvanpham%40ku.edu%7Cde613490bee44b1296d908d9aa7e63c5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637728282092917187%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=zdHLOvKbHWQHW7G17zW1GN1%2Bq5Vj%2FajNuTGk0LVx8F4%3D&reserved=0> >> to get more information >> on how to properly use CMakeLists.txt >> >> 2.) You may either just use a simple text editor such as Atom or >> notepad++ or you can try setting up VS Code (an IDE) which however, is a >> little bit more involved to configure. Note that you can either edit your >> files under Windows (as shown in the windows explorer) or using the Ubuntu >> subsytem. Whatever works better for you. >> >> See Point 3 in our wiki on how to get VS Code >> https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/wikis/Windows-Subsystem-for-DuMux >> < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.iws.uni-stuttgart.de%2Fdumux-repositories%2Fdumux%2F-%2Fwikis%2FWindows-Subsystem-for-DuMux&data=04%7C01%7Cvuongvanpham%40ku.edu%7Cde613490bee44b1296d908d9aa7e63c5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637728282092927180%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=gLWMDVj2UyWQPUESnsfD2QvorfIAifDLjJefjt%2BTzX0%3D&reserved=0 >> > >> >> >> >> PS: Please always respond to the mailing list ( >> [email protected]<mailto:[email protected]>, >> I also forgot to do that in my first mail) such that others can profit from >> our discussion, too. >> >> Best wishes >> Kilian >> On 17.11.21 20:56, Pham, Vuong Van wrote: >> Dear Kilian, >> I am glad to receive your swift response. Following the use of DuMuX (at >> this point I installed all folders and ran the test successfully), I have >> the concerns listed as below: >> >> 1. The core structure of a ?DuMux? job contains files as the >> attached figure. I believe that I have to compile the ?CMakeLists.txt? >> using CMake prior to any further execution. May you assist me how to >> compile such that ?CMakeLists.txt? properly? >> <image002.png> >> >> 2. By far, I only know how to modify contents in a file (within >> Ubuntu subsystem) using Vim editor. However, I may need either Python/C++ >> later to modify such files. May you suggest me an IDE to use with C++ in >> Ubuntu subsystem? >> >> I hope that my concerns are appropriate. >> >> Best regards, >> Vuong Van Pham >> Graduate Research Assistant (GRA) >> Department of Chemical and Petroleum Engineering (CPE), University of >> Kansas >> Email: [email protected]<mailto:[email protected]> >> Phone: +1-(785)-979-2664 >> >> >> >> From: Kilian Weishaupt <[email protected]><mailto: >> [email protected]> >> Sent: Wednesday, November 17, 2021 10:28 AM >> To: Pham, Vuong Van <[email protected]><mailto:[email protected]> >> Subject: Re: [DuMux] (no subject) >> >> >> Dear Vuong Van, >> >> we recently updated our wiki for installing Dumux under Windows 10. >> >> There seems to be an issue with git clone which can be fixed as described >> in the wiki. >> >> >> https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/-/wikis/Windows-Subsystem-for-DuMux >> < >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit.iws.uni-stuttgart.de%2Fdumux-repositories%2Fdumux%2F-%2Fwikis%2FWindows-Subsystem-for-DuMux&data=04%7C01%7Cvuongvanpham%40ku.edu%7Cde613490bee44b1296d908d9aa7e63c5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637728282092927180%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=gLWMDVj2UyWQPUESnsfD2QvorfIAifDLjJefjt%2BTzX0%3D&reserved=0 >> > >> >> Best wishes >> Kilian >> On 12.11.21 01:39, Pham, Vuong Van wrote: >> To the DuMux development team, >> >> My name is VUONG VAN PHAM and I am an interested DuMux user for my >> research purpose. When I was tempted to install the simulator using >> installdumux.py, the installation was paused and the .log file is attached. >> >> Please assist me on how to install DuMux correctly. Also please note that >> I was tempted to install in ubuntu subsystem within Windows 10 (I do not >> know whether that impacts the installation process, however, I inform that >> fact just in case). >> >> Best regards, >> Vuong Van Pham >> Graduate Research Assistant (GRA) >> Department of Chemical and Petroleum Engineering (CPE), University of >> Kansas >> Email: [email protected]<mailto:[email protected]> >> Phone: +1-(785)-979-2664 >> >> >> >> >> >> >> _______________________________________________ >> >> DuMux mailing list >> >> [email protected]<mailto:[email protected]> >> >> https://listserv.uni-stuttgart.de/mailman/listinfo/dumux< >> https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Flistserv.uni-stuttgart.de%2Fmailman%2Flistinfo%2Fdumux&data=04%7C01%7Cvuongvanpham%40ku.edu%7Cde613490bee44b1296d908d9aa7e63c5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637728282092937174%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=whr9VH%2FhoPCO4bBa8mK5NALr3QDCh7P%2B92nFwyUki2U%3D&reserved=0 >> > >> >> -- >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> Kilian Weishaupt >> >> Institut f?r Wasser- und Umweltsystemmodellierung (IWS) >> >> Lehrstuhl f?r Hydromechanik und Hydrosystemmodellierung >> >> Universit?t Stuttgart, Pfaffenwaldring 61, 70569 Stuttgart >> >> Email: [email protected]<mailto: >> [email protected]> >> >> Telefon: 0049 711 685-60461 ** fax: 0049-711-685-60430 >> >> http://www.hydrosys.uni-stuttgart.de< >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.hydrosys.uni-stuttgart.de%2F&data=04%7C01%7Cvuongvanpham%40ku.edu%7Cde613490bee44b1296d908d9aa7e63c5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637728282092947175%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=dbZlT866YezZ%2BYsOA6y3kJOJhPOItupRjINH5LHHPvI%3D&reserved=0 >> > >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> -- >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> Kilian Weishaupt >> >> Institut f?r Wasser- und Umweltsystemmodellierung (IWS) >> >> Lehrstuhl f?r Hydromechanik und Hydrosystemmodellierung >> >> Universit?t Stuttgart, Pfaffenwaldring 61, 70569 Stuttgart >> >> Email: [email protected]<mailto: >> [email protected]> >> >> Telefon: 0049 711 685-60461 ** fax: 0049-711-685-60430 >> >> http://www.hydrosys.uni-stuttgart.de< >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.hydrosys.uni-stuttgart.de%2F&data=04%7C01%7Cvuongvanpham%40ku.edu%7Cde613490bee44b1296d908d9aa7e63c5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637728282092947175%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=dbZlT866YezZ%2BYsOA6y3kJOJhPOItupRjINH5LHHPvI%3D&reserved=0 >> > >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> -- >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> >> Kilian Weishaupt >> >> Institut f?r Wasser- und Umweltsystemmodellierung (IWS) >> >> Lehrstuhl f?r Hydromechanik und Hydrosystemmodellierung >> >> Universit?t Stuttgart, Pfaffenwaldring 61, 70569 Stuttgart >> >> Email: [email protected]<mailto: >> [email protected]> >> >> Telefon: 0049 711 685-60461 ** fax: 0049-711-685-60430 >> >> http://www.hydrosys.uni-stuttgart.de< >> https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.hydrosys.uni-stuttgart.de%2F&data=04%7C01%7Cvuongvanpham%40ku.edu%7Cde613490bee44b1296d908d9aa7e63c5%7C3c176536afe643f5b96636feabbe3c1a%7C0%7C0%7C637728282092957170%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=QBDlHB8UdqRmhnwyAA%2FRwkrR%2FQy4zEYz8vX8WW6ycoU%3D&reserved=0 >> > >> >> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% >> _______________________________________________ >> DuMux mailing list >> [email protected]<mailto:[email protected]> >> https://listserv.uni-stuttgart.de/mailman/listinfo/dumux >> -------------- next part -------------- >> An HTML attachment was scrubbed... >> URL: < >> http://listserv.uni-stuttgart.de/pipermail/dumux/attachments/20211118/39f00e03/attachment.htm >> > >> >> ------------------------------ >> >> Subject: Digest Footer >> >> _______________________________________________ >> DuMux mailing list >> [email protected] >> https://listserv.uni-stuttgart.de/mailman/listinfo/dumux >> >> >> ------------------------------ >> >> End of DuMux Digest, Vol 128, Issue 12 >> ************************************** >> > > _______________________________________________ > DuMux mailing > [email protected]https://listserv.uni-stuttgart.de/mailman/listinfo/dumux > >
_______________________________________________ DuMux mailing list [email protected] https://listserv.uni-stuttgart.de/mailman/listinfo/dumux
