On 24.05.2018 13:42, [email protected]<mailto:[email protected]> wrote: Hi Timo,
I think the errors from build_tests are not that important for me anyways. The fact that the tracer test and some other models are not properly linked to the build-cmake folder is the bigger problem, as they simply cannot be build: Here is the output when trying to build the tracer test: macbook-pro:1ptracer berkn$ pwd /Users/berkn/dune_today/dumux/build-cmake/test/porousmediumflow/tracer/1ptracer macbook-pro:1ptracer berkn$ make test_cctracer make: *** No rule to make target `test_cctracer'. Stop. Hi Berk, I cannot reproduce this problem on my machine. Maybe try to rename the target in the CMakeLists.txt and run cmake build-cmake from the top folder again. Then build this new target. For my tracer example, it's actually the second error I am not able to resolve, fixing the first one is no problem. Please always solve errors one after each other as they are often related. The second error also says exactly whats wrong. You are putting variables of the wrong type or the wrong number of parameters in the problem constructor. Timo Best, Berk -----Timo <[email protected]<mailto:[email protected]>> schrieb: ----- An: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Von: Timo <[email protected]<mailto:[email protected]>> Datum: 24.05.2018 13:28 Betreff: Re: Antwort: Re: Antwort: Re: Antwort: Re: Antwort: Re: Antwort: Re: [DuMuX] Antwort: Re: Antwort: Re: Antwort: Re: Couple tracer model with 1p_1p test Hi Berk, the error you get from build_tests was a bug with clang that has already been fixed on master but the multidomain branch is lacking a few commits behind, a rebase will fix. But as I said, we don't expect everything to compile now as we have to clean up the commit history on the multidomain branch first, which we'll do before we want to merge. I'm sorry I can't help you more here. But we don't have the time right now to fix everything right away, after all it's still an unmerged feature branch. What is the error message, when you compile the tracer test? For your tracer example the error message tells you exactly what is wrong: You use a variable "fvGridGeometry" but you haven't defined it anywhere before. Please read the compiler error messages carefully they will point you (most of the time) right to the problem. Timo On 24.05.2018 13:19, [email protected]<mailto:[email protected]> wrote: Hi Timo, I installed UGGrid and deleted the build-cmake folders in all the modules before successfully rebuilding them. The make build_tests command is still returning errors. Please find the output file for make build_tests attached to this mail. Also more specifically, I am still facing the main problem of not being able to build the 1ptracer (test_cctracer code) from the build-cmake/test/... folder. However, I've been working on writing a cpp-file to couple tracer and bloodflow (1p_1p_tracer as it's only blood flow+tracer, no tracer for the tissue yet), and have been debugging this code for a few days now. When compiling this 1p_1p_tracer code, there are two errors left I cannot really resolve, so I attached the output file for this as well. Please have a look and let me know. Best, Berk -----Timo <[email protected]<mailto:[email protected]>> schrieb: ----- An: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Von: Timo <[email protected]<mailto:[email protected]>> Datum: 23.05.2018 15:55 Betreff: Re: Antwort: Re: Antwort: Re: Antwort: Re: Antwort: Re: [DuMuX] Antwort: Re: Antwort: Re: Antwort: Re: Couple tracer model with 1p_1p test Hi Berk, first error says that UGGrid is not installed. Sorry that there is no better error message but we'll fix that before merging into master. Install the dune-uggrid module (git clone https://gitlab.dune-project.org/staging/dune-uggrid.git) to fix that error. However building all tests might fail anyway because some of the newly introduced tests are not in an up-to-date state. So maybe just build the tracer tests you wanted to look at and attach the output if something doesn't work. Timo On 23.05.2018 15:49, [email protected]<mailto:[email protected]> wrote: Dear Timo, I attached the output file to this e-mail. Best, Berk -----Timo <[email protected]<mailto:[email protected]>> schrieb: ----- An: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>>, "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Von: Timo <[email protected]<mailto:[email protected]>> Datum: 23.05.2018 14:59 Betreff: Re: Antwort: Re: Antwort: Re: Antwort: Re: [DuMuX] Antwort: Re: Antwort: Re: Antwort: Re: Couple tracer model with 1p_1p test Hi Berk, I would need the error message to be able to say something (leave out the -j2). Timo On 23.05.2018 14:57, [email protected]<mailto:[email protected]> wrote: Dear Timo, Running ./dune-common/bin/dunecontrol --module=dune-grid bexec make -j2 build_tests and ./dune-common/bin/dunecontrol --module=dune-grid bexec ctest -j2 works fine. Everything is build perfectly and the tests pass. However, I tried to run make -j2 build_tests in the dumux/build-cmake folder, and had the following output: 2 warnings generated. [ 24%] Linking CXX executable test_1p_richards [ 24%] Built target test_1p_richards make[1]: *** [CMakeFiles/build_tests.dir/rule] Error 2 make: *** [build_tests] Error 2 after which the compiling process was stopped. The cmake version I am using is 3.9.4. Thank you for taking the time. Best, Berk -----Timo <[email protected]<mailto:[email protected]>> schrieb: ----- An: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Von: Timo <[email protected]<mailto:[email protected]>> Datum: 18.05.2018 17:56 Kopie: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Betreff: Re: Antwort: Re: Antwort: Re: [DuMuX] Antwort: Re: Antwort: Re: Antwort: Re: Couple tracer model with 1p_1p test Hi Berk, it's hard to help. The output looks fine. It's weird that some application seem to build and some don't. What about the the Dune tests? Can you run ./dune-common/bin/dunecontrol --module=dune-grid bexec make -j2 build_tests ./dune-common/bin/dunecontrol --module=dune-grid bexec ctest -j2 to see if the tests build and pass? If yes also try running make -j2 build_tests in your dumux/build-cmake folder. I don't have a macOS system here to try if it's related to that. Which CMake version do you have? (cmake --version) Timo On 18.05.2018 14:07, [email protected]<mailto:[email protected]> wrote: Sorry, forgot attaching the file. Best, Berk -----Timo <[email protected]<mailto:[email protected]>> schrieb: ----- An: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Von: Timo <[email protected]<mailto:[email protected]>> Datum: 17.05.2018 19:17 Kopie: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Betreff: Re: Antwort: Re: [DuMuX] Antwort: Re: Antwort: Re: Antwort: Re: Couple tracer model with 1p_1p test Hi Berk, the branch just adds the multidomain infrastructure. The other models stay untouched. The tracer model works fine for me. So something is going wrong in your local setup. Did you completely remove the build-cmake folder? Try also deleting it for all the dune modules and the run dunecontrol again. You can also attach the output of dunecontrol after deleting all build directories if it still doesn't work so I can have a look at a possible problem. Timo On 17.05.2018 12:58, [email protected]<mailto:[email protected]> wrote: Dear Timo, after doing the git pull, I could finally run the 1p_1p test and plug my network data in, which worked perfectly. However, only the models in the 1d3d folder seem to work, the tracer and all the other models are not running, there seems to be a CMake linking problem, as I cannot build the code through the build-cmake folder ("No rule to make target `test_3d2p' "). Already tried building the build-cmake folder again a few times. I guess these problems are all linked to the actual changes due to the development in this branch. Any ideas ? Best, Berk -----Timo <[email protected]<mailto:[email protected]>> schrieb: ----- An: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Von: Timo <[email protected]<mailto:[email protected]>> Datum: 16.05.2018 11:17 Kopie: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Betreff: Re: [DuMuX] Antwort: Re: Antwort: Re: Antwort: Re: Couple tracer model with 1p_1p test Hi Berk, can you do a git pull origin feature/multidomain-on-3.0 on the feature/multidomain-on-3.0 branch? As this branch is currently under heavy development there are a lot of changes and it might happen that temporarily not everything compiles. We'll clean that up later. After the git pull, the 1p_1p example should hopefully work again. Timo On 16.05.2018 11:03, [email protected]<mailto:[email protected]> wrote: Dear Timo, I cloned the dune-foamgrid module and rebuild the build-cmake folder after deleting the old one in dumux. The foam grid module has been found as an optional module. Still getting errors (this time " error: no matching member function for call to 'updateCouplingContext' "), but different ones. I attached a part of the output to the email as it was very long. Thank you again. Best, Berk -----Timo <[email protected]<mailto:[email protected]>> schrieb: ----- An: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Von: Timo <[email protected]<mailto:[email protected]>> Datum: 16.05.2018 10:23 Kopie: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Betreff: Re: Antwort: Re: Antwort: Re: [DuMuX] Couple tracer model with 1p_1p test Dear Berk, you need the dune-foamgrid module (https://gitlab.dune-project.org/extensions/dune-foamgrid) which is a grid manager for surface and network grids to run this example. You need to rerun the dunecontrol script. You might need to delete the build folders first. The CMake output of the dumux module will print if dune-foamgrid has been found as an additional module. Timo Viele Grüße, Timo Am 16.05.2018 um 10:08 schrieb <[email protected]<mailto:[email protected]>> <[email protected]<mailto:[email protected]>>: Dear Timo, please find the terminal output of make test_1p_1p attached to this e-mail. Also thank you for the hint, I have rebuild the build-cmake folder with the optic.opts option file now (the output when trying to build test_1p_1p is still the same). Best, Berk -----Timo <[email protected]<mailto:[email protected]>> schrieb: ----- An: DuMuX User Forum <[email protected]<mailto:[email protected]>> Von: Timo <[email protected]<mailto:[email protected]>> Datum: 15.05.2018 17:51 Kopie: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Betreff: Re: Antwort: Re: [DuMuX] Couple tracer model with 1p_1p test On 15.05.2018 17:43, [email protected]<mailto:[email protected]> wrote: Dear Timo, Thank you very much for the hints. I know what you mean with the different versions and branches now, but I used dune1 and dune2 in the email because I wasn't sure which dune and dumux versions I was actually using. I now downloaded the newest versions of dune and dumux (dune 2.6 and dumux 2.12, as "git clone -b releases/3.0-git https://git.iws.uni-stuttgart.de/dumux-repositories/dumux.git"; dumux did not work), and switched to the branch you mentioned (feature/multidomain-on-3.0). I think that as you said this will resolve the stupid problems I was having. I seem to have some troubles when compiling everything with "./dune-common/bin/dunecontrol --opts=dumux/debug.opts all " though, the build-cmake folder etc. is build without errors, but when entering /build-cmake/test/multidomain/embedded/1d3d/1p_1p or 1p_richards, I am getting many errors when compiling with "make test_1p_1p" or "make test 1p_richards". Hi Berk, there is no release branch yet for 3.0 because it's not released yet. The branch is simply called master. The branch with the multidomain code is feature/multidomain-on-3.0 as you noticed correctly. Can you attach the output of make test_1p_1p? BTW using the debug option file will produce very slow code. You can also use the optim.opts option file and then switch setting the CMAKE_BUILD_TYPE variable for the specific application you want to debug. To this end add set(CMAKE_BUILD_TYPE Debug) in the CMakeLists.txt of the application. Analogously, set(CMAKE_BUILD_TYPE Release) will use compiler flags that produce optimized binaries. Timo Do you have any ideas why this is happening ? Thank you again for the help. Best, Berk -----Timo <[email protected]<mailto:[email protected]>> schrieb: ----- An: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Von: Timo <[email protected]<mailto:[email protected]>> Datum: 14.05.2018 16:28 Kopie: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Betreff: Re: [DuMuX] Couple tracer model with 1p_1p test Hi Berk, a small addition: the multidomain branch (feature/multidomain-on-3.0) has been updated today to the master branch version (3.0-git). You can look at the 1ptracer test on branch master (or also on feature/multidomain-on-3.0) (https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/tree/master/test/porousmediumflow/tracer/1ptracer) and the 1p_1p test on branch feature/multidomain-on-3.0 (https://git.iws.uni-stuttgart.de/dumux-repositories/dumux/tree/feature/multidomain-on-3.0/test/multidomain/embedded/1d3d/1p_1p) Maybe this resolves some of the interface changes you were talking about. Please make sure that your Dumux version is correct (3.0-git) and compatible with your Dune version (2.6 release). Timo On 11.05.2018 15:48, Timo wrote: Dear Berk, it's a bit hard to follow. There is no dune1 and dune2. The newest release of Dune is Dune 2.6 for example. But the Dune version has nothing to do with the Dumux version. The branch the 1p_1p test is on is based on Dumux version 3.0 and the 1ptracer test is available on the master branch (also Dumux 3.0). These are unstable branches and the release will be around July. The latest release brach is 2.12 but it doesn't have the mixeddimensional 1d3d problem you are looking for yet. I'm working on a very similar model than your and yes this is no problem as I tried to explain in my previous mail. So which interfaces changed? And where do you think you need major changes? Here again is short what you have to do: Follow the 1ptracer example except in the first step you solve the 1p_1p problem. Then compute the fluxes and sources. The solve a tracer_tracer problem for the oxygen transport. The tracer_tracer problem will be similar to the 1p_1p problem except the subproblems (tissue/vessel) use the tracer model instead of the 1p model. Timo Am 11.05.2018 um 13:42 schrieb <[email protected]<mailto:[email protected]>> <[email protected]<mailto:[email protected]>>: Dear DuMux developers, When trying to couple the tracer model (localized in /dune2/dumux/test/porousmediumflow/tracer/1ptracer) with the 1p_1p test case (localized in /dune1/dumux/test/mixeddimension/embedded/1p_1p), I realized that these two models are in different versions of dumux, and that the functions used in the tracer model-code (in dune2 for me) are not defined anywhere in the dune1 version. This basically means for me, that there is no way of using this tracer model in the dune version I am actually using, without rewriting all the code necessary for every function the tracer problem uses. Am I getting this right ? Did anyone ever successfully couple the tracer model to another model in a different dune version with or without making major changes ? Thank you very much in advance. Best, Berk Nergiz _______________________________________________ Dumux mailing list [email protected]<mailto:[email protected]> https://listserv.uni-stuttgart.de/mailman/listinfo/dumux _______________________________________________ Dumux mailing list [email protected]<mailto:[email protected]> https://listserv.uni-stuttgart.de/mailman/listinfo/dumux <Output make test_1p_1p.pdf> _______________________________________________ Dumux mailing list [email protected]<mailto:[email protected]> https://listserv.uni-stuttgart.de/mailman/listinfo/dumux
_______________________________________________ Dumux mailing list [email protected] https://listserv.uni-stuttgart.de/mailman/listinfo/dumux
