I decided to follow with the installation on the virtual linux machine because in this case I don’t get any complaints about additional software and I don’t need to comment any line in the installation script. I also commented the line in add_subdirectory(stokesdarcy) from the test/multidomain/boundary/CMakeLists.txt and I delete the folder build-cmake from the dumux directory and I still get the errors below on this laptop. I ran also the ./test_dumux. Sh and I got the following: Compiling a one-phase test using a cell-centered TPFA discretization (might take a while)... make: *** No rule to make target 'test_1pcctpfa'. Stop. Running simulation... ./test_dumux.sh: line 8: ./test_1pcctpfa: No such file or directory OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU OpenGL Warning: vboxCall failed with VBox status code VERR_BUFFER_OVERFLOW
OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU The errros at executing the installation script are shown below: CMake Error at /home/maria/projects/DuMuX/dumux/dune-common/cmake/modules/DuneTestMacros.cmake:255 (add_executable): add_executable cannot create target "test_stokes1pdarcy2pvertical" because another target with the same name already exists. The existing target is an executable created in source directory "/home/maria/projects/DuMuX/dumux/dumux/test/multidomain/boundary/stokesdarcy/1p_2p". See documentation for policy CMP0002 for more details. Call Stack (most recent call first): test/multidomain/boundary/stokesdarcy/1p_2p/CMakeLists.txt:5 (dune_add_test) CMake Error at /home/maria/projects/DuMuX/dumux/dune-common/cmake/modules/DuneTestMacros.cmake:255 (add_executable): add_executable cannot create target "test_stokes1p2cdarcy1p2chorizontal" because another target with the same name already exists. The existing target is an executable created in source directory "/home/maria/projects/DuMuX/dumux/dumux/test/multidomain/boundary/stokesdarcy/1p2c_1p2c/horizontalflow". See documentation for policy CMP0002 for more details. Call Stack (most recent call first): test/multidomain/boundary/stokesdarcy/1p2c_1p2c/horizontalflow/CMakeLists.txt:5 (dune_add_test) CMake Error at /home/maria/projects/DuMuX/dumux/dune-common/cmake/modules/DuneTestMacros.cmake:255 (add_executable): add_executable cannot create target "test_stokes1p2cdarcy2p2chorizontal" because another target with the same name already exists. The existing target is an executable created in source directory "/home/maria/projects/DuMuX/dumux/dumux/test/multidomain/boundary/stokesdarcy/1p2c_2p2c". See documentation for policy CMP0002 for more details. Call Stack (most recent call first): test/multidomain/boundary/stokesdarcy/1p2c_2p2c/CMakeLists.txt:5 (dune_add_test) CMake Error at /home/maria/projects/DuMuX/dumux/dune-common/cmake/modules/DuneTestMacros.cmake:255 (add_executable): add_executable cannot create target "test_stokes1pdarcy2pvertical" because another target with the same name already exists. The existing target is an executable created in source directory "/home/maria/projects/DuMuX/dumux/dumux/test/multidomain/boundary/stokesdarcy/1p_2p". See documentation for policy CMP0002 for more details. Call Stack (most recent call first): test/multidomain/boundary/stokesdarcy/1p_2p/CMakeLists.txt:5 (dune_add_test) CMake Error at /home/maria/projects/DuMuX/dumux/dune-common/cmake/modules/DuneTestMacros.cmake:255 (add_executable): add_executable cannot create target "test_stokes1p2cdarcy1p2chorizontal" because another target with the same name already exists. The existing target is an executable created in source directory "/home/maria/projects/DuMuX/dumux/dumux/test/multidomain/boundary/stokesdarcy/1p2c_1p2c/horizontalflow". See documentation for policy CMP0002 for more details. Call Stack (most recent call first): test/multidomain/boundary/stokesdarcy/1p2c_1p2c/horizontalflow/CMakeLists.txt:5 (dune_add_test) CMake Error at /home/maria/projects/DuMuX/dumux/dune-common/cmake/modules/DuneTestMacros.cmake:255 (add_executable): add_executable cannot create target "test_stokes1p2cdarcy2p2chorizontal" because another target with the same name already exists. The existing target is an executable created in source directory "/home/maria/projects/DuMuX/dumux/dumux/test/multidomain/boundary/stokesdarcy/1p2c_2p2c". See documentation for policy CMP0002 for more details. Call Stack (most recent call first): test/multidomain/boundary/stokesdarcy/1p2c_2p2c/CMakeLists.txt:5 (dune_add_test) From: Timo Koch <[email protected]> Sent: 16. juli 2018 13:35 To: Maria Bonto <[email protected]> Cc: [email protected] Subject: Re: [DuMuX] Error while installing dumux Hi Maria, you can choose your compiler in the file “cmake.opts” that was downloaded to the newly created folder. Replace the lines /usr/bin/g++ and /usr/bin/gcc by a path to a newer compiler, maybe /usr/bin/gcc is still pointing to 4.2.1. By the way gcc 4.9 is still ancient. There is gcc 8.1, you can install it with homebrew. After you replace the lines, delete the build directories by typing “rm -rf d*/build-cmake” and run dune control again “./dune-common/bin/dunecontrol —opts=cmake.opts all”. Maybe that helps. Timo On 16. Jul 2018, at 13:20, Maria Bonto <[email protected]<mailto:[email protected]>> wrote: I just eliminated paraview from that line. However, I had to comment the paragraph below because it says that gcc version is 4.2.1 and it needs at least 4.9.0. I downloaded a new one and added it to the path. When I type gcc --version it says 4.9.4. However, in the installation I still got the same error. see below: DuMuX mac$ gcc --version gcc (Homebrew GCC 4.9.4_1) 4.9.4 Copyright (C) 2015 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. Moreover, I tried the installation (with all the lines in the script) on another laptop on a virtual linux environment. I don't get any complaints about gcc, paraview etc, but I get exactly the same error related to Cmake, as the error I get on my Mac. ________________________________ De: Timo Koch <[email protected]<mailto:[email protected]>> Enviado: lunes, 16 de julio de 2018 13:14:39 Para: [email protected]<mailto:[email protected]>; Maria Bonto Asunto: Re: [DuMuX] Error while installing dumux Hi Maria, most likely it cannot find paraview because it's installed as an app on macOS. Can you only delete paraview from the script in that line and not comment the whole line. The other checks are important. You probably need a newer compiler. Can you type the output of gcc --version? Timo On 16.07.2018 13:09, Maria Bonto wrote: This does not work. I get the following errors below. When I first started installing the software on the Mac I got an error about paraview. It was saying that paraview was not installed when it actually was installed. So I was told to comment that line where the script checks paraview. I can see in the last line that it complains again about paraview. /Volumes/MARY/DuMuX/dumux/dune-alugrid/dune/alugrid/common/memory.hh:184:14: error: thread-local storage is not supported for the current target static thread_local MemoryPoolType pool; ^ In file included from /Volumes/MARY/DuMuX/dumux/dumux/test/porousmediumflow/1p/implicit/test_1pfv.cc:35<http://test_1pfv.cc:35/>: In file included from /Volumes/MARY/DuMuX/dumux/dumux/test/porousmediumflow/1p/implicit/1ptestproblem.hh:30: In file included from /Volumes/MARY/DuMuX/dumux/dumux/dumux/discretization/cellcentered/tpfa/properties.hh:30: In file included from /Volumes/MARY/DuMuX/dumux/dumux/dumux/common/boundaryflag.hh:36: In file included from /Volumes/MARY/DuMuX/dumux/dune-subgrid/dune/subgrid/subgrid.hh:28: /Volumes/MARY/DuMuX/dumux/dune-subgrid/dune/subgrid/subgrid/subgridleafintersectioniterator.hh:5:10: fatal error: 'tr1/memory' file not found #include <tr1/memory> ^ 2 errors generated. make[3]: *** [test/porousmediumflow/1p/implicit/CMakeFiles/test_1pcctpfa.dir/test_1pfv.cc.o] Error 1 make[2]: *** [test/porousmediumflow/1p/implicit/CMakeFiles/test_1pcctpfa.dir/all] Error 2 make[1]: *** [test/porousmediumflow/1p/implicit/CMakeFiles/test_1pcctpfa.dir/rule] Error 2 make: *** [test/porousmediumflow/1p/implicit/CMakeFiles/test_1pcctpfa.dir/rule] Error 2 Running simulation... ./test_dumux.sh: line 8: ./test_1pcctpfa: No such file or directory ./test_dumux.sh: line 9: paraview: command not found ________________________________ De: Bernd Flemisch <[email protected]><mailto:[email protected]> Enviado: lunes, 16 de julio de 2018 12:59:25 Para: Maria Bonto; DuMuX User Forum Asunto: Re: [DuMuX] Error while installing dumux Ok. Try a cd /Volumes/MARY/DuMuX/dumux ./test_dumux.sh Bernd On 07/16/2018 12:55 PM, Maria Bonto wrote: I did that. I didn't get any errors in this case. Configuring done -- Generating done -- Build files have been written to: /Volumes/MARY/DuMuX/dumux/dumux/build-cmake --- calling make for dumux --- build directory: build-cmake cmake --build . -- --- dumux done --- --- done --- ________________________________ De: Bernd Flemisch <[email protected]><mailto:[email protected]> Enviado: lunes, 16 de julio de 2018 12:49:26 Para: Maria Bonto; DuMuX User Forum Asunto: Re: [DuMuX] Error while installing dumux Can you remove the line, then do a cd /Volumes/MARY/DuMuX/dumux/ rm -rf dumux/build-cmake ./dune-common/bin/dunecontrol --opts=cmake.opts --only=dumux all and see if that works? Bernd On 07/16/2018 12:33 PM, Maria Bonto wrote: Dear Bernd, I did what you suggested and I still get the same errors. After running the script again I saw that the folder is created again and also the line that I removed. I tried the same procedure several times but I still get the following errors: CMake Error at /Volumes/MARY/DuMuX/dumux/dune-common/cmake/modules/DuneTestMacros.cmake:255 (add_executable): add_executable cannot create target "test_stokes1pdarcy2pvertical" because another target with the same name already exists. The existing target is an executable created in source directory "/Volumes/MARY/DuMuX/dumux/dumux/test/multidomain/boundary/stokesdarcy/1p_2p". See documentation for policy CMP0002 for more details. Call Stack (most recent call first): test/multidomain/boundary/stokesdarcy/1p_2p/CMakeLists.txt:5 (dune_add_test) CMake Error at /Volumes/MARY/DuMuX/dumux/dune-common/cmake/modules/DuneTestMacros.cmake:255 (add_executable): add_executable cannot create target "test_stokes1p2cdarcy1p2chorizontal" because another target with the same name already exists. The existing target is an executable created in source directory "/Volumes/MARY/DuMuX/dumux/dumux/test/multidomain/boundary/stokesdarcy/1p2c_1p2c/horizontalflow". See documentation for policy CMP0002 for more details. Call Stack (most recent call first): test/multidomain/boundary/stokesdarcy/1p2c_1p2c/horizontalflow/CMakeLists.txt:5 (dune_add_test) CMake Error at /Volumes/MARY/DuMuX/dumux/dune-common/cmake/modules/DuneTestMacros.cmake:255 (add_executable): add_executable cannot create target "test_stokes1p2cdarcy2p2chorizontal" because another target with the same name already exists. The existing target is an executable created in source directory "/Volumes/MARY/DuMuX/dumux/dumux/test/multidomain/boundary/stokesdarcy/1p2c_2p2c". See documentation for policy CMP0002 for more details. Call Stack (most recent call first): test/multidomain/boundary/stokesdarcy/1p2c_2p2c/CMakeLists.txt:5 (dune_add_test) Regards, María. ________________________________ De: Bernd Flemisch <[email protected]><mailto:[email protected]> Enviado: lunes, 16 de julio de 2018 11:56:19 Para: Maria Bonto; DuMuX User Forum Asunto: Re: [DuMuX] Error while installing dumux Ok, thank you. Apparently, the constructions that we do in the CMakeLists.txt of test/multidomain/boundary/stokesdarcy/1p_2p and test/multidomain/boundary/stokesdarcy/1p2c_2p2c result in problems on your Mac. As a temporary workaround to get things running, it should be ok to comment/remove the line add_subdirectory(stokesdarcy) from test/multidomain/boundary/CMakeLists.txt, remove the folder build-cmake from your dumux directory and run the script again. Meanwhile, we will try to fix the problem in the offending CMakeLists.txt. Kind regards Bernd On 07/16/2018 11:45 AM, Maria Bonto wrote: Dear Bernd, I started again from the beginning but I still get the same errors. Regards, María. ________________________________ De: Bernd Flemisch <[email protected]><mailto:[email protected]> Enviado: lunes, 16 de julio de 2018 11:34:33 Para: Maria Bonto; DuMuX User Forum Asunto: Re: [DuMuX] Error while installing dumux Can you maybe try to restart from scratch? Kind regards Bernd On 07/16/2018 11:25 AM, Maria Bonto wrote: I installed gfortran 4.9.2, but I still get errors. I attach the new console output. ________________________________ De: Bernd Flemisch <[email protected]><mailto:[email protected]> Enviado: lunes, 16 de julio de 2018 10:50:26 Para: Maria Bonto Asunto: Re: [DuMuX] Error while installing dumux Ok, you need a Fortran compiler. On Mac, you might want to want to consider https://scicomp.stackexchange.com/questions/2469/how-should-i-install-a-fortran-compiler-on-a-mac-os-x-10-x-x-4 [Image removed by sender.]<https://scicomp.stackexchange.com/questions/2469/how-should-i-install-a-fortran-compiler-on-a-mac-os-x-10-x-x-4> How should I install a Fortran compiler on a Mac? (OS X 10 ...<https://scicomp.stackexchange.com/questions/2469/how-should-i-install-a-fortran-compiler-on-a-mac-os-x-10-x-x-4> scicomp.stackexchange.com<http://scicomp.stackexchange.com/> Related question: State of the Mac OS in Scientific Computing and HPC A significant number of software packages in computational science are written in Fortran, and Fortran isn't going away. Kind regards Bernd On 07/16/2018 10:37 AM, Maria Bonto wrote: Dear Bernd, Attached please find a txt. file with the console messages after running the installation script. Regards, María. ________________________________ De: Bernd Flemisch <[email protected]><mailto:[email protected]> Enviado: lunes, 16 de julio de 2018 10:28:20 Para: DuMuX User Forum; Maria Bonto Asunto: Re: [DuMuX] Error while installing dumux Hi Maria, can you please also post the console output that you get from the install script or from running dunecontrol directly? Kind regards Bernd On 07/16/2018 10:13 AM, Maria Bonto wrote: Dear Sir/Madam, I was trying to install dumux on a Mac OS X 10.10 for the dumux course but I get the following error: failed to build the dune libraries. I am attaching the error log file I get. Thank you in advance. Best regards, María. _______________________________________________ Dumux mailing list [email protected]<mailto:[email protected]> https://listserv.uni-stuttgart.de/mailman/listinfo/dumux -- _______________________________________________________________ Bernd Flemisch phone: +49 711 685 69162 IWS, Universität Stuttgart fax: +49 711 685 60430 Pfaffenwaldring 61 email: [email protected]<mailto:[email protected]> D-70569 Stuttgart url: www.hydrosys.uni-stuttgart.de<http://www.hydrosys.uni-stuttgart.de/> _______________________________________________________________ -- _______________________________________________________________ Bernd Flemisch phone: +49 711 685 69162 IWS, Universität Stuttgart fax: +49 711 685 60430 Pfaffenwaldring 61 email: [email protected]<mailto:[email protected]> D-70569 Stuttgart url: www.hydrosys.uni-stuttgart.de<http://www.hydrosys.uni-stuttgart.de/> _______________________________________________________________ -- _______________________________________________________________ Bernd Flemisch phone: +49 711 685 69162 IWS, Universität Stuttgart fax: +49 711 685 60430 Pfaffenwaldring 61 email: [email protected]<mailto:[email protected]> D-70569 Stuttgart url: www.hydrosys.uni-stuttgart.de<http://www.hydrosys.uni-stuttgart.de/> _______________________________________________________________ -- _______________________________________________________________ Bernd Flemisch phone: +49 711 685 69162 IWS, Universität Stuttgart fax: +49 711 685 60430 Pfaffenwaldring 61 email: [email protected]<mailto:[email protected]> D-70569 Stuttgart url: www.hydrosys.uni-stuttgart.de<http://www.hydrosys.uni-stuttgart.de/> _______________________________________________________________ -- _______________________________________________________________ Bernd Flemisch phone: +49 711 685 69162 IWS, Universität Stuttgart fax: +49 711 685 60430 Pfaffenwaldring 61 email: [email protected]<mailto:[email protected]> D-70569 Stuttgart url: www.hydrosys.uni-stuttgart.de<http://www.hydrosys.uni-stuttgart.de/> _______________________________________________________________ -- _______________________________________________________________ Bernd Flemisch phone: +49 711 685 69162 IWS, Universität Stuttgart fax: +49 711 685 60430 Pfaffenwaldring 61 email: [email protected]<mailto:[email protected]> D-70569 Stuttgart url: www.hydrosys.uni-stuttgart.de<http://www.hydrosys.uni-stuttgart.de/> _______________________________________________________________ _______________________________________________ Dumux mailing list [email protected]<mailto:[email protected]> https://listserv.uni-stuttgart.de/mailman/listinfo/dumux
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