Re: [DuMuX] Dumux with UMFpack
mber function ‘void Dune::SuperLU<Dune::BCRSMatrix<Dune::FieldMatrix<K, n, p>, TA> >::apply(Dune::SuperLU<Dune::BCRSMatrix<Dune::FieldMatrix<K, n, p>, TA> >::domain_type&, Dune::SuperLU<Dune::BCRSMatrix<Dune::FieldMatrix<K, n, p>, TA> >::range_type&, Dune::InverseOperatorResult&)’: /home/anowamooz/jda-332-aa/apps/Dumux_pile/dune-istl/dune/istl/superlu.hh:598:24: error: ‘DOUBLE’ was not declared in this scope options.IterRefine=DOUBLE; 4)Could all these errors be related to the version of gcc/g++ that I use? (gcc 4.8) Kind regards Ali Nowamooz *Subject: *** Re: [DuMuX] Dumux with UMFpack *Date: *** Wed, 1 Jun 2016 09:21:53 +0200 *From: *** Bernd Flemisch <be...@iws.uni-stuttgart.de> <mailto:be...@iws.uni-stuttgart.de> *Reply-To: *** DuMuX User Forum <dumux@listserv.uni-stuttgart.de> <mailto:dumux@listserv.uni-stuttgart.de> *To: *** DuMuX User Forum <dumux@listserv.uni-stuttgart.de> <mailto:dumux@listserv.uni-stuttgart.de> Hi Ali, can you post the output of make VERBOSE=1 test_windTunnelTopClosed And check whether in your folder /software6/libs/suitesparse/4.2.1_gcc/lib there is a library containing the routines, grep 'cholmod_start' *.so Kind regards Bernd On 05/22/2016 02:19 AM, Ali Nowamooz wrote: Dear Dumux users, I compiled Dumux with UMFpack to run the multi-domain simulations presented by Fetzer et al. 2016 (i.e., Effect of Turbulence and Roughness on Coupled Porous-Medium/Free-Flow Exchange Processes). I got the following errors that I couldn’t find any solution for them yet. I would like to know if anyone experienced the same problem and can help me with it. [anowamooz@colosse2 windTunnel]$ make Linking CXX executable test_windTunnelTopClosed /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_start' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_finish' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_free_factor' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_print_common' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `SuiteSparse_time' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_free_factor' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_free_sparse' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_transpose' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_analyze' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_transpose' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_free_sparse' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_finish' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_print_common' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_start' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_analyze' collect2: error: ld returned 1 exit status make[2]: *** [appl/multidomain/windTunnel/test_windTunnelTopClosed] Error 1 make[1]: *** [appl/multidomain/windTunnel/CMakeFiles/test_windTunnelTopClosed.dir/all] Error 2 make: *** [all] Error 2 Thanks in advance for your help Ali Nowamooz Research associate Université Laval Department of Geology and Geological Engineering Faculty of Science and Engineering Quebec (Quebec) – Canada ___ Dumux mailing list Dumux@listserv.uni-stuttgart.de <mailto:Dumux@listserv.uni-stuttgart.de> https://listserv.uni-stuttgart.de/mailman/listinfo/dumux -- ___ Bernd Flemisch phone: +49 711 685 69162 IWS, Universität Stuttgart fax: +49 711 685 60430 Pfaffenwaldring 61email:be...@iws.uni-stuttgart.de <mailto:be...@iws.uni-stuttgart.de> D-70569 Stuttgarturl:www.hydrosys.uni-stuttgart.de <http://www.hydrosys.uni-stuttgart.de> ___ ___ Dumux mailing list Dumux@listserv.uni-stuttgart.de https://listserv.uni-stuttgart.de/mailman/listinfo/dumux ___ Dumux mailing list Dumux@listserv.uni-stuttgart.de https://listserv.uni-stuttgart.de/mailman/listinfo/dumux
Re: [DuMuX] Dumux with UMFpack
ld-gcc/lib/libdunegeometry.a /rap/jda-332-aa/apps/Dumux_Pile_SS/dune-common/build-gcc/lib/libdunecommon.a -lmkl_gf_lp64 -lmkl_intel_lp64 -lmkl_gnu_thread -lmkl_core -lgomp -lpthread -lm /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_start' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_finish' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_free_factor' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_print_common' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `SuiteSparse_time' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_free_factor' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_free_sparse' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_transpose' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_analyze' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_transpose' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_free_sparse' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_finish' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_print_common' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_start' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_analyze' collect2: error: ld returned 1 exit status make[3]: *** [appl/multidomain/windTunnel/test_windTunnelTopClosed] Error 1 make[3]: Leaving directory `/rap/jda-332-aa/apps/Dumux_Pile_SS/dumux-Fetzer2015a/build-gcc' make[2]: *** [appl/multidomain/windTunnel/CMakeFiles/test_windTunnelTopClosed.dir/all] Error 2 make[2]: Leaving directory `/rap/jda-332-aa/apps/Dumux_Pile_SS/dumux-Fetzer2015a/build-gcc' make[1]: *** [appl/multidomain/windTunnel/CMakeFiles/test_windTunnelTopClosed.dir/rule] Error 2 make[1]: Leaving directory `/rap/jda-332-aa/apps/Dumux_Pile_SS/dumux-Fetzer2015a/build-gcc' make: *** [appl/multidomain/windTunnel/CMakeFiles/test_windTunnelTopClosed.dir/rule] Error 2 3) I also tried to compile the code using superlu but I got the following error (using superlu 4.3): In file included from /home/anowamooz/jda-332-aa/apps/Dumux_pile/dumux/dumux/linear/seqsolverbackend.hh:28:0, from /home/anowamooz/jda-332-aa/apps/Dumux_pile/dumux/dumux/linear/boxlinearsolver.hh:32, from /home/anowamooz/jda-332-aa/apps/Dumux_pile/dumux/dumux/nonlinear/newtoncontroller.hh:32, from /home/anowamooz/jda-332-aa/apps/Dumux_pile/dumux/dumux/implicit/common/implicitpropertydefaults.hh:29, from /home/anowamooz/jda-332-aa/apps/Dumux_pile/dumux/dumux/implicit/box/boxpropertydefaults.hh:29, from /home/anowamooz/jda-332-aa/apps/Dumux_pile/dumux/dumux/implicit/box/boxproperties.hh:59, from /home/anowamooz/jda-332-aa/apps/Dumux_pile/dumux/dumux/multidomain/common/multidomainlocaloperator.hh:30, from /home/anowamooz/jda-332-aa/apps/Dumux_pile/dumux/dumux/multidomain/common/subdomainpropertydefaults.hh:37, from /home/anowamooz/jda-332-aa/apps/Dumux_pile/dumux/dumux/multidomain/common/multidomainpropertydefaults.hh:44, from /home/anowamooz/jda-332-aa/apps/Dumux_pile/dumux/dumux/multidomain/common/multidomainmodel.hh:29, from /home/anowamooz/jda-332-aa/apps/Dumux_pile/dumux/dumux/multidomain/common/multidomainproblem.hh:29, from /home/anowamooz/jda-332-aa/apps/Dumux_pile/dumux-Fetzer2015a/appl/multidomain/windTunnel/2cnizeroeq2p2cniproblem.hh:34, from /home/anowamooz/jda-332-aa/apps/Dumux_pile/dumux-Fetzer2015a/appl/multidomain/windTunnel/test_windTunnelTopClosed.cc:36: /home/anowamooz/jda-332-aa/apps/Dumux_pile/dune-istl/dune/istl/superlu.hh: In member function ‘void Dune::SuperLU<Dune::BCRSMatrix<Dune::FieldMatrix<K, n, p>, TA> >::apply(Dune::SuperLU<Dune::BCRSMatrix<Dune::FieldMatrix<K, n, p>, TA> >::domain_type&, Dune::SuperLU<Dune::BCRSMatrix<Dune::FieldMatrix<K, n, p>, TA> >::range_type&, Dune::InverseOperatorResult&)’: /home/anowamooz/jda-332-aa/apps/Dumux_pile/dune-istl/dune/istl/superlu.hh:598:24: error: ‘DOUBLE’ was not declared in this scope options.IterRefine=DOUBLE; 4) Could all these errors be related to the version of gcc/g++ that I use? (gcc 4.8) Kind regards Ali Nowamooz Subject: Re: [DuMuX] Dumux with UMFpack Date: Wed, 1 Jun 2016 09:21:53 +0200 From: Bernd Flemisch <be...@iws.uni-stuttgart.de><mailto:be...@iw
Re: [DuMuX] Dumux with UMFpack
Hi Ali, SuiteSparse is package of several linear algebra algorithms including UMFPack. They are packaged in different ways depending on the SuiteSparse version and the Linux distribution. 1 ) You can add -lcholmod to the linker line, somewhere near the -lumfpack line. You get the linker line with VERBOSE=1 as mentioned by Bernd. 2) You can try building with static libraries. I haven't done this for a long time, I am not sure whether it works out of the box or what special flags are or avail. 3) Maybe it is worth a try to download the source code and built SuiteSparce. Then the libraries are not oddly chopped by the distribution. I assume this advice will not finally help. If you choose one way and run into further troubles, please report back. Bye Christoph -- The method has been developed for use on a high-speed electronic computer and would be impractical for hand-solution purposes. [Harlow & Welch 1965] signature.asc Description: OpenPGP digital signature ___ Dumux mailing list Dumux@listserv.uni-stuttgart.de https://listserv.uni-stuttgart.de/mailman/listinfo/dumux
[DuMuX] Dumux with UMFpack
Dear Dumux users, I compiled Dumux with UMFpack to run the multi-domain simulations presented by Fetzer et al. 2016 (i.e., Effect of Turbulence and Roughness on Coupled Porous-Medium/Free-Flow Exchange Processes). I got the following errors that I couldn't find any solution for them yet. I would like to know if anyone experienced the same problem and can help me with it. [anowamooz@colosse2 windTunnel]$ make Linking CXX executable test_windTunnelTopClosed /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_start' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_finish' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_free_factor' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_print_common' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `SuiteSparse_time' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_free_factor' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_free_sparse' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_transpose' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_analyze' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_transpose' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_free_sparse' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_finish' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_print_common' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_l_start' /software6/libs/suitesparse/4.2.1_gcc/lib/libumfpack.so: undefined reference to `cholmod_analyze' collect2: error: ld returned 1 exit status make[2]: *** [appl/multidomain/windTunnel/test_windTunnelTopClosed] Error 1 make[1]: *** [appl/multidomain/windTunnel/CMakeFiles/test_windTunnelTopClosed.dir/all] Error 2 make: *** [all] Error 2 Thanks in advance for your help Ali Nowamooz Research associate Université Laval Department of Geology and Geological Engineering Faculty of Science and Engineering Quebec (Quebec) - Canada ___ Dumux mailing list Dumux@listserv.uni-stuttgart.de https://listserv.uni-stuttgart.de/mailman/listinfo/dumux
