Feature/fs1519 suitesparse ldl spqr

What is the reason to have this no-op method? Is there some value to gain from having all suitesparse wrappers fulfill the same interface? Is there an ldl control array and it is just not implemented?

Hi @dominic . Are you referring to setOption? If so, I added it in order to have exactly the same methods of umfpack. I think it is necessary because you can change the solver in your code with only a typedef without the need of commenting out any methods. I don't think there is a ldl control array but I can take a look again to see if I have missed it.

@marco.agnese istl does not have any type of parameter interface. To some extent this is what we want to achieve in the feature/istl-ini branch, where all components will get an additional interface to configure via a ParameterTree

@christi I don't get your comment. setOption is already used by UMFPack bindings. How is ParameterTree related to Marco's code?

Same question here.

Same answer here

Those additional solvers use ColCompMatrix as internal matrix structure and set the StoresColumnCompressed capability to true. I would conclude, that it is possible without further adjustments to plug them into the overlapping schwarz code. It would be nice if this could be tested. The guard in https://gitlab.dune-project.org/core/dune-istl/blob/master/dune/istl/overlappingschwarz.hh#L313 has to be changed for that though (btw I think this guarding could be safely deleted!)

Yes, I can remove the guard and add a preprocessor variable into https://gitlab.dune-project.org/core/dune-istl/blob/master/dune/istl/test/overlappingschwarztest.cc in order to choose the direct solver in the test. What do you think?

Yes, it would be very nice if that works out of the box.

@dominic Since I cannot push any change to the branch do you want to do the change yourself or how it works?

@marco.agnese I have given you developer status, which allows you to push to feature branches.

Added 9 commits:

4a0f4cdb...f8774757 - 8 commits from branch master
6105a90a - Merge branch 'master' into feature/FS1519-suitesparse-ldl-spqr

Added 1 commit:

be1c8442 - test overlappingschwartz also with SPQR and LDL

@dominic I have implemented the change but I have trouble testing it since the build-system found SuperLU but it seems that there are some missing headers so it fails to compile the test. May you test it?

I have tested your branch. There seems to be some problem in SPQR:

/home/dominic/dune/dune-istl/dune/istl/spqr.hh: In member function ‘virtual void Dune::SPQR<Dune::BCRSMatrix<Dune::FieldMatrix<K, n, p>, TA> >::apply(Dune::SPQR<Dune::BCRSMatrix<Dune::FieldMatrix<K, n, p>, TA> >::domain_type&, Dune::SPQR<Dune::BCRSMatrix<Dune::FieldMatrix<K, n, p>, TA> >::range_type&, Dune::InverseOperatorResult&)’:
/home/dominic/dune/dune-istl/dune/istl/spqr.hh:154:42: error: ‘cholmod_common’ has no member named ‘SPQR_flopcount’
         std::cout<<"Flops Taken: "<<cc_->SPQR_flopcount<<std::endl;
                                          ^
/home/dominic/dune/dune-istl/dune/istl/spqr.hh:155:44: error: ‘cholmod_common’ has no member named ‘SPQR_analyze_time’
         std::cout<<"Analysis Time: "<<cc_->SPQR_analyze_time<<" s"<<std::endl;
                                            ^
/home/dominic/dune/dune-istl/dune/istl/spqr.hh:156:45: error: ‘cholmod_common’ has no member named ‘SPQR_factorize_time’
         std::cout<<"Factorize Time: "<<cc_->SPQR_factorize_time<<" s"<<std::endl;
                                             ^
/home/dominic/dune/dune-istl/dune/istl/spqr.hh:157:45: error: ‘cholmod_common’ has no member named ‘SPQR_solve_time’
         std::cout<<"Backsolve Time: "<<cc_->SPQR_solve_time<<" s"<<std::endl;

I have also problem with spqrtest. At linking stage I have these errors:

/usr/local_machine/suitesparse-4.4.0/lib/libspqr.a(spqr_larftb.o): In function `void spqr_larftb<double>(int, long, long, long, long, long, double*, double*, double*, double*, cholmod_common_struct*)':
spqr_larftb.cpp:(.text._Z11spqr_larftbIdEvilllllPT_S1_S1_S1_P21cholmod_common_struct[_Z11spqr_larftbIdEvilllllPT_S1_S1_S1_P21cholmod_common_struct]+0x2c3): undefined reference to `dlarfb_'
spqr_larftb.cpp:(.text._Z11spqr_larftbIdEvilllllPT_S1_S1_S1_P21cholmod_common_struct[_Z11spqr_larftbIdEvilllllPT_S1_S1_S1_P21cholmod_common_struct]+0x3b9): undefined reference to `dlarft_'
spqr_larftb.cpp:(.text._Z11spqr_larftbIdEvilllllPT_S1_S1_S1_P21cholmod_common_struct[_Z11spqr_larftbIdEvilllllPT_S1_S1_S1_P21cholmod_common_struct]+0x673): undefined reference to `dlarft_'
spqr_larftb.cpp:(.text._Z11spqr_larftbIdEvilllllPT_S1_S1_S1_P21cholmod_common_struct[_Z11spqr_larftbIdEvilllllPT_S1_S1_S1_P21cholmod_common_struct]+0x711): undefined reference to `dlarft_'
spqr_larftb.cpp:(.text._Z11spqr_larftbIdEvilllllPT_S1_S1_S1_P21cholmod_common_struct[_Z11spqr_larftbIdEvilllllPT_S1_S1_S1_P21cholmod_common_struct]+0x7a8): undefined reference to `dlarft_'
/usr/local_machine/suitesparse-4.4.0/lib/libspqr.a(spqr_larftb.o): In function `void spqr_larftb<std::complex<double> >(int, long, long, long, long, long, std::complex<double>*, std::complex<double>*, std::complex<double>*, std::complex<double>*, cholmod_common_struct*)':
spqr_larftb.cpp:(.text._Z11spqr_larftbISt7complexIdEEvilllllPT_S3_S3_S3_P21cholmod_common_struct[_Z11spqr_larftbISt7complexIdEEvilllllPT_S3_S3_S3_P21cholmod_common_struct]+0x2c3): undefined reference to `zlarfb_'
spqr_larftb.cpp:(.text._Z11spqr_larftbISt7complexIdEEvilllllPT_S3_S3_S3_P21cholmod_common_struct[_Z11spqr_larftbISt7complexIdEEvilllllPT_S3_S3_S3_P21cholmod_common_struct]+0x3b9): undefined reference to `zlarft_'
spqr_larftb.cpp:(.text._Z11spqr_larftbISt7complexIdEEvilllllPT_S3_S3_S3_P21cholmod_common_struct[_Z11spqr_larftbISt7complexIdEEvilllllPT_S3_S3_S3_P21cholmod_common_struct]+0x673): undefined reference to `zlarft_'
spqr_larftb.cpp:(.text._Z11spqr_larftbISt7complexIdEEvilllllPT_S3_S3_S3_P21cholmod_common_struct[_Z11spqr_larftbISt7complexIdEEvilllllPT_S3_S3_S3_P21cholmod_common_struct]+0x711): undefined reference to `zlarft_'
spqr_larftb.cpp:(.text._Z11spqr_larftbISt7complexIdEEvilllllPT_S3_S3_S3_P21cholmod_common_struct[_Z11spqr_larftbISt7complexIdEEvilllllPT_S3_S3_S3_P21cholmod_common_struct]+0x7a8): undefined reference to `zlarft_'
/usr/local_machine/suitesparse-4.4.0/lib/libspqr.a(spqr_front.o): In function `long spqr_front<double>(long, long, long, double, long, long, double*, long*, char*, double*, double*, double*, double*, cholmod_common_struct*)':
spqr_front.cpp:(.text._Z10spqr_frontIdElllldllPT_PlPcS1_S1_PdS4_P21cholmod_common_struct[_Z10spqr_frontIdElllldllPT_PlPcS1_S1_PdS4_P21cholmod_common_struct]+0x656): undefined reference to `dlarfg_'
spqr_front.cpp:(.text._Z10spqr_frontIdElllldllPT_PlPcS1_S1_PdS4_P21cholmod_common_struct[_Z10spqr_frontIdElllldllPT_PlPcS1_S1_PdS4_P21cholmod_common_struct]+0x936): undefined reference to `dlarf_'
/usr/local_machine/suitesparse-4.4.0/lib/libspqr.a(spqr_front.o): In function `long spqr_front<std::complex<double> >(long, long, long, double, long, long, std::complex<double>*, long*, char*, std::complex<double>*, std::complex<double>*, double*, double*, cholmod_common_struct*)':
spqr_front.cpp:(.text._Z10spqr_frontISt7complexIdEElllldllPT_PlPcS3_S3_PdS6_P21cholmod_common_struct[_Z10spqr_frontISt7complexIdEElllldllPT_PlPcS3_S3_PdS6_P21cholmod_common_struct]+0x67e): undefined reference to `zlarfg_'
spqr_front.cpp:(.text._Z10spqr_frontISt7complexIdEElllldllPT_PlPcS3_S3_PdS6_P21cholmod_common_struct[_Z10spqr_frontISt7complexIdEElllldllPT_PlPcS3_S3_PdS6_P21cholmod_common_struct]+0x9c2): undefined reference to `zlarf_'

Do you experience something similar?

Does spqrtest work for you both? It works for be, but I get the following compiler error:

[  0%] Building CXX object dune/istl/test/CMakeFiles/overlappingschwarztest.dir/overlappingschwarztest.cc.o
In file included from /temp/gruenich/dune/complete/dune-istl/dune/istl/test/overlappingschwarztest.cc:12:
/temp/gruenich/dune/complete/dune-istl/dune/istl/overlappingschwarz.hh:1248:18: error: no matching member function for call to 'apply'
        sdsolver.apply(assigner.lhs(), assigner.rhs());
        ~~~~~~~~~^~~~~
/temp/gruenich/dune/complete/dune-istl/dune/istl/overlappingschwarz.hh:662:19: note: in instantiation of function template specialization 'Dune::SeqOverlappingSchwarz<Dune::BCRSMatrix<Dune::FieldMatrix<double, 1, 1>, std::allocator<Dune::FieldMatrix<double, 1, 1> > >,
      Dune::BlockVector<Dune::FieldVector<double, 1>, std::allocator<Dune::FieldVector<double, 1> > >, Dune::AdditiveSchwarzMode, Dune::SPQR<Dune::BCRSMatrix<Dune::FieldMatrix<double, 1, 1>, std::allocator<Dune::FieldMatrix<double, 1, 1> > > >,
      std::allocator<Dune::BlockVector<Dune::FieldVector<double, 1>, std::allocator<Dune::FieldVector<double, 1> > > > >::apply<true>' requested here
      sm.template apply<true>(v, b);
                  ^
/temp/gruenich/dune/complete/dune-istl/dune/istl/overlappingschwarz.hh:1217:58: note: in instantiation of member function 'Dune::SeqOverlappingSchwarzApplier<Dune::SeqOverlappingSchwarz<Dune::BCRSMatrix<Dune::FieldMatrix<double, 1, 1>,
      std::allocator<Dune::FieldMatrix<double, 1, 1> > >, Dune::BlockVector<Dune::FieldVector<double, 1>, std::allocator<Dune::FieldVector<double, 1> > >, Dune::AdditiveSchwarzMode, Dune::SPQR<Dune::BCRSMatrix<Dune::FieldMatrix<double, 1, 1>,
      std::allocator<Dune::FieldMatrix<double, 1, 1> > > >, std::allocator<Dune::BlockVector<Dune::FieldVector<double, 1>, std::allocator<Dune::FieldVector<double, 1> > > > > >::apply' requested here
    SeqOverlappingSchwarzApplier<SeqOverlappingSchwarz>::apply(*this, x, b);
                                                         ^
/temp/gruenich/dune/complete/dune-istl/dune/istl/test/overlappingschwarztest.cc:176:29: note: in instantiation of member function 'Dune::SeqOverlappingSchwarz<Dune::BCRSMatrix<Dune::FieldMatrix<double, 1, 1>, std::allocator<Dune::FieldMatrix<double, 1, 1> > >,
      Dune::BlockVector<Dune::FieldVector<double, 1>, std::allocator<Dune::FieldVector<double, 1> > >, Dune::AdditiveSchwarzMode, Dune::SPQR<Dune::BCRSMatrix<Dune::FieldMatrix<double, 1, 1>, std::allocator<Dune::FieldMatrix<double, 1, 1> > > >,
      std::allocator<Dune::BlockVector<Dune::FieldVector<double, 1>, std::allocator<Dune::FieldVector<double, 1> > > > >::apply' requested here
      Dune::SPQR<BCRSMat> > spqr_prec0(mat, domains, 1);
                            ^
/temp/gruenich/dune/complete/dune-istl/dune/istl/spqr.hh:134:18: note: candidate function not viable: requires 3 arguments, but 2 were provided
    virtual void apply(domain_type& x, range_type& b, InverseOperatorResult& res)
                 ^
/temp/gruenich/dune/complete/dune-istl/dune/istl/spqr.hh:164:18: note: candidate function not viable: requires 4 arguments, but 2 were provided
    virtual void apply (domain_type& x, range_type& b, double reduction, InverseOperatorResult& res)
                 ^
1 error generated.

@gruenich it compiles but it does NOT link, see my previous message. Do you have any clue what is wrong? I am using SPQR in DUNE-FEM and I don't have any linking issue so FindSuiteSparse seems perfectly working.

I edited your comments to use ``` around the copied error messages, its so hard to read otherwise.

Wow, 3 testers, 3 different errors. I have SuiteSparse 4.2.1, Marcos has 4.4.0. This might be a problem source.

Concerning Marcos error, I guess that the Suitesparse check does not gather the correct set of libraries to link for SPQR.

Mine, I have no clue.

Christophs, I think, revealed the hidden assumption of the overlapping schwarz code, that the solver has an apply method taking to plain c arrays (no idea why that is so).

@dominic When I implemented the wrappers I was using SuiteSparse 4.2.1 therefore I am pretty sure that cc_->SPQR_flopcount and the other members are available also in that version

Title changed from Feature/fs1519 suitesparse ldl spqr to [WIP] Feature/fs1519 suitesparse ldl spqr

Added 15 commits:

be1c8442...f9aede6e - 13 commits from branch master
4bac91be - Merge branch 'master' into feature/FS1519-suitesparse-ldl-spqr
ab1d4887 - Merge branch 'master' into feature/FS1519-suitesparse-ldl-spqr

Added 1 commit:

4c9e6cf4 - fix includes, remove useless preprocessor variables and use std::exceptions

Added 1 commit:

1c4164a5 - fix include config

Added 11 commits:

3a5c3d6a - [bugfix] Produce a linker error when pardiso lib is not found
8fa53e4b - [fixup] correctly nest namespace and ifdef directive
05561591 - [pardiso] update the Pardiso preconditioner to current Dune and Pardiso versions
a3ae2c23 - Typo
ca6e0ddb - bvector: Fix NaN behaviour of infinity_norm()
ef237c59 - bcrsmatrix: Fix NaN behaviour of infinity_norm()
56be52b3 - matrix: Fix NaN behaviour of infinity_norm()
349df800 - Test complex for floating point T only
8d58bc2d - [bugfix] fix broken assertion.
033153ea - fix includes, remove useless preprocessor variables and use std::exceptions
37ac9466 - Merge branch 'feature/FS1519-suitesparse-ldl-spqr' of ssh://gitlab.dune-project.…

According to Tim Davis (the developer of SuiteSparse) to fix my linking error: "You have to link SPQR to LAPACK". I tried to edit manually the CMake cache but it didn't work. What do I have to change into FindSuiteSparse in order to link lapack to SPQR? I tried different things but the error was always there.

You have to execute find_package(LAPACK). After that you can use the variables exported, which are listed in cmake --help-module FindLAPACK.

Marco, please give dune-common's feature/fs1519-add-lapack-to-suitesparse a try. It is not properly tested by myself, as I have a broken SuiteSparse package on this computer.

Hi @gruenich, thank you for your help. This was exactly what I tried. It add the lapack flag to the linker but the error is still present and it is exactly the same. Maybe a problem of flag ordering?

The fun part is that the wrapper for SPQR which I wrote inside dune-fem links correctly. How is this possible since it uses FindSuiteSparse of dune-common?

Have you deleted the build directory of both common and istl? What code from dune-fem are you referring to? I could not find an executable including SPQR when I had a quick look into fem's repository.
You can compare how the linker was invoked with make yourtarget VERBOSE=true and then compare or post both here.

Yes I have delete the build directory of both common and istl. In dune-fem there are only the wrappers but there aren't any tests yet. I am using SPQR in one of my codes which are based on dune-fem. If I compile spqrtest the linking flags are

/usr/bin/c++   -O3 -Wall -funroll-loops -finline-functions -fomit-frame-pointer -ffast-math -mfpmath=sse -msse3 -std=c++11     -Wl,-no-as-needed -pthread CMakeFiles/spqrtest.dir/spqrtest.cc.o  -o spqrtest -rdynamic /usr/local_machine/dune-trunk/build/dune-common/lib/libdunecommon.a /usr/local_machine/suitesparse-4.4.0/lib/libumfpack.a /usr/local_machine/suitesparse-4.4.0/lib/libcholmod.a /usr/local_machine/suitesparse-4.4.0/lib/libamd.a /usr/local_machine/suitesparse-4.4.0/lib/libcamd.a /usr/local_machine/suitesparse-4.4.0/lib/libcolamd.a /usr/local_machine/suitesparse-4.4.0/lib/libccolamd.a /usr/local_machine/suitesparse-4.4.0/lib/libldl.a /usr/local_machine/suitesparse-4.4.0/lib/libspqr.a /usr/local_machine/suitesparse-4.4.0/lib/libsuitesparseconfig.a /usr/local_machine/suitesparse-4.4.0/lib/libumfpack.a /usr/local_machine/suitesparse-4.4.0/lib/libcholmod.a /usr/local_machine/suitesparse-4.4.0/lib/libamd.a /usr/local_machine/suitesparse-4.4.0/lib/libcamd.a /usr/local_machine/suitesparse-4.4.0/lib/libcolamd.a /usr/local_machine/suitesparse-4.4.0/lib/libccolamd.a /usr/local_machine/suitesparse-4.4.0/lib/libsuitesparseconfig.a -lsuperlu /usr/lib/libf77blas.so.3gf /usr/lib/libatlas.so.3gf /usr/local_machine/parmetis-4.0.3/lib/libparmetis.a /usr/local_machine/parmetis-4.0.3/lib/libmetis.a -lm -pthread /usr/local_machine/openmpi-1.8.4/lib/libmpi.so /usr/local_machine/parmetis-4.0.3/lib/libmetis.a -lm -lgmp -lgmpxx -pthread /usr/local_machine/openmpi-1.8.4/lib/libmpi.so /usr/local_machine/suitesparse-4.4.0/lib/libldl.a /usr/local_machine/suitesparse-4.4.0/lib/libspqr.a -lsuperlu /usr/lib/libf77blas.so.3gf /usr/lib/libatlas.so.3gf /usr/local_machine/parmetis-4.0.3/lib/libparmetis.a /usr/local_machine/parmetis-4.0.3/lib/libmetis.a -lm /usr/local_machine/openmpi-1.8.4/lib/libmpi.so -lgmp -lgmpxx /usr/local_machine/parmetis-4.0.3/lib/libmetis.a -lm /usr/local_machine/openmpi-1.8.4/lib/libmpi.so -lgmp -lgmpxx -Wl,-rpath,/usr/local_machine/openmpi-1.8.4/lib

while with dune-fem are

/usr/bin/c++   -O3 -Wall -funroll-loops -finline-functions -fomit-frame-pointer -ffast-math -mfpmath=sse -msse3 -std=c++11     -Wl,-no-as-needed -pthread CMakeFiles/dune-navier-stokes.dir/dune-navier-stokes.cc.o  -o dune-navier-stokes -rdynamic /usr/local_machine/dune-trunk/build/dune-fem/lib/libdunefem.a /usr/local_machine/dune-trunk/build/dune-alugrid/lib/libdunealugrid.a /usr/local_machine/dune-trunk/build/dune-grid/lib/libdunealbertagrid_3d.a /usr/local_machine/dune-trunk/build/dune-grid/lib/libdunealbertagrid_2d.a /usr/local_machine/dune-trunk/build/dune-grid/lib/libdunealbertagrid_1d.a /usr/local_machine/dune-trunk/build/dune-grid/lib/libdunegrid.a /usr/local_machine/dune-trunk/build/dune-geometry/lib/libdunegeometry.a /usr/local_machine/dune-trunk/build/dune-common/lib/libdunecommon.a /usr/local_machine/suitesparse-4.4.0/lib/libumfpack.a /usr/local_machine/suitesparse-4.4.0/lib/libspqr.a /usr/local_machine/suitesparse-4.4.0/lib/libldl.a /usr/local_machine/suitesparse-4.4.0/lib/libcholmod.a /usr/local_machine/suitesparse-4.4.0/lib/libamd.a /usr/local_machine/suitesparse-4.4.0/lib/libcamd.a /usr/local_machine/suitesparse-4.4.0/lib/libcolamd.a /usr/local_machine/suitesparse-4.4.0/lib/libccolamd.a /usr/local_machine/suitesparse-4.4.0/lib/libsuitesparseconfig.a /usr/local_machine/petsc-3.5.3/lib/libpetsc.so /usr/local_machine/petsc-3.5.3/lib/libHYPRE.a /usr/local_machine/petsc-3.5.3/lib/libsuperlu_dist_3.3.a -llapack -lblas /usr/local_machine/parmetis-4.0.3/lib/libparmetis.a /usr/local_machine/parmetis-4.0.3/lib/libmetis.a -lX11 -lssl -lcrypto /usr/local_machine/openmpi-1.8.4/lib/libmpi_usempi.so /usr/local_machine/openmpi-1.8.4/lib/libmpi_mpifh.so -lgfortran -lquadmath -lm /usr/local_machine/openmpi-1.8.4/lib/libmpi_cxx.so -lstdc++ /usr/local_machine/openmpi-1.8.4/lib/libmpi.so -lgcc_s -lpthread -ldl /usr/local_machine/zoltan-3.8/lib/libzoltan.a /usr/local_machine/parmetis-4.0.3/lib/libparmetis.a /usr/local_machine/parmetis-4.0.3/lib/libmetis.a -lm -pthread /usr/local_machine/openmpi-1.8.4/lib/libmpi.so -pthread /usr/local_machine/openmpi-1.8.4/lib/libmpi.so -lz /usr/local_machine/suitesparse-4.4.0/lib/libumfpack.a /usr/local_machine/suitesparse-4.4.0/lib/libcholmod.a /usr/local_machine/suitesparse-4.4.0/lib/libamd.a /usr/local_machine/suitesparse-4.4.0/lib/libcamd.a /usr/local_machine/suitesparse-4.4.0/lib/libcolamd.a /usr/local_machine/suitesparse-4.4.0/lib/libccolamd.a /usr/local_machine/suitesparse-4.4.0/lib/libldl.a /usr/local_machine/suitesparse-4.4.0/lib/libspqr.a /usr/local_machine/suitesparse-4.4.0/lib/libsuitesparseconfig.a /usr/local_machine/suitesparse-4.4.0/lib/libumfpack.a /usr/local_machine/suitesparse-4.4.0/lib/libcholmod.a /usr/local_machine/suitesparse-4.4.0/lib/libamd.a /usr/local_machine/suitesparse-4.4.0/lib/libcamd.a /usr/local_machine/suitesparse-4.4.0/lib/libcolamd.a /usr/local_machine/suitesparse-4.4.0/lib/libccolamd.a /usr/local_machine/suitesparse-4.4.0/lib/libsuitesparseconfig.a -lsuperlu /usr/lib/libf77blas.so.3gf /usr/lib/libatlas.so.3gf /usr/local_machine/parmetis-4.0.3/lib/libparmetis.a /usr/local_machine/parmetis-4.0.3/lib/libmetis.a -lm -pthread /usr/local_machine/openmpi-1.8.4/lib/libmpi.so /usr/local_machine/parmetis-4.0.3/lib/libmetis.a -lm -lm /usr/local_machine/dune-trunk/build/dune-grid/lib/libdunegrid.a /usr/local_machine/ug-3.11.0/lib/libugS2.a /usr/local_machine/ug-3.11.0/lib/libugS3.a /usr/local_machine/ug-3.11.0/lib/libdevS.a /usr/local_machine/dune-trunk/build/dune-geometry/lib/libdunegeometry.a /usr/local_machine/dune-trunk/build/dune-common/lib/libdunecommon.a /usr/local_machine/parmetis-4.0.3/lib/libparmetis.a /usr/local_machine/parmetis-4.0.3/lib/libmetis.a -lm -pthread /usr/local_machine/openmpi-1.8.4/lib/libmpi.so /usr/local_machine/parmetis-4.0.3/lib/libmetis.a -lm -lgmp -lgmpxx -pthread /usr/local_machine/openmpi-1.8.4/lib/libmpi.so /usr/local_machine/petsc-3.5.3/lib/libpetsc.so /usr/local_machine/petsc-3.5.3/lib/libHYPRE.a /usr/local_machine/petsc-3.5.3/lib/libsuperlu_dist_3.3.a -llapack -lblas /usr/local_machine/parmetis-4.0.3/lib/libparmetis.a /usr/local_machine/parmetis-4.0.3/lib/libmetis.a -lX11 -lssl -lcrypto /usr/local_machine/openmpi-1.8.4/lib/libmpi_usempi.so /usr/local_machine/openmpi-1.8.4/lib/libmpi_mpifh.so -lgfortran -lquadmath -lm /usr/local_machine/openmpi-1.8.4/lib/libmpi_cxx.so -lstdc++ /usr/local_machine/openmpi-1.8.4/lib/libmpi.so -lgcc_s -lpthread -ldl /usr/local_machine/dune-trunk/build/dune-fem/lib/libdunefem.a /usr/local_machine/dune-trunk/build/dune-alugrid/lib/libdunealugrid.a /usr/local_machine/dune-trunk/build/dune-grid/lib/libdunealbertagrid_3d.a /usr/local_machine/dune-trunk/build/dune-grid/lib/libdunealbertagrid_2d.a /usr/local_machine/dune-trunk/build/dune-grid/lib/libdunealbertagrid_1d.a /usr/local_machine/dune-trunk/build/dune-grid/lib/libdunegrid.a /usr/local_machine/dune-trunk/build/dune-geometry/lib/libdunegeometry.a /usr/local_machine/dune-trunk/build/dune-common/lib/libdunecommon.a /usr/local_machine/dune-trunk/build/dune-grid/lib/libdunealbertagrid_2d.a /usr/local_machine/alberta-3.0.0/lib/libalberta_2d.so /usr/local_machine/dune-trunk/build/dune-grid/lib/libdunegrid.a /usr/local_machine/dune-trunk/build/dune-fem/lib/libdunefem.a /usr/local_machine/dune-trunk/build/dune-alugrid/lib/libdunealugrid.a /usr/local_machine/dune-trunk/build/dune-grid/lib/libdunealbertagrid_3d.a /usr/local_machine/dune-trunk/build/dune-grid/lib/libdunealbertagrid_2d.a /usr/local_machine/dune-trunk/build/dune-grid/lib/libdunealbertagrid_1d.a /usr/local_machine/dune-trunk/build/dune-grid/lib/libdunegrid.a /usr/local_machine/dune-trunk/build/dune-geometry/lib/libdunegeometry.a /usr/local_machine/dune-trunk/build/dune-common/lib/libdunecommon.a /usr/local_machine/alberta-3.0.0/lib/libalberta_utilities.so -lm -lltdl /usr/lib/libf77blas.so.3gf /usr/lib/libatlas.so.3gf /usr/local_machine/suitesparse-4.4.0/lib/libumfpack.a /usr/local_machine/suitesparse-4.4.0/lib/libcholmod.a /usr/local_machine/suitesparse-4.4.0/lib/libamd.a /usr/local_machine/suitesparse-4.4.0/lib/libcamd.a /usr/local_machine/suitesparse-4.4.0/lib/libcolamd.a /usr/local_machine/suitesparse-4.4.0/lib/libccolamd.a /usr/local_machine/suitesparse-4.4.0/lib/libsuitesparseconfig.a /usr/local_machine/suitesparse-4.4.0/lib/libspqr.a /usr/local_machine/suitesparse-4.4.0/lib/libldl.a /usr/local_machine/petsc-3.5.3/lib/libpetsc.so /usr/local_machine/petsc-3.5.3/lib/libHYPRE.a /usr/local_machine/petsc-3.5.3/lib/libsuperlu_dist_3.3.a -llapack -lblas /usr/local_machine/parmetis-4.0.3/lib/libparmetis.a /usr/local_machine/parmetis-4.0.3/lib/libmetis.a -lX11 -lssl -lcrypto /usr/local_machine/openmpi-1.8.4/lib/libmpi_usempi.so /usr/local_machine/openmpi-1.8.4/lib/libmpi_mpifh.so -lgfortran -lquadmath -lm /usr/local_machine/openmpi-1.8.4/lib/libmpi_cxx.so -lstdc++ /usr/local_machine/openmpi-1.8.4/lib/libmpi.so -lgcc_s -lpthread -ldl /usr/local_machine/zoltan-3.8/lib/libzoltan.a -lm -lsuperlu /usr/local_machine/ug-3.11.0/lib/libugS2.a /usr/local_machine/ug-3.11.0/lib/libugS3.a /usr/local_machine/ug-3.11.0/lib/libdevS.a -lgmp -lgmpxx /usr/local_machine/alberta-3.0.0/lib/libalberta_2d.so /usr/local_machine/alberta-3.0.0/lib/libalberta_utilities.so -lm -lltdl -lz -Wl,-rpath,/usr/local_machine/petsc-3.5.3/lib:/usr/local_machine/openmpi-1.8.4/lib:/usr/local_machine/alberta-3.0.0/lib 
/usr/bin/ld: warning: libblas.so.3gf, needed by /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libsuperlu.so, may conflict with libblas.so.3
/usr/bin/ld: warning: libblas.so.3gf, needed by /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libsuperlu.so, may conflict with libblas.so.3
/usr/bin/ld: warning: libblas.so.3gf, needed by /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../../lib/libsuperlu.so, may conflict with libblas.so.3

The second one works, but it is crazy long so could be difficult to compare against the first one.

PS It is truncated because is too long; if you edit it, you can see the full line!

Can you try my branch with reversed order of the libraries? From ${BLAS_LIBRARIES} ${LAPACK_LIBRARIES} ${SuiteSparse_LIBRARIES} change to ${SuiteSparse_LIBRARIES} ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES}

Always the same error :(

Added 14 commits:

37ac9466...35c9a1bf - 13 commits from branch master
7c3bea4d - Merge branch 'master' into feature/FS1519-suitesparse-ldl-spqr

Added 22 commits:

b250bf60 - Adjust Doxygen comments.
7a4c7de8 - [suitesparse] Create test for SPQR
673d1a60 - [suitesparse] Create wrapper for SPQR solver
a34d685c - [suitesparse] Create wrapper for LDL linear solver
e9986a89 - [umfpack] Factorization extraction, make colcomp public
8394a69a - [suitesparse] Cleanup of SPQR wrapper
7846d481 - [suitesparse] Fixed segmentation fault in SPQR
a973fabb - [suitesparse] LDL wrapper derived from Dune::InverseOperator
2e74d580 - [suitesparse][cleanup] Remove useless parantheses
69b9d30c - [suitesparse] Activate SPQR test
f1d7c040 - [suitesparse] Add test for LDL wrapper
aa96d622 - [suitesparse] Add setOption to LDL wrapper for compatibility
0fec2806 - [suitesparse][cleanup] Remove useless class variable in SPQR wrapper
f229b274 - [suitesparse][cleanup] Format includes, white space changes.
9ec8cbf8 - [CMake][suitesparse] Add ldltest and spqr test to build system
7102ea6e - [SuiteSparse] Enable CMake checks for LDL and SPQR
fe80c39a - test overlappingschwartz also with SPQR and LDL
9e953de2 - fix includes, remove useless preprocessor variables and use std::exceptions
c623d17d - fix include config
844e2c06 - [bugfix] Produce a linker error when pardiso lib is not found
bf9378c7 - [fixup] correctly nest namespace and ifdef directive
ca3de931 - [pardiso] update the Pardiso preconditioner to current Dune and Pardiso versions

Added 19 commits:

4edb4d52 - Adjust Doxygen comments.
3fdfba90 - [suitesparse] Create test for SPQR
858d1c9e - [suitesparse] Create wrapper for SPQR solver
6f037b8a - [suitesparse] Create wrapper for LDL linear solver
a2b8e1d2 - [umfpack] Factorization extraction, make colcomp public
51ab8358 - [suitesparse] Cleanup of SPQR wrapper
3f6f3457 - [suitesparse] Fixed segmentation fault in SPQR
6868b618 - [suitesparse] LDL wrapper derived from Dune::InverseOperator
334aafe0 - [suitesparse][cleanup] Remove useless parantheses
6193b962 - [suitesparse] Activate SPQR test
ea1ad1bb - [suitesparse] Add test for LDL wrapper
c5d21c89 - [suitesparse] Add setOption to LDL wrapper for compatibility
bd1e6c44 - [suitesparse][cleanup] Remove useless class variable in SPQR wrapper
253b29b0 - [suitesparse][cleanup] Format includes, white space changes.
69baaf8f - [CMake][suitesparse] Add ldltest and spqr test to build system
6fa91d76 - [SuiteSparse] Enable CMake checks for LDL and SPQR
7f30864f - test overlappingschwartz also with SPQR and LDL
3db040a0 - fix includes, remove useless preprocessor variables and use std::exceptions
6a47c649 - fix include config

I rebased the branch again and removed the unrelated commits from Bernd and Dominic.
I am inclined to remove the last three commits of Marco. The overlapping Schwartz does no work and we can have this as a new branch. ldltest and spqrtest work for all of us, so why wait?

@gruenich Yes I agree with you. My issue with spqrtest is a linking issue caused by FindSuiteSparse. I am going to open an issue in dune-common. The only commit that I would remove from the merge is 7f30864f. Please do the merge.

Hi @gruenich, can we merge this?

Added 29 commits:

6a47c649...6b890e74 - 13 commits from branch master
9ddfaccb - Adjust Doxygen comments.
a39bd5a8 - [suitesparse] Create test for SPQR
36a20860 - [suitesparse] Create wrapper for SPQR solver
10c05e6f - [suitesparse] Create wrapper for LDL linear solver
7f1f5934 - [umfpack] Factorization extraction, make colcomp public
9d25e1af - [suitesparse] Cleanup of SPQR wrapper
1edf9bda - [suitesparse] Fixed segmentation fault in SPQR
28e812ee - [suitesparse] LDL wrapper derived from Dune::InverseOperator
94acdc9c - [suitesparse][cleanup] Remove useless parantheses
8a0fba38 - [suitesparse] Activate SPQR test
8ff42cf9 - [suitesparse] Add test for LDL wrapper
9efd2742 - [suitesparse] Add setOption to LDL wrapper for compatibility
b0d1e24f - [suitesparse][cleanup] Remove useless class variable in SPQR wrapper
4bb59d9a - [suitesparse][cleanup] Format includes, white space changes.
823a76c5 - [CMake][suitesparse] Add ldltest and spqr test to build system
d0b42794 - [SuiteSparse] Enable CMake checks for LDL and SPQR

Title changed from [WIP] Feature/fs1519 suitesparse ldl spqr to Feature/fs1519 suitesparse ldl spqr

mentioned in commit ea087758

Status changed to merged

Marco, thanks again for your patches!

Thank you for the merge!

mentioned in merge request !20 (merged)

mentioned in commit a6f130c0

@gruenich I was a bit slow to react here. Your assumption that spqrtest works for everybody was wrong. My above error is alive and kickin:

/home/dominic/dune/dune-istl/dune/istl/spqr.hh: In member function ‘virtual void Dune::SPQR<Dune::BCRSMatrix<Dune::FieldMatrix<K, n, p>, TA> >::apply(Dune::SPQR<Dune::BCRSMatrix<Dune::FieldMatrix<K, n, p>, TA> >::domain_type&, Dune::SPQR<Dune::BCRSMatrix<Dune::FieldMatrix<K, n, p>, TA> >::range_type&, Dune::InverseOperatorResult&)’:
/home/dominic/dune/dune-istl/dune/istl/spqr.hh:154:42: error: ‘cholmod_common’ has no member named ‘SPQR_flopcount’
         std::cout<<"Flops Taken: "<<cc_->SPQR_flopcount<<std::endl;
                                          ^
/home/dominic/dune/dune-istl/dune/istl/spqr.hh:155:44: error: ‘cholmod_common’ has no member named ‘SPQR_analyze_time’
         std::cout<<"Analysis Time: "<<cc_->SPQR_analyze_time<<" s"<<std::endl;
                                            ^
/home/dominic/dune/dune-istl/dune/istl/spqr.hh:156:45: error: ‘cholmod_common’ has no member named ‘SPQR_factorize_time’
         std::cout<<"Factorize Time: "<<cc_->SPQR_factorize_time<<" s"<<std::endl;
                                             ^
/home/dominic/dune/dune-istl/dune/istl/spqr.hh:157:45: error: ‘cholmod_common’ has no member named ‘SPQR_solve_time’
         std::cout<<"Backsolve Time: "<<cc_->SPQR_solve_time<<" s"<<std::endl;

To be honest, I have no idea, why it would work for you. Why should cholmod_common have a SPQR-related methods? I use libsuitesparse-dev from Debian 8.2 in version 4.2.1.

@dominic With SuiteSparse 4.4.0 I don't experience the error. But, also with SuiteSparse 4.2.1 everything worked. I have always compiled SuiteSparse from the source, that is the only difference which I can see.

mentioned in issue #5 (closed)

See #5 (closed) from now on.

     */
    void apply(T* x, T* b)
+   {
      const int dimMat(ldlMatrix_.N());
      ldl_perm(dimMat, Y_, b, P_);
      ldl_lsolve(dimMat, Y_, Lp_, Li_, Lx_);
      ldl_dsolve(dimMat, Y_, D_);
      ldl_ltsolve(dimMat, Y_, Lp_, Li_, Lx_);
      ldl_permt(dimMat, x, Y_, P_);
+   }
    void setOption(unsigned int option, double value)
+   {
      DUNE_UNUSED_PARAMETER(option);
      DUNE_UNUSED_PARAMETER(value);
+   }

        std::cout<<"Rank Estimate: "<<cc_->SPQR_istat[4]<<std::endl<<std::endl;
+     }
+   }
    /** \copydoc InverseOperator::apply(X&,Y&,double,InverseOperatorResult&) */
    virtual void apply (domain_type& x, range_type& b, double reduction, InverseOperatorResult& res)
+   {
      DUNE_UNUSED_PARAMETER(reduction);
      apply(x, b, res);
+   }
    void setOption(unsigned int option, double value)
+   {
      DUNE_UNUSED_PARAMETER(option);
      DUNE_UNUSED_PARAMETER(value);
+   }

Feature/fs1519 suitesparse ldl spqr

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