Trouble getting UMFPACK to work

[John]

Hello everyone,

I am currently using Deal II version 8.0.0. When I try to run a project I am getting the following:

----------------------------------------------------
Exception on processing:

--------------------------------------------------------
An error occurred in line <379> of file </home/sean/Downloads/deal.II/source/lac/sparse_direct.cc> in function
    void dealii::SparseDirectUMFPACK::factorize(const Matrix&) [with Matrix = dealii::SparseMatrix<double>]
The violated condition was:
    false
The name and call sequence of the exception was:
    ExcMessage("To call this function you need UMFPACK, but configured deal.II without passing the necessary switch to 'cmake'. Please consult the installation instructions in doc/readme.html.")
Additional Information:
To call this function you need UMFPACK, but configured deal.II without passing the necessary switch to 'cmake'. Please consult the installation instructions in doc/readme.html.

Stacktrace:
-----------
#0  /Downloads/deal.II/lib/libdeal_II.so.8.0.0: void dealii::SparseDirectUMFPACK::factorize<dealii::SparseMatrix<double> >(dealii::SparseMatrix<double> const&)
#1  step-3: TmsProblem::solve()
#2  step-3: TmsProblem::run()
#3  step-3: main
--------------------------------------------------------

Aborting!
----------------------------------------------------
CMake Error at CMakeFiles/run_target.cmake:6 (MESSAGE):
 

  Program terminated with exit code: 1


CMakeFiles/run.dir/build.make:57: recipe for target 'CMakeFiles/run' failed
make[3]: *** [CMakeFiles/run] Error 1
CMakeFiles/Makefile2:264: recipe for target 'CMakeFiles/run.dir/all' failed
make[2]: *** [CMakeFiles/run.dir/all] Error 2
CMakeFiles/Makefile2:271: recipe for target 'CMakeFiles/run.dir/rule' failed
make[1]: *** [CMakeFiles/run.dir/rule] Error 2
Makefile:196: recipe for target 'run' failed
make: *** [run] Error 2



I have tried "cmake -DDEAL_II_WITH_UMFPACK=ON" and "cmake -DDEAL_II_WITH_UMFPACK=ON -DUMFPACK_DIR=/Downloads/deal.II/bundled/umfpack ." and also  "cmake -DDEAL_II_WITH_UMFPACK=ON -DUMFPACK_DIR=/Downloads/deal.II/bundled/umfpack/UMFPACK ." and then following each of these with "make" and "make run". However, all of these still end up giving me the same error as above. Can anyone help me with getting umfpack to work? Thank you in advance.

[Timo Heister]

John,

> I am currently using Deal II version 8.0.0.

I would like to encourage you to update to the latest release. Many
things have changed and improved over the years. That probably also
includes handling of dependencies like UMFPACK.

> I have tried "cmake -DDEAL_II_WITH_UMFPACK=ON" and "cmake
> -DDEAL_II_WITH_UMFPACK=ON -DUMFPACK_DIR=/Downloads/deal.II/bundled/umfpack
> ." and also "cmake -DDEAL_II_WITH_UMFPACK=ON
> -DUMFPACK_DIR=/Downloads/deal.II/bundled/umfpack/UMFPACK ." and then
> following each of these with "make" and "make run".

Just to be sure: you did this in your deal.II build directory and you
then compiled and installed deal.II, right? (using "make install")
Please be sure that no other errors were reported in between.

--
Timo Heister
http://www.math.clemson.edu/~heister/

[John]

 Timo,

I do eventually plan on updating the code to the latest release.
I was doing the commands inside a folder in deal.II (similar to if I was in deal.II/examples/step-1). I already have deal.II installed and compiled. I have been going through a few of the examples perfectly fine. Should I be trying to run the commands elsewhere? Everything else in the code has been running just fine until it reaches the point it needs UMFPACK. Thank you for responding.

[Bruno Turcksin]

John,

On Thursday, August 31, 2017 at 3:52:44 PM UTC-4, John wrote:

I was doing the commands inside a folder in deal.II (similar to if I was in deal.II/examples/step-1).

That won't work you need to reconfigure, recompile, and reinstall deal.II to get UMFPACK to work. Otherwise, the wrappers to UMFPACK are not compiled and you can't use it. Adding configuration options when you are configuring a step (or your code) is too late.

Best,

Bruno

[曾元圆]

hi John,

have you solve this problem? I encountered the same problem as you. Actually I'm following an FEM open course on coursera and I'm trying to compile the source code in the homework. I have installed the dealii just a few days ago so I don't think it has something to do with the version of dealii.

在 2017年9月1日星期五 UTC+8上午3:52:44，John写道：

[John]

I still have yet to resolve the issue. As suggested, I have been trying to delete deal.II and then reinstalling and configuring with -DDEAL_II_WITH_UMFPACK=ON, but am still having trouble with it. I will write back to you if/when I figure it out!

[Bruno Turcksin]

John,

2017-09-02 11:07 GMT-04:00 John <thesma...@gmail.com>:
> I still have yet to resolve the issue. As suggested, I have been trying to
> delete deal.II and then reinstalling and configuring with
> -DDEAL_II_WITH_UMFPACK=ON, but am still having trouble with it. I will write
> back to you if/when I figure it out!

Please send the detailed.log file and the error message.

Best,

Bruno

[Wolfgang Bangerth]

As a general rule, there is no need to compile deal.II and then try to run any
programs with it if you want to find out whether your UMFPACK will work or
not. All you need to do is to run the
cmake ....
command you run to configure deal.II. At the end, it prints out a summary that
shows what packages it found. if UMFPACK is not listed as ON, then compiling
deal.II to test it is not necessary -- UMFPACK has not been enabled.

Now, if you do find that UMFPACK has not been enabled, even though you specificed
-DDEAL_II_WITH_UMFPACK=ON
then you need to go higher up in the cmake output to find what precisely it
was that cmake couldn't figure out. The usual cause is that UMFPACK requires
BLAS and LAPACK, and if your system does not have these libraries available,
or has them in places where cmake can't find them, then UMFPACK can not be
enabled.

What it is in your case that doesn't work, I don't know of course. But you can
find out by looking through the cmake output.

Best
W.

--
------------------------------------------------------------------------
Wolfgang Bangerth email: bang...@colostate.edu
www: http://www.math.colostate.edu/~bangerth/

[John]

I've actually deleted deal.II version 8.0.0 since last writing. I got UMFPACK to work by installing BLAS and LAPACK, but then I kept getting an error that it was unable to find the MPI library even though I had just installed openmpi. Since I could not find a way around this, I ended up updating the code to deal.II version 8.1.0, which it is currently running successfully on, and am now working on updating to 8.5. Thank you for all of your help!

[John]

Wolfgang, you are absolutely correct. My mistake was not having BLAS and LAPACK, so it was unable to use UMFPACK. Thank you for all of your help!

[曾元圆]

Hi Wolfgang,

Now I used the command you mentioned to check whether UMFPACK is enabled and it shows like this:

#      ( DEAL_II_WITH_HDF5 = OFF )

#      ( DEAL_II_WITH_LAPACK = OFF )

#      ( DEAL_II_WITH_METIS = OFF )

#      ( DEAL_II_WITH_MPI = OFF )

#        DEAL_II_WITH_MUPARSER set up with bundled packages

#      ( DEAL_II_WITH_NANOFLANN = OFF )

#      ( DEAL_II_WITH_NETCDF = OFF )

#      ( DEAL_II_WITH_OPENCASCADE = OFF )

#      ( DEAL_II_WITH_P4EST = OFF )

#      ( DEAL_II_WITH_PETSC = OFF )

#      ( DEAL_II_WITH_SLEPC = OFF )

#      ( DEAL_II_WITH_SUNDIALS = OFF )

#        DEAL_II_WITH_THREADS set up with bundled packages

#      ( DEAL_II_WITH_TRILINOS = OFF )

#      ( DEAL_II_WITH_UMFPACK = OFF )

So UMFPACK is not installed, right? But what to do next?  How can I know whether my Ubuntu OS already installed the lapack and blas package?

 (I tried to search lapack library under /usr/lib and it showed that there is only a FindLAPACK.cmake file whose name contains lapack, no files such as liblapack is found. I also found  a folder named Lapack under /usr/include/CGAL which contains a file named Linear_algebra_lapack.h, and a LAPACK.h under the path  /usr/include/CGAL/auto_link 

The above is all I can find but seems no lib like liblapack exits)

I can intall lapack and blas myself, but I don't know how to compile and install UMFPACK. I think I have found the source files which are needed under   /home/dyfluid/dealii/bundled/umfpack/UMFPACK  

.

[Bruno Turcksin]

2017-09-11 0:30 GMT-04:00 曾元圆 <2012...@gmail.com>:
> So UMFPACK is not installed, right? But what to do next? How can I know
> whether my Ubuntu OS already installed the lapack and blas package?

No UMFPACK has not been installed and lapack has not been found. You
need to install the dev version of lapack otherwise the headers are
not installed. Without the headers, lapack cannot be used by deal. So
make sure you get ( DEAL_II_WITH_LAPACK = ON ) You can also add
-DDEAL_II_WITH_LAPACK=ON when configuring deal.II and cmake will let
you know if there is a problem.

> I can intall lapack and blas myself, but I don't know how to compile and
> install UMFPACK.

You don't need to install UMFPACK yourself. It will be installed by deal.II.

Best,

Bruno

[曾元圆]

more specifically？

在 2017年9月11日星期一 UTC+8下午8:22:11，Bruno Turcksin写道：

[Jean-Paul Pelteret]

Probably something like




sudo apt-get install libblas-dev liblapack-dev liblapacke-dev 

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[曾元圆]

thank you but, nothing need to do with UMFPACK? 

在 2017年9月11日星期一 UTC+8下午11:13:24，Jean-Paul Pelteret写道：

[Wolfgang Bangerth]

On 09/11/2017 10:40 AM, 曾元圆 wrote:
> thank you but, nothing need to do with UMFPACK?

No -- deal.II has its own copy of UMFPACK. So, whenever deal.II can find
BLAS and LAPACK, it uses its own copy of UMFPACK. (It uses a copy of
UMFPACK if one is found on your system, but because it has its own copy,
it doesn't *need* to find one installed on the system.)

[曾元圆]

Now suppose I have installed blas and lapack by execute command in terminal. Then the remaining part is UMPACK. Since "DEAL_II_WITH_UMFPACK = OFF" is apparently not expected. What I want to know is what I should do to change it to  " DEAL_II_WITH_UMFPACK set up with bundled packages", which is what we want.

    

在 2017年9月11日星期一 UTC+8下午8:22:11，Bruno Turcksin写道：

2017-09-11 0:30 GMT-04:00 曾元圆 <2012...@gmail.com>:

[曾元圆]

Because I have already installed dealii, I don't quite understand what you mean by saying "configuring". Do you mean I need to recompile the whole dealii then it can know where to find lapack?  LAPACK is a third party library right? so all I need to do is to tell the compiler where is the header and library. I suppose perhaps I don't need to configure dealii again?  sorry I really don't know much about cmake. Forgive me if I asked you some silly questions. 

best regards.

在 2017年9月11日星期一 UTC+8下午8:22:11，Bruno Turcksin写道：

2017-09-11 0:30 GMT-04:00 曾元圆 <2012...@gmail.com>:

[Bruno Turcksin]

2017-09-11 13:11 GMT-04:00 曾元圆 <2012...@gmail.com>:
> Because I have already installed dealii, I don't quite understand what you
> mean by saying "configuring". Do you mean I need to recompile the whole
> dealii then it can know where to find lapack? LAPACK is a third party
> library right? so all I need to do is to tell the compiler where is the
> header and library. I suppose perhaps I don't need to configure dealii
> again? sorry I really don't know much about cmake. Forgive me if I asked
> you some silly questions.

To install deal.II, you have basically two steps: 1) the configuration
(that's when you use cmake and give all the options that you want for
example -DDEAL_II_WITH_UMFPACK=ON) 2) the compilation itself.
In step 1, all the compiler commands are generated and they are
executed during step 2. Like you correctly said, you need to tell the
compiler where the header and the library are, this is done during
step 1. However, this is slightly more complicated that just giving a
path, because some part of deal.II are only activated if some
libraries are present. For example, if you are using UMFPACK some
files will need to be compiled but if you are not using UMFPACK they
won't be compiled. So having deal.II compiled without UMFPACK support
and then, adding the flags to the library won't work because the files
that allow to use UMFPACK from deal.II won't be compiled. Basically
deal.II would not be aware that UMDPACK is installed. So what you need
to do is to reinstall deal.II from the very beginning in a new
directory.
Does it make sense?

Best,

Bruno

[曾元圆]

 Thank you very much! So you mean every time I want to use another library, I have to recompile and reinstall dealii again?

在 2017年9月12日星期二 UTC+8上午1:25:25，Bruno Turcksin写道：

[Bruno Turcksin]

2017-09-11 23:45 GMT-04:00 曾元圆 <2012...@gmail.com>:
>  Thank you very much! So you mean every time I want to use another library,
> I have to recompile and reinstall dealii again?

Every time you add a new library you need to reconfigure and recompile deal. Now if you want to use PETSc and Trilinos you can turn on both of them at the same time. You don't need to recompile deal twice. Ideally, the first time you configure deal, you would turn on the support for the all libraries that you will need. This way you only have to compile deal.II once.

Best,

Bruno

[曾元圆]

If I want to run all the 57 steps, should I install all the mentioned libraries? How can I know in advance which library I may need? Perhaps now I don't need PETSc, but maybe someday in the future I will need. 

在 2017年9月12日星期二 UTC+8下午8:08:14，Bruno Turcksin写道：

[Bruno Turcksin]

2017-09-12 9:49 GMT-04:00 曾元圆 <2012...@gmail.com>:

If I want to run all the 57 steps, should I install all the mentioned libraries? How can I know in advance which library I may need? Perhaps now I don't need PETSc, but maybe someday in the future I will need.

No you don't. You can use candi or spack to install everything and then, you won't have to worry about missing a library.

Best,

Bruno

[Darius Barreto]

Hi John,

I am exactly getting the same error message?. How were you able to rectify it?.

Could you please help?.

Thanks

[Jean-Paul Pelteret]

Dear Darius,

Your installation of deal.II has not been compiled with UMFPACK supplied as an external library. The bundled version has also not been built, likely because you do not have the required dependencies installed. I believe that you need to have LAPACK installed for it to work, so you should install LAPACK and then try to configure and then build deal.II again. At the end of the configuration step you should see a line similar to this in the summary printed to the console:

#        DEAL_II_WITH_UMFPACK successfully set up with bundled packages.

or

#        DEAL_II_WITH_UMFPACK set up with external dependencies

I hope that this helps you resolve your issue.

Best,

Jean-Paul

[Jean-Paul Pelteret]

Dear Darius,

template <int dim, int spacedim>

void elastic_rod<dim, spacedim>::solve(){

        SparseDirectUMFPACK A_direct;

A_direct.initialize(system_matrix) ;

A_direct.vmult(solution, system_rhs);

}

Since I am new to dealii, so instead of creating a new  CMakeLists.txt file I have just copied my code in step-29 example(as It uses this UMFPACK), of course I have ensured to change the name in the .txt file. I am getting the error. I have attached the error message.  Do I actually need to make changes( unlike other tutorials) while  entering the cmake command in the terminal?(cmake -DDEAL_II_WITH_DIR=/path/to/installed/deal.II). I have also included the header file for the sparse direct solver UMFPACK(#include <deal.II/lac/sparse_direct.h>). My other tutorials are just running fine in dealii, except the ones which use an UMFPACK.

You suggested me to install an external LAPACK on the group, but I have difficulties in installing it. I was unable to find a proper source in google regarding its installation procedure. So could it be the only reason of not having an external LAPACK?.

I’m gathering from the picture that you sent me that the operating system that you’re running is Ubuntu 18.04 or thereabouts. You should be able to install LAPACK with the command “sudo apt install liblapack-dev”. After that, you should recompile deal.II itself (not the tutorial example, or your code, but the actual library). It is during the configuration stage for deal.II that UMFPACK is detected and, therefore, enabled within deal.II. It also at this point that you should see the messages that I mentioned earlier, if the detection of UMFPACK was successful. If you’re having trouble installing deal.II itself, then you should consider installing deal.II using candi (https://github.com/dealii/candi) or spack (https://github.com/spack/spack / https://github.com/dealii/dealii/wiki/deal.II-in-Spack).

I hope that this clarify what you need to do.

Best,

Jean-Paul

[Darius Barreto]

Dear Jean-Paul,

Thanks for the reply. 

[Jean-Paul Pelteret]

Dear Darius,

I just thought I’d ask whether you were able to solve your problem?

Best,

Jean-Paul

[Darius Barreto]

Dear Jean-Paul, 

Yes,  I was able to solve that problem.  I installed LAPACK using the command and later I compiled the entire deal.II library. Thanks for the help.

Regards,

Darius Barreto.

[ME20D503 NEWTON]

Hello everyone,

which command i have to use to check whether UMFPACK is enabled or not?? if it is OFF how to turn it ON??

Thank you in advance.

[Daniel Arndt]

What does the log for running

cmake -DDEAL_II_WITH_UMFPACK=ON .

look like? The summary printed at the end should tell you if `UMFPACK` really was found. N=Any problems in finding a compatible library should be contained in the output printed when running the CMake command.

Best,

Daniel

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[ME20D503 NEWTON]

Dear Daniel,

i am getting this while running cmake-DDEAL_II_WITH_UMFPACK=ON, can you please see  the highlighted output?

....................................

 No source or binary directory provided.  Both will be assumed to be the
  same as the current working directory, but note that this warning will
  become a fatal error in future CMake releases.


-- This is CMake 3.16.3
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/setup_external_macros.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_add_flags.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_check_compiler_setup.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_check_cxx_compiler_bug.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_check_mpi_interface.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_clear_cmake_required.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_configure_feature.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_add_definitions.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_add_library.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_add_test.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_find_file.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_find_library.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_find_path.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_find_program.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_initialize_cached_variables.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_insource_setup_target.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_invoke_autopilot.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_package_handle.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_pickup_tests.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_query_git_information.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_deal_ii_setup_target.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_decorate_with_stars.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_enable_if_links.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_enable_if_supported.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_enable_language_optional.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_evaluate_expression.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_expand_instantiations.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_filter_system_libraries.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_find_package.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_find_system_library.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_item_matches.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_purge_feature.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_register_feature.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_remove_duplicates.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_replace_flag.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_reset_cmake_required.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_set_if_empty.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_setup_source_list.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_setup_unity_target.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_strip_flag.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_switch_library_preference.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_to_string.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_to_string_and_add_prefix.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_unset_if_changed.cmake
-- Include /home/newton/fem/dealii-9.2.0/cmake/macros/macro_verbose_include.cmake
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/setup_cached_variables.cmake
-- Prepending ${CUDA_NVCC_FLAGS} to ${DEAL_II_CUDA_FLAGS}
-- The CXX compiler identification is GNU 9.4.0
-- The C compiler identification is GNU 9.4.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- No working Fortran compiler found, disabling Fortran
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/setup_deal_ii.cmake
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/setup_compiler_flags.cmake
-- Performing Test DEAL_II_HAVE_USABLE_USER_FLAGS_DEBUG
-- Performing Test DEAL_II_HAVE_USABLE_USER_FLAGS_DEBUG - Success
-- Performing Test DEAL_II_HAVE_USABLE_USER_FLAGS_RELEASE
-- Performing Test DEAL_II_HAVE_USABLE_USER_FLAGS_RELEASE - Success
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/setup_compiler_flags_gnu.cmake
-- Performing Test DEAL_II_HAVE_FLAG_pedantic
-- Performing Test DEAL_II_HAVE_FLAG_pedantic - Success
-- Performing Test DEAL_II_HAVE_FLAG_fPIC
-- Performing Test DEAL_II_HAVE_FLAG_fPIC - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wl__as_needed
-- Performing Test DEAL_II_HAVE_FLAG_Wl__as_needed - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wall
-- Performing Test DEAL_II_HAVE_FLAG_Wall - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wextra
-- Performing Test DEAL_II_HAVE_FLAG_Wextra - Success
-- Performing Test DEAL_II_HAVE_FLAG_Woverloaded_virtual
-- Performing Test DEAL_II_HAVE_FLAG_Woverloaded_virtual - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wpointer_arith
-- Performing Test DEAL_II_HAVE_FLAG_Wpointer_arith - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wsign_compare
-- Performing Test DEAL_II_HAVE_FLAG_Wsign_compare - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wsuggest_override
-- Performing Test DEAL_II_HAVE_FLAG_Wsuggest_override - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wswitch
-- Performing Test DEAL_II_HAVE_FLAG_Wswitch - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wsynth
-- Performing Test DEAL_II_HAVE_FLAG_Wsynth - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wwrite_strings
-- Performing Test DEAL_II_HAVE_FLAG_Wwrite_strings - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wplacement_new
-- Performing Test DEAL_II_HAVE_FLAG_Wplacement_new - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wdeprecated_declarations
-- Performing Test DEAL_II_HAVE_FLAG_Wdeprecated_declarations - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wliteral_suffix
-- Performing Test DEAL_II_HAVE_FLAG_Wliteral_suffix - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wpsabi
-- Performing Test DEAL_II_HAVE_FLAG_Wpsabi - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wclass_memaccess
-- Performing Test DEAL_II_HAVE_FLAG_Wclass_memaccess - Success
-- Performing Test DEAL_II_HAVE_FLAG_funroll_loops
-- Performing Test DEAL_II_HAVE_FLAG_funroll_loops - Success
-- Performing Test DEAL_II_HAVE_FLAG_funroll_all_loops
-- Performing Test DEAL_II_HAVE_FLAG_funroll_all_loops - Success
-- Performing Test DEAL_II_HAVE_FLAG_fstrict_aliasing
-- Performing Test DEAL_II_HAVE_FLAG_fstrict_aliasing - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wunused_local_typedefs
-- Performing Test DEAL_II_HAVE_FLAG_Wunused_local_typedefs - Success
-- Performing Test DEAL_II_HAVE_FLAG_ggdb
-- Performing Test DEAL_II_HAVE_FLAG_ggdb - Success
--
-- Include /home/newton/fem/dealii-9.2.0/bundled/setup_bundled.cmake
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/checks/check_01_cpu_features.cmake
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Performing Test DEAL_II_HAVE_SSE2
-- Performing Test DEAL_II_HAVE_SSE2 - Success
-- Performing Test DEAL_II_HAVE_AVX
-- Performing Test DEAL_II_HAVE_AVX - Failed
-- Performing Test DEAL_II_HAVE_AVX512
-- Performing Test DEAL_II_HAVE_AVX512 - Failed
-- Performing Test DEAL_II_HAVE_ALTIVEC
-- Performing Test DEAL_II_HAVE_ALTIVEC - Failed
-- Performing Test DEAL_II_HAVE_OPENMP_SIMD
-- Performing Test DEAL_II_HAVE_OPENMP_SIMD - Success
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/checks/check_01_cxx_features.cmake
-- Performing Test DEAL_II_HAVE_FLAG_stdcxx17
-- Performing Test DEAL_II_HAVE_FLAG_stdcxx17 - Success
-- Using C++ version flag "-std=c++17"
-- Performing Test DEAL_II_HAVE_CXX17_ATTRIBUTES
-- Performing Test DEAL_II_HAVE_CXX17_ATTRIBUTES - Success
-- Performing Test DEAL_II_HAVE_CXX17_IF_CONSTEXPR
-- Performing Test DEAL_II_HAVE_CXX17_IF_CONSTEXPR - Success
-- Performing Test DEAL_II_NON_CONSTEXPR_LAMBDA
-- Performing Test DEAL_II_NON_CONSTEXPR_LAMBDA - Success
-- Performing Test DEAL_II_HAVE_CXX14_MAKE_UNIQUE
-- Performing Test DEAL_II_HAVE_CXX14_MAKE_UNIQUE - Success
-- Performing Test DEAL_II_HAVE_CXX14_CONSTEXPR_STDMAXMIN
-- Performing Test DEAL_II_HAVE_CXX14_CONSTEXPR_STDMAXMIN - Success
-- Performing Test DEAL_II_HAVE_CXX14_CLANGAUTODEBUG_BUG_OK
-- Performing Test DEAL_II_HAVE_CXX14_CLANGAUTODEBUG_BUG_OK - Success
-- Performing Test DEAL_II_HAVE_CXX11_FEATURES
-- Performing Test DEAL_II_HAVE_CXX11_FEATURES - Success
-- Performing Test DEAL_II_HAVE_CXX11_FUNCTIONAL_LLVMBUG20084_OK
-- Performing Test DEAL_II_HAVE_CXX11_FUNCTIONAL_LLVMBUG20084_OK - Success
-- Performing Test DEAL_II_HAVE_CXX11_MACOSXC99BUG_OK
-- Performing Test DEAL_II_HAVE_CXX11_MACOSXC99BUG_OK - Success
-- Performing Test DEAL_II_HAVE_CXX11_ICCNUMERICLIMITSBUG_OK
-- Performing Test DEAL_II_HAVE_CXX11_ICCNUMERICLIMITSBUG_OK - Success
-- Performing Test DEAL_II_HAVE_CXX11_ICCLIBSTDCPP47CXX11BUG_OK
-- Performing Test DEAL_II_HAVE_CXX11_ICCLIBSTDCPP47CXX11BUG_OK - Success
-- Performing Test DEAL_II_COMPILER_DEFAULTS_TO_CXX11_OR_NEWER
-- Performing Test DEAL_II_COMPILER_DEFAULTS_TO_CXX11_OR_NEWER - Success
-- DEAL_II_WITH_CXX14 successfully set up
-- DEAL_II_WITH_CXX17 successfully set up
-- Performing Test DEAL_II_HAVE_CXX17_ATTRIBUTE_FALLTHROUGH
-- Performing Test DEAL_II_HAVE_CXX17_ATTRIBUTE_FALLTHROUGH - Success
-- Performing Test DEAL_II_HAVE_ATTRIBUTE_FALLTHROUGH
-- Performing Test DEAL_II_HAVE_ATTRIBUTE_FALLTHROUGH - Success
-- Performing Test DEAL_II_HAVE_CXX11_IS_TRIVIALLY_COPYABLE
-- Performing Test DEAL_II_HAVE_CXX11_IS_TRIVIALLY_COPYABLE - Success
-- Performing Test DEAL_II_HAVE_FP_EXCEPTIONS
-- Performing Test DEAL_II_HAVE_FP_EXCEPTIONS - Success
-- Performing Test DEAL_II_HAVE_COMPLEX_OPERATOR_OVERLOADS
-- Performing Test DEAL_II_HAVE_COMPLEX_OPERATOR_OVERLOADS - Failed
-- Performing Test DEAL_II_HAVE_CXX14_CONSTEXPR
-- Performing Test DEAL_II_HAVE_CXX14_CONSTEXPR - Success
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/checks/check_02_compiler_features.cmake
-- Performing Test DEAL_II_COMPILER_USE_VECTOR_ARITHMETICS
-- Performing Test DEAL_II_COMPILER_USE_VECTOR_ARITHMETICS - Success
-- Performing Test DEAL_II_VECTOR_ITERATOR_IS_POINTER_OK
-- Performing Test DEAL_II_VECTOR_ITERATOR_IS_POINTER_OK - Success
-- Test successful, do not define DEAL_II_VECTOR_ITERATOR_IS_POINTER
-- Performing Test DEAL_II_HAVE_BUILTIN_EXPECT
-- Performing Test DEAL_II_HAVE_BUILTIN_EXPECT - Success
-- Performing Test DEAL_II_HAVE_GLIBC_STACKTRACE
-- Performing Test DEAL_II_HAVE_GLIBC_STACKTRACE - Success
-- Performing Test DEAL_II_HAVE_FLAG_rdynamic
-- Performing Test DEAL_II_HAVE_FLAG_rdynamic - Success
-- Performing Test DEAL_II_HAVE_LIBSTDCXX_DEMANGLER
-- Performing Test DEAL_II_HAVE_LIBSTDCXX_DEMANGLER - Success
-- Performing Test DEAL_II_COMPILER_HAS_ATTRIBUTE_PRETTY_FUNCTION
-- Performing Test DEAL_II_COMPILER_HAS_ATTRIBUTE_PRETTY_FUNCTION - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wa__compress_debug_sections
-- Performing Test DEAL_II_HAVE_FLAG_Wa__compress_debug_sections - Success
-- Performing Test DEAL_II_COMPILER_HAS_CXX14_ATTRIBUTE_DEPRECATED
-- Performing Test DEAL_II_COMPILER_HAS_CXX14_ATTRIBUTE_DEPRECATED - Success
-- Performing Test DEAL_II_COMPILER_HAS_ATTRIBUTE_DEPRECATED
-- Performing Test DEAL_II_COMPILER_HAS_ATTRIBUTE_DEPRECATED - Success
-- Performing Test DEAL_II_COMPILER_HAS_ATTRIBUTE_ALWAYS_INLINE
-- Performing Test DEAL_II_COMPILER_HAS_ATTRIBUTE_ALWAYS_INLINE - Success
-- Performing Test DEAL_II_COMPILER_HAS_RESTRICT_KEYWORD
-- Performing Test DEAL_II_COMPILER_HAS_RESTRICT_KEYWORD - Success
-- Performing Test DEAL_II_COMPILER_HAS_DIAGNOSTIC_PRAGMA
-- Performing Test DEAL_II_COMPILER_HAS_DIAGNOSTIC_PRAGMA - Success
-- Performing Test DEAL_II_COMPILER_HAS_FUSE_LD_LLD
-- Performing Test DEAL_II_COMPILER_HAS_FUSE_LD_LLD - Failed
-- Performing Test DEAL_II_COMPILER_HAS_FUSE_LD_GOLD
-- Performing Test DEAL_II_COMPILER_HAS_FUSE_LD_GOLD - Success
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/checks/check_02_system_features.cmake
-- Looking for C++ include sys/resource.h
-- Looking for C++ include sys/resource.h - found
-- Looking for C++ include unistd.h
-- Looking for C++ include unistd.h - found
-- Looking for gethostname
-- Looking for gethostname - found
-- Looking for getpid
-- Looking for getpid - found
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/checks/check_03_compiler_bugs.cmake
-- Performing Test DEAL_II_TEMPL_SPEC_FRIEND_BUG_OK
-- Performing Test DEAL_II_TEMPL_SPEC_FRIEND_BUG_OK - Success
-- Test successful, do not define DEAL_II_TEMPL_SPEC_FRIEND_BUG
-- Performing Test DEAL_II_MEMBER_ARRAY_SPECIALIZATION_BUG_OK
-- Performing Test DEAL_II_MEMBER_ARRAY_SPECIALIZATION_BUG_OK - Success
-- Test successful, do not define DEAL_II_MEMBER_ARRAY_SPECIALIZATION_BUG
-- Performing Test DEAL_II_CONST_MEMBER_DEDUCTION_BUG_OK
-- Performing Test DEAL_II_CONST_MEMBER_DEDUCTION_BUG_OK - Success
-- Test successful, do not define DEAL_II_CONST_MEMBER_DEDUCTION_BUG
-- Performing Test DEAL_II_BIND_NO_CONST_OP_PARENTHESES_OK
-- Performing Test DEAL_II_BIND_NO_CONST_OP_PARENTHESES_OK - Success
-- Test successful, do not define DEAL_II_BIND_NO_CONST_OP_PARENTHESES
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/configure/configure_1_cuda.cmake
-- DEAL_II_WITH_CUDA is set to off.
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/configure/configure_1_lapack.cmake
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Could NOT find BLAS (missing: BLAS_LIBRARIES)
-- LAPACK requires BLAS
-- A library with LAPACK API not found. Please specify library location.
-- Performing Test gfortran_LIBRARY
-- Performing Test gfortran_LIBRARY - Failed
-- Performing Test m_LIBRARY
-- Performing Test m_LIBRARY - Success
-- Performing Test quadmath_LIBRARY
-- Performing Test quadmath_LIBRARY - Success
-- Performing Test c_LIBRARY
-- Performing Test c_LIBRARY - Success
--   LAPACK_LIBRARIES: *** Required variable "_lapack_libraries" empty ***
--   LAPACK_LINKER_FLAGS:
--   LAPACK_INCLUDE_DIRS:
--   LAPACK_USER_INCLUDE_DIRS:
-- Could NOT find LAPACK
-- DEAL_II_WITH_LAPACK has unmet external dependencies.
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/configure/configure_1_mpi.cmake
-- DEAL_II_WITH_MPI is set to off.
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/configure/configure_1_threads.cmake
-- TBB_LIBRARY not found! Call:
--     FIND_LIBRARY(TBB_LIBRARY NAMES tbb HINTS PATH_SUFFIXES lib lib64 lib)
-- TBB_DEBUG_LIBRARY not found! Call:
--     FIND_LIBRARY(TBB_DEBUG_LIBRARY NAMES tbb_debug HINTS PATH_SUFFIXES lib lib64 lib)
-- TBB_INCLUDE_DIR not found! Call:
--     FIND_PATH(TBB_INCLUDE_DIR tbb/tbb_stddef.h HINTS PATH_SUFFIXES include include/tbb tbb)
--   TBB_LIBRARIES: *** Required variable "TBB_LIBRARY" set to NOTFOUND ***
--   TBB_INCLUDE_DIRS: *** Required variable "TBB_INCLUDE_DIR" set to NOTFOUND ***
--   TBB_USER_INCLUDE_DIRS: *** Required variable "TBB_INCLUDE_DIR" set to NOTFOUND ***
-- Could NOT find TBB
-- The externally provided TBB library is older than version 4.2.0, which cannot be used with deal.II.
-- DEAL_II_WITH_THREADS has unmet external dependencies.
-- Performing Test DEAL_II_HAVE_FLAG_pthread
-- Performing Test DEAL_II_HAVE_FLAG_pthread - Success
-- Performing Test DEAL_II_HAVE_MT_POSIX_BARRIERS
-- Performing Test DEAL_II_HAVE_MT_POSIX_BARRIERS - Success
-- Performing Test DEAL_II_HAVE_FLAG_Wparentheses
-- Performing Test DEAL_II_HAVE_FLAG_Wparentheses - Success
-- DEAL_II_WITH_THREADS successfully set up with bundled packages.
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/configure/configure_1_zlib.cmake
-- Could NOT find ZLIB (missing: ZLIB_LIBRARY ZLIB_INCLUDE_DIR)
--   ZLIB_LIBRARIES: *** Required variable "ZLIB_LIBRARY" set to NOTFOUND ***
--   ZLIB_INCLUDE_DIRS: *** Required variable "ZLIB_INCLUDE_DIR" set to NOTFOUND ***
-- Could NOT find ZLIB
-- DEAL_II_WITH_ZLIB has unmet external dependencies.
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/configure/configure_2_boost.cmake
-- Could NOT find Boost (missing: Boost_INCLUDE_DIR serialization system thread) (Required is at least version "1.59")
--   BOOST_LIBRARIES: *** Required variable "Boost_LIBRARIES" empty ***
--   BOOST_INCLUDE_DIRS: *** Required variable "Boost_INCLUDE_DIRS" set to NOTFOUND ***
--   BOOST_USER_INCLUDE_DIRS: *** Required variable "Boost_INCLUDE_DIRS" set to NOTFOUND ***
-- Could NOT find BOOST
-- DEAL_II_WITH_BOOST has unmet external dependencies.
-- Performing Test rt_LIBRARY
-- Performing Test rt_LIBRARY - Success
-- Performing Test DEAL_II_HAS_AUTO_PTR
-- Performing Test DEAL_II_HAS_AUTO_PTR - Failed
-- DEAL_II_WITH_BOOST successfully set up with bundled packages.
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/configure/configure_2_ginkgo.cmake
-- GINKGO_LIBRARY not found! Call:
--     FIND_LIBRARY(GINKGO_LIBRARY NAMES ginkgo HINTS PATH_SUFFIXES lib lib64 lib build/Linux-x86_64/libginkgo)
-- GINKGO_REFERENCE_LIBRARY not found! Call:
--     FIND_LIBRARY(GINKGO_REFERENCE_LIBRARY NAMES ginkgo_reference HINTS PATH_SUFFIXES lib lib64 lib build/Linux-x86_64/libginkgo_reference)
-- GINKGO_OMP_LIBRARY not found! Call:
--     FIND_LIBRARY(GINKGO_OMP_LIBRARY NAMES ginkgo_omp HINTS PATH_SUFFIXES lib lib64 lib build/Linux-x86_64/libginkgo_omp)
-- GINKGO_CUDA_LIBRARY not found! Call:
--     FIND_LIBRARY(GINKGO_CUDA_LIBRARY NAMES ginkgo_cuda HINTS PATH_SUFFIXES lib lib64 lib build/Linux-x86_64/libginkgo_cuda)
-- GINKGO_INCLUDE_DIR not found! Call:
--     FIND_PATH(GINKGO_INCLUDE_DIR ginkgo/ginkgo.hpp HINTS PATH_SUFFIXES include)
--   GINKGO_LIBRARIES: *** Required variable "GINKGO_LIBRARY" set to NOTFOUND ***
--   GINKGO_INCLUDE_DIRS: *** Required variable "GINKGO_INCLUDE_DIR" set to NOTFOUND ***
--   GINKGO_USER_INCLUDE_DIRS: *** Required variable "GINKGO_INCLUDE_DIR" set to NOTFOUND ***
-- Could NOT find GINKGO
-- DEAL_II_WITH_GINKGO has unmet external dependencies.
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/configure/configure_2_metis.cmake
-- METIS_LIBRARY not found! Call:
--     FIND_LIBRARY(METIS_LIBRARY NAMES metis HINTS PATH_SUFFIXES lib lib64 lib build/Linux-x86_64/libmetis)
-- METIS_INCLUDE_DIR not found! Call:
--     FIND_PATH(METIS_INCLUDE_DIR metis.h HINTS PATH_SUFFIXES metis include/metis include)
--   METIS_LIBRARIES: *** Required variable "METIS_LIBRARY" set to NOTFOUND ***
--   METIS_INCLUDE_DIRS: *** Required variable "METIS_INCLUDE_DIR" set to NOTFOUND ***
--   METIS_USER_INCLUDE_DIRS: *** Required variable "METIS_INCLUDE_DIR" set to NOTFOUND ***
-- Could NOT find METIS
-- DEAL_II_WITH_METIS has unmet external dependencies.
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/configure/configure_2_trilinos.cmake
-- EPETRA_CONFIG_H not found! Call:
--     FIND_FILE(EPETRA_CONFIG_H Epetra_config.h HINTS NO_DEFAULT_PATH NO_CMAKE_ENVIRONMENT_PATH NO_CMAKE_PATH NO_SYSTEM_ENVIRONMENT_PATH NO_CMAKE_SYSTEM_PATH NO_CMAKE_FIND_ROOT_PATH)
--   TRILINOS_LIBRARIES:
--   TRILINOS_INCLUDE_DIRS: *** Required variable "Trilinos_INCLUDE_DIRS" empty ***
--   TRILINOS_USER_INCLUDE_DIRS: *** Required variable "Trilinos_INCLUDE_DIRS" empty ***
--   TRILINOS_LINKER_FLAGS:
-- Could NOT find TRILINOS
-- DEAL_II_WITH_TRILINOS has unmet external dependencies.
--
-- Include /home/newton/fem/dealii-9.2.0/cmake/configure/configure_2_umfpack.cmake
CMake Error at cmake/macros/macro_configure_feature.cmake:196 (MESSAGE):
 

  DEAL_II_WITH_UMFPACK has unmet configuration requirements:
  DEAL_II_WITH_LAPACK has to be set to "ON".

 

Call Stack (most recent call first):
  cmake/configure/configure_2_umfpack.cmake:46 (CONFIGURE_FEATURE)
  cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
  CMakeLists.txt:124 (VERBOSE_INCLUDE)


-- Configuring incomplete, errors occurred!
See also "/home/newton/fem/dealii-9.2.0/CMakeFiles/CMakeOutput.log".
See also "/home/newton/fem/dealii-9.2.0/CMakeFiles/CMakeError.log".

[陈敏]

You can install lapack/blas of netlib version or openblas version or intel mkl version

best 

chen

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