error installing dealii

[Mahmoud Ajbar]

Dear Community,

After installing dealii development package in ubuntu, I tried to compile a code that requires MPI, Trilinos and Trilinos with Sacado, while all these are OFF.

I have read in the documentation that I should pass the -DDEAL_II_WITH_MPI=ON argument to cmake. Could anyone walk me through this process please I am new to dealii and ubuntu.

Thank you in advanced for your help.

Greetings

[Bruno Turcksin]

Hello,

It looks like you installed deal.II in /home/ajbar/Bureau/dealii How did you configure it? To get the code to compile, you need to reconfigure, recompile, and reinstall deal.II This time when you configure deal.II, make sure that the configuration line contains -DDEAL_II_WITH_MPI=ON and -DDEAL_II_WITH_TRILINOS=ON.

Best,

Bruno

[Mahmoud Ajbar]

Hello Bruno,

Thank you for your quick reply.

I have downloaded the deal.ii 9.4.0-1ubuntu1 source package in Ubuntu available here : https://launchpad.net/ubuntu/+source/deal.ii/9.4.0-1ubuntu1.

I tried to put ON both for MPI and Trilinos on the file "deal.IIConfig.cmake" which I found on the build/cmake/config folder after passing the command "cmake -DCMAKE_INSTALL_PREFIX=/home/ajbar/deal.ii-9.4.0 /home/ajbar/Téléchargements/deal.ii-9.4.0" and then launch the intallation process, unfortunately, I ended up with the same error message.

Could you please inform about the file I should modify to have the correct configuration?

Regards,

Mahmoud

[Bruno Turcksin]

Mahmoud,

You should add  -DDEAL_II_WITH_MPI=ON and -DDEAL_II_WITH_TRILINOS=ON  to the cmake command. Then, you can compile and install deal.II You should not modify deal.IIConfig.cmake (or any other file for that matter). Th cmake like should look like:

cmake -DDEAL_II_WITH_MPI_MPI=ON -DDEAL_II_WITH_TRILINOS=ON -DCMAKE_INSTALL_PREFIX=/path ..

Best,

Bruno

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[Mahmoud Ajbar]

Hello Bruno,

Thank you for the explanation.

Now I am getting another issue when building cmake :

-- Include /home/ajbar/Téléchargements/deal.ii-9.4.0/cmake/setup_finalize.cmake
-- Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG
-- Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG - Failed
-- Unable to compile a simple test program. Trying to drop "-fuse-ld=gold" from the linker flags.
-- Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG
-- Performing Test DEAL_II_HAVE_USABLE_FLAGS_DEBUG - Failed
CMake Error at cmake/setup_finalize.cmake:137 (MESSAGE):
 

    Configuration error: Cannot compile a test program with the final set of
    compiler and linker flags:
      CXX flags (DEBUG): -pedantic -fPIC -Wall -Wextra -Wmissing-braces -Woverloaded-virtual -Wpointer-arith -Wsign-compare -Wsuggest-override -Wswitch -Wsynth -Wwrite-strings -Wno-placement-new -Wno-deprecated-declarations -Wno-literal-suffix -Wno-psabi -Wno-class-memaccess -fopenmp-simd -pthread -Wno-unused-local-typedefs -O0 -ggdb -Wa,--compress-debug-sections
      LD flags  (DEBUG): -rdynamic  -lpthread -pthread -ggdb
      LIBRARIES (DEBUG): /usr/lib/x86_64-linux-gnu/openmpi/lib/libopen-pal.so;/usr/lib/x86_64-linux-gnu/libboost_iostreams.so;/usr/lib/x86_64-linux-gnu/libboost_serialization.so;/usr/lib/x86_64-linux-gnu/libboost_system.so;/usr/lib/x86_64-linux-gnu/libboost_thread.so;/usr/lib/x86_64-linux-gnu/libboost_regex.so;/usr/lib/x86_64-linux-gnu/libboost_chrono.so;/usr/lib/x86_64-linux-gnu/libboost_date_time.so;/usr/lib/x86_64-linux-gnu/libboost_atomic.so;/usr/lib/x86_64-linux-gnu/libtrilinos_pike-blackbox.so;/usr/lib/x86_64-linux-gnu/libtrilinos_trilinoscouplings.so;/usr/lib/x86_64-linux-gnu/libtrilinos_piro.so;/usr/lib/x86_64-linux-gnu/libtrilinos_rol.so;/usr/lib/x86_64-linux-gnu/libtrilinos_stokhos_muelu.so;/usr/lib/x86_64-linux-gnu/libtrilinos_stokhos_ifpack2.so;/usr/lib/x86_64-linux-gnu/libtrilinos_stokhos_amesos2.so;/usr/lib/x86_64-linux-gnu/libtrilinos_stokhos_tpetra.so;/usr/lib/x86_64-linux-gnu/libtrilinos_stokhos_sacado.so;/usr/lib/x86_64-linux-gnu/libtrilinos_stokhos.so;/usr/lib/x86_64-linux-gnu/libtrilinos_rythmos.so;/usr/lib/x86_64-linux-gnu/libtrilinos_shylu_ddcommon.so;/usr/lib/x86_64-linux-gnu/libtrilinos_shylu_ddfrosch.so;/usr/lib/x86_64-linux-gnu/libtrilinos_muelu-adapters.so;/usr/lib/x86_64-linux-gnu/libtrilinos_muelu-interface.so;/usr/lib/x86_64-linux-gnu/libtrilinos_muelu.so;/usr/lib/x86_64-linux-gnu/libtrilinos_moertel.so;/usr/lib/x86_64-linux-gnu/libtrilinos_locathyra.so;/usr/lib/x86_64-linux-gnu/libtrilinos_locaepetra.so;/usr/lib/x86_64-linux-gnu/libtrilinos_localapack.so;/usr/lib/x86_64-linux-gnu/libtrilinos_loca.so;/usr/lib/x86_64-linux-gnu/libtrilinos_noxepetra.so;/usr/lib/x86_64-linux-gnu/libtrilinos_noxlapack.so;/usr/lib/x86_64-linux-gnu/libtrilinos_nox.so;/usr/lib/x86_64-linux-gnu/libtrilinos_phalanx.so;/usr/lib/x86_64-linux-gnu/libtrilinos_intrepid2.so;/usr/lib/x86_64-linux-gnu/libtrilinos_intrepid.so;/usr/lib/x86_64-linux-gnu/libtrilinos_teko.so;/usr/lib/x86_64-linux-gnu/libtrilinos_stratimikos.so;/usr/lib/x86_64-linux-gnu/libtrilinos_stratimikosbelos.so;/usr/lib/x86_64-linux-gnu/libtrilinos_stratimikosamesos2.so;/usr/lib/x86_64-linux-gnu/libtrilinos_stratimikosaztecoo.so;/usr/lib/x86_64-linux-gnu/libtrilinos_stratimikosamesos.so;/usr/lib/x86_64-linux-gnu/libtrilinos_stratimikosml.so;/usr/lib/x86_64-linux-gnu/libtrilinos_stratimikosifpack.so;/usr/lib/x86_64-linux-gnu/libtrilinos_ifpack2-adapters.so;/usr/lib/x86_64-linux-gnu/libtrilinos_ifpack2.so;/usr/lib/x86_64-linux-gnu/libtrilinos_anasazitpetra.so;/usr/lib/x86_64-linux-gnu/libtrilinos_ModeLaplace.so;/usr/lib/x86_64-linux-gnu/libtrilinos_anasaziepetra.so;/usr/lib/x86_64-linux-gnu/libtrilinos_anasazi.so;/usr/lib/x86_64-linux-gnu/libtrilinos_komplex.so;/usr/lib/x86_64-linux-gnu/libtrilinos_amesos2.so;/usr/lib/x86_64-linux-gnu/libtrilinos_shylu_nodetacho.so;/usr/lib/x86_64-linux-gnu/libtrilinos_shylu_nodehts.so;/usr/lib/x86_64-linux-gnu/libtrilinos_belosxpetra.so;/usr/lib/x86_64-linux-gnu/libtrilinos_belostpetra.so;/usr/lib/x86_64-linux-gnu/libtrilinos_belosepetra.so;/usr/lib/x86_64-linux-gnu/libtrilinos_belos.so;/usr/lib/x86_64-linux-gnu/libtrilinos_ml.so;/usr/lib/x86_64-linux-gnu/libtrilinos_ifpack.so;/usr/lib/x86_64-linux-gnu/libtrilinos_zoltan2.so;/usr/lib/x86_64-linux-gnu/libtrilinos_pamgen_extras.so;/usr/lib/x86_64-linux-gnu/libtrilinos_pamgen.so;/usr/lib/x86_64-linux-gnu/libtrilinos_amesos.so;/usr/lib/x86_64-linux-gnu/libtrilinos_galeri-xpetra.so;/usr/lib/x86_64-linux-gnu/libtrilinos_galeri-epetra.so;/usr/lib/x86_64-linux-gnu/libtrilinos_aztecoo.so;/usr/lib/x86_64-linux-gnu/libtrilinos_dpliris.so;/usr/lib/x86_64-linux-gnu/libtrilinos_isorropia.so;/usr/lib/x86_64-linux-gnu/libtrilinos_optipack.so;/usr/lib/x86_64-linux-gnu/libtrilinos_xpetra-sup.so;/usr/lib/x86_64-linux-gnu/libtrilinos_xpetra.so;/usr/lib/x86_64-linux-gnu/libtrilinos_thyratpetra.so;/usr/lib/x86_64-linux-gnu/libtrilinos_thyraepetraext.so;/usr/lib/x86_64-linux-gnu/libtrilinos_thyraepetra.so;/usr/lib/x86_64-linux-gnu/libtrilinos_thyracore.so;/usr/lib/x86_64-linux-gnu/libtrilinos_epetraext.so;/usr/lib/x86_64-linux-gnu/libtrilinos_trilinosss.so;/usr/lib/x86_64-linux-gnu/libtrilinos_tpetraext.so;/usr/lib/x86_64-linux-gnu/libtrilinos_tpetrainout.so;/usr/lib/x86_64-linux-gnu/libtrilinos_tpetra.so;/usr/lib/x86_64-linux-gnu/libtrilinos_kokkostsqr.so;/usr/lib/x86_64-linux-gnu/libtrilinos_tpetraclassiclinalg.so;/usr/lib/x86_64-linux-gnu/libtrilinos_tpetraclassicnodeapi.so;/usr/lib/x86_64-linux-gnu/libtrilinos_tpetraclassic.so;/usr/lib/x86_64-linux-gnu/libtrilinos_triutils.so;/usr/lib/x86_64-linux-gnu/libtrilinos_globipack.so;/usr/lib/x86_64-linux-gnu/libtrilinos_shards.so;/usr/lib/x86_64-linux-gnu/libtrilinos_zoltan.so;/usr/lib/x86_64-linux-gnu/libtrilinos_epetra.so;/usr/lib/x86_64-linux-gnu/libtrilinos_sacado.so;/usr/lib/x86_64-linux-gnu/libtrilinos_rtop.so;/usr/lib/x86_64-linux-gnu/libtrilinos_kokkoskernels.so;/usr/lib/x86_64-linux-gnu/libtrilinos_teuchoskokkoscomm.so;/usr/lib/x86_64-linux-gnu/libtrilinos_teuchoskokkoscompat.so;/usr/lib/x86_64-linux-gnu/libtrilinos_teuchosremainder.so;/usr/lib/x86_64-linux-gnu/libtrilinos_teuchosnumerics.so;/usr/lib/x86_64-linux-gnu/libtrilinos_teuchoscomm.so;/usr/lib/x86_64-linux-gnu/libtrilinos_teuchosparameterlist.so;/usr/lib/x86_64-linux-gnu/libtrilinos_teuchosparser.so;/usr/lib/x86_64-linux-gnu/libtrilinos_teuchoscore.so;/usr/lib/x86_64-linux-gnu/libtrilinos_kokkosalgorithms.so;/usr/lib/x86_64-linux-gnu/libtrilinos_kokkoscontainers.so;/usr/lib/x86_64-linux-gnu/libtrilinos_kokkoscore.so;/usr/lib/x86_64-linux-gnu/libsmumps.so;/usr/lib/x86_64-linux-gnu/libdmumps.so;/usr/lib/x86_64-linux-gnu/libcmumps.so;/usr/lib/x86_64-linux-gnu/libzmumps.so;/usr/lib/x86_64-linux-gnu/libpord.so;/usr/lib/x86_64-linux-gnu/libmumps_common.so;/usr/lib/x86_64-linux-gnu/libtbb.so;/usr/lib/x86_64-linux-gnu/libptscotch.so;/usr/lib/x86_64-linux-gnu/libptscotcherr.so;/usr/lib/x86_64-linux-gnu/libscotch.so;/usr/lib/x86_64-linux-gnu/libscotcherr.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so;/usr/lib/x86_64-linux-gnu/libamd.so;rt;/usr/lib/x86_64-linux-gnu/hdf5/openmpi/libhdf5.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;dl;m;/usr/lib/x86_64-linux-gnu/libscalapack-openmpi.so;/usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_usempif08.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_usempi_ignore_tkr.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_mpifh.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so;
   

 Call Stack (most recent call first):
  cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
  CMakeLists.txt:136 (VERBOSE_INCLUDE)

-- Configuring incomplete, errors occurred!
See also "/home/ajbar/Téléchargements/deal.ii-9.4.0/build/CMakeFiles/CMakeOutput.log".
See also "/home/ajbar/Téléchargements/deal.ii-9.4.0/build/CMakeFiles/CMakeError.log".

Could you please help me with that?

Thank you in advanced for your help.

Greetings.

Mahmoud

[Bruno Turcksin]

Mahmoud,

Make sure you write the cmake command from an empty directory. Otherwise you can sometimes get weird results. If that doesn't help, please send the CMakeOutput.log and the CMakeError.log files.

Best,

Bruno

To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/a5c86105-5725-457c-86a5-a98fc264ac21n%40googlegroups.com.

[Mahmoud Ajbar]

Bruno,

I tried to run the cmake command from an empty directory yet still not working.

Please find attached the CMakeOutput.log and CMakeError.log files.

Regards,

Mahmoud

[Bruno Turcksin]

It looks like there is a problem with MUMPS dependencies. The compiler complains that it cannot find

/usr/lib/x86_64-linux-gnu/libptscotch.so

Can you check that this file exists. If it doesn't, try sudo apt install libmumps-ptscotch-dev or sudo apt install libptscotch-dev.

Bruno

To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/6a2d7fec-d2a3-4a95-b28f-e9ac2bc10b81n%40googlegroups.com.

[Jau-Uei Chen]

Dear all,

Recently, I also try to re-install dealii via candi on a Linux machine but encounter the same error message (CMakeError.log is different). On the machine, I have the following modules:

1) ubt18   2) gcc/9.2   3) mkl/19.0   4) mpich2/3.2   5) phdf5/1.10.5   6) paraview/5.7.0-MPI-Linux-Python2.7   7) matlab/r2022a   8) boost/1.69.0   9) cmake/3.20.0

Please see the attachment for .log files and the candi.sh file.

Any suggestion or comment is greatly appreciated.

Best Regards,

Jau-Uei

bruno.t...@gmail.com 在 2022年7月28日 星期四上午8:16:42 [UTC-5] 的信中寫道：

[Wolfgang Bangerth]

> Recently, I also try to re-install dealii via candi on a Linux machine but
> encounter the same error message (CMakeError.log is different). On the
> machine, I have the following modules:
> 1) ubt18   2) gcc/9.2   3) mkl/19.0   4) mpich2/3.2   5) phdf5/1.10.5   6)
> paraview/5.7.0-MPI-Linux-Python2.7   7) matlab/r2022a   8) boost/1.69.0   9)
> cmake/3.20.0
>
> Please see the attachment for .log files and the candi.sh file.
>
> Any suggestion or comment is greatly appreciated.

I don't know what exactly it is that is going wrong here, but this warning
here is suspicious:

/usr/bin/ld: warning: libmpi.so.20, needed by
/usr/lib/x86_64-linux-gnu/libscalapack-openmpi.so, may conflict with libmpi.so.12
/usr/bin/ld: warning: libgfortran.so.4, needed by
/usr/lib/x86_64-linux-gnu/libscalapack-openmpi.so, may conflict with
libgfortran.so.5

It suggests that you have been using different versions of MPI and/or the
compiler to compile different parts of the whole system. This will not likely
work. On cluster systems like the one you appear to be on, this may happen if
you load different modules at different times during the compilation process.
My suggestion would be to remove everything, make sure you put the 'module
load' commands into your .bashrc or .cshrc (so that you don't have to do it by
hand every time), and then restart the compilation process from scratch.

Best
W.


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

[Jau-Uei Chen]

Dear Dr. Wolfgang,

Thanks for the reply!

I tried to re-install again but still, end up with the same error. However, I found that I can successfully build dealii using candi with version 9.4.0-r2 with the same .cfg file (I was using the latest version). I am not quite sure what is going on but I am happy with the result.

Best Regards,

Jau-Uei Chen

Wolfgang Bangerth 在 2022年11月23日 星期三下午1:49:55 [UTC-6] 的信中寫道：