Errors during dealii installation

ASPECT
1

Dear all,
I am experiencing some issues during the installation of dependencies for the new ASPECT version on Ubuntu 16.04.
Specifically, it seems to be related to a test during the installation of dealii via candi (maybe something wrong with gfortran?).

Below I copy-paste some error messages:

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-deprecated-declarations -Wno-literal-suffix -Wno-psabi -fopenmp-simd -Wno-parentheses -Wno-unused-local-typedefs -O0 -ggdb -Wa,–compress-debug-sections
LD flags (DEBUG): -Wl,–as-needed -rdynamic -lgfortran -ggdb
LIBRARIES (DEBUG): /usr/local/lib/libz.so;/home/aspect/trilinos-release-12-18-1/lib/librol.so;/home/aspect/trilinos-release-12-18-1/lib/libtempus.so;/home/aspect/trilinos-release-12-18-1/lib/libmuelu-adapters.so;/home/aspect/trilinos-release-12-18-1/lib/libmuelu-interface.so;/home/aspect/trilinos-release-12-18-1/lib/libmuelu.so;/home/aspect/trilinos-release-12-18-1/lib/liblocathyra.so;/home/aspect/trilinos-release-12-18-1/lib/liblocaepetra.so;/home/aspect/trilinos-release-12-18-1/lib/liblocalapack.so;/home/aspect/trilinos-release-12-18-1/lib/libloca.so;/home/aspect/trilinos-release-12-18-1/lib/libnoxepetra.so;/home/aspect/trilinos-release-12-18-1/lib/libnoxlapack.so;/home/aspect/trilinos-release-12-18-1/lib/libnox.so;/home/aspect/trilinos-release-12-18-1/lib/libintrepid2.so;/home/aspect/trilinos-release-12-18-1/lib/libintrepid.so;/home/aspect/trilinos-release-12-18-1/lib/libteko.so;/home/aspect/trilinos-release-12-18-1/lib/libstratimikos.so;/home/aspect/trilinos-release-12-18-1/lib/libstratimikosbelos.so;/home/aspect/trilinos-release-12-18-1/lib/libstratimikosamesos2.so;/home/aspect/trilinos-release-12-18-1/lib/libstratimikosaztecoo.so;/home/aspect/trilinos-release-12-18-1/lib/libstratimikosamesos.so;/home/aspect/trilinos-release-12-18-1/lib/libstratimikosml.so;/home/aspect/trilinos-release-12-18-1/lib/libstratimikosifpack.so;/home/aspect/trilinos-release-12-18-1/lib/libanasazitpetra.so;/home/aspect/trilinos-release-12-18-1/lib/libModeLaplace.so;/home/aspect/trilinos-release-12-18-1/lib/libanasaziepetra.so;/home/aspect/trilinos-release-12-18-1/lib/libanasazi.so;/home/aspect/trilinos-release-12-18-1/lib/libamesos2.so;/home/aspect/trilinos-release-12-18-1/lib/libshylu_nodetacho.so;/home/aspect/trilinos-release-12-18-1/lib/libbelosxpetra.so;/home/aspect/trilinos-release-12-18-1/lib/libbelostpetra.so;/home/aspect/trilinos-release-12-18-1/lib/libbelosepetra.so;/home/aspect/trilinos-release-12-18-1/lib/libbelos.so;/home/aspect/trilinos-release-12-18-1/lib/libml.so;/home/aspect/trilinos-release-12-18-1/lib/libifpack.so;/home/aspect/trilinos-release-12-18-1/lib/libzoltan2.so;/home/aspect/trilinos-release-12-18-1/lib/libpamgen_extras.so;/home/aspect/trilinos-release-12-18-1/lib/libpamgen.so;/home/aspect/trilinos-release-12-18-1/lib/libamesos.so;/home/aspect/trilinos-release-12-18-1/lib/libgaleri-xpetra.so;/home/aspect/trilinos-release-12-18-1/lib/libgaleri-epetra.so;/home/aspect/trilinos-release-12-18-1/lib/libaztecoo.so;/home/aspect/trilinos-release-12-18-1/lib/libisorropia.so;/home/aspect/trilinos-release-12-18-1/lib/libxpetra-sup.so;/home/aspect/trilinos-release-12-18-1/lib/libxpetra.so;/home/aspect/trilinos-release-12-18-1/lib/libthyratpetra.so;/home/aspect/trilinos-release-12-18-1/lib/libthyraepetraext.so;/home/aspect/trilinos-release-12-18-1/lib/libthyraepetra.so;/home/aspect/trilinos-release-12-18-1/lib/libthyracore.so;/home/aspect/trilinos-release-12-18-1/lib/libtrilinosss.so;/home/aspect/trilinos-release-12-18-1/lib/libtpetraext.so;/home/aspect/trilinos-release-12-18-1/lib/libtpetrainout.so;/home/aspect/trilinos-release-12-18-1/lib/libtpetra.so;/home/aspect/trilinos-release-12-18-1/lib/libkokkostsqr.so;/home/aspect/trilinos-release-12-18-1/lib/libtpetraclassiclinalg.so;/home/aspect/trilinos-release-12-18-1/lib/libtpetraclassicnodeapi.so;/home/aspect/trilinos-release-12-18-1/lib/libtpetraclassic.so;/home/aspect/trilinos-release-12-18-1/lib/libepetraext.so;/home/aspect/trilinos-release-12-18-1/lib/libtriutils.so;/home/aspect/trilinos-release-12-18-1/lib/libshards.so;/home/aspect/trilinos-release-12-18-1/lib/libzoltan.so;/home/aspect/trilinos-release-12-18-1/lib/libepetra.so;/home/aspect/trilinos-release-12-18-1/lib/libsacado.so;/home/aspect/trilinos-release-12-18-1/lib/librtop.so;/home/aspect/trilinos-release-12-18-1/lib/libkokkoskernels.so;/home/aspect/trilinos-release-12-18-1/lib/libteuchoskokkoscomm.so;/home/aspect/trilinos-release-12-18-1/lib/libteuchoskokkoscompat.so;/home/aspect/trilinos-release-12-18-1/lib/libteuchosremainder.so;/home/aspect/trilinos-release-12-18-1/lib/libteuchosnumerics.so;/home/aspect/trilinos-release-12-18-1/lib/libteuchoscomm.so;/home/aspect/trilinos-release-12-18-1/lib/libteuchosparameterlist.so;/home/aspect/trilinos-release-12-18-1/lib/libteuchosparser.so;/home/aspect/trilinos-release-12-18-1/lib/libteuchoscore.so;/home/aspect/trilinos-release-12-18-1/lib/libkokkosalgorithms.so;/home/aspect/trilinos-release-12-18-1/lib/libkokkoscontainers.so;/home/aspect/trilinos-release-12-18-1/lib/libkokkoscore.so;/home/aspect/trilinos-release-12-18-1/lib/libgtest.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;/home/aspect/hdf5-1.10.7/lib/libhdf5_hl.so;/home/aspect/hdf5-1.10.7/lib/libhdf5.so;/home/aspect/oce-OCE-0.18.2/lib/libTKBO.so;/home/aspect/oce-OCE-0.18.2/lib/libTKBool.so;/home/aspect/oce-OCE-0.18.2/lib/libTKBRep.so;/home/aspect/oce-OCE-0.18.2/lib/libTKernel.so;/home/aspect/oce-OCE-0.18.2/lib/libTKFeat.so;/home/aspect/oce-OCE-0.18.2/lib/libTKFillet.so;/home/aspect/oce-OCE-0.18.2/lib/libTKG2d.so;/home/aspect/oce-OCE-0.18.2/lib/libTKG3d.so;/home/aspect/oce-OCE-0.18.2/lib/libTKGeomAlgo.so;/home/aspect/oce-OCE-0.18.2/lib/libTKGeomBase.so;/home/aspect/oce-OCE-0.18.2/lib/libTKHLR.so;/home/aspect/oce-OCE-0.18.2/lib/libTKIGES.so;/home/aspect/oce-OCE-0.18.2/lib/libTKMath.so;/home/aspect/oce-OCE-0.18.2/lib/libTKMesh.so;/home/aspect/oce-OCE-0.18.2/lib/libTKOffset.so;/home/aspect/oce-OCE-0.18.2/lib/libTKPrim.so;/home/aspect/oce-OCE-0.18.2/lib/libTKShHealing.so;/home/aspect/oce-OCE-0.18.2/lib/libTKSTEP.so;/home/aspect/oce-OCE-0.18.2/lib/libTKSTEPAttr.so;/home/aspect/oce-OCE-0.18.2/lib/libTKSTEPBase.so;/home/aspect/oce-OCE-0.18.2/lib/libTKSTEP209.so;/home/aspect/oce-OCE-0.18.2/lib/libTKSTL.so;/home/aspect/oce-OCE-0.18.2/lib/libTKTopAlgo.so;/home/aspect/oce-OCE-0.18.2/lib/libTKXSBase.so;/home/aspect/slepc-3.13.2/lib/libslepc.so;/home/aspect/petsc-3.13.1/lib/libpetsc.so;/home/aspect/petsc-3.13.1/lib/libHYPRE.so;/home/aspect/petsc-3.13.1/lib/libcmumps.a;/home/aspect/petsc-3.13.1/lib/libdmumps.a;/home/aspect/petsc-3.13.1/lib/libsmumps.a;/home/aspect/petsc-3.13.1/lib/libzmumps.a;/home/aspect/petsc-3.13.1/lib/libmumps_common.a;/home/aspect/petsc-3.13.1/lib/libpord.a;/home/aspect/petsc-3.13.1/lib/libscalapack.a;/usr/lib/liblapack.so;/usr/lib/libblas.so;/home/aspect/parmetis-4.0.3/lib/libparmetis.so;/home/aspect/parmetis-4.0.3/lib/libmetis.so;/usr/lib/openmpi/lib/libmpi_usempif08.so;/usr/lib/openmpi/lib/libmpi_usempi_ignore_tkr.so;/usr/lib/openmpi/lib/libmpi_mpifh.so;/usr/lib/openmpi/lib/libmpi.so;gfortran;m;quadmath;dl;/home/aspect/p4est-2.2/DEBUG/lib/libp4est.so;/home/aspect/p4est-2.2/DEBUG/lib/libsc.so

Please let me know if some other information are needed and thank you very much for your help!

All the best,
Nora

2

Hi Elena,

I’m not sure what the exact source of the error is here, but I have had no trouble compiling deal.II via Candi recently on more recent Ubuntu stable releases (18/20).

Would it be possible to upgrade your machine to Ubuntu 20.04?

Can you also post what version of gnu (gcc, gfortran, etc) you are using? Have they been updated recently?

Cheers,
John

3

Dear John,
thanks a lot for this reply! I am afraid it will not be possible to upgrade Ubuntu in my case…however, gcc, g++ are version 9.4, whereas I have now realized that gfortran is still 5.5 (even if I installed 9.4 this morning to have the same version for all the three and do not know why it is still 5.5…). It could be the cause of the issue?

I also tried to install dealii alone, but at the end of the installation (which indeed succeded) I realized that it should have been installed with the support of trilinos and p4est, thus I guess I would just need candi.

Thanks!
Nora

4

Hi Nora,

There may be a version of gfortran that was installed outside of the ubuntu package management system, and that folder is in your path.

Can you do the following via terminal and report the results?

  • which gfortran
  • gfortran --version
  • echo $PATH

John

5

Dear John,
results of the commands you sent are:
-/usr/bin/gfortran
-GNU Fortran (Ubuntu 9.4.0-1ubuntu1~16.04) 9.4.0 (I managed to update it)
-/home/aspect/bin:/home/aspect/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/aspect/deal.ii-candi/deal.II-v8.5.1:/home/aspect/ParaView-5.5.0/bin/

I guess there are problems with the last result…

Thanks!

Nora

6

Hi Nora,

Good news that the updated gfortran is the one that showed up.

I suggest deleting the old candi build directory and starting again, as candi determine at the beginning what compilers to use (i.e., just restarting the candi compilation may still cause issues).

Can you give that a shot and report back?

Cheers,
John

7

Dear John,
I really have to thank you a lot for this suggestion: finally, after a very-long installation, the issue is solved and the brand new version of ASPECT is installed on my computer!

Thank you so much for your help!!

Nora

8

Dear Nora,

Excellent, glad to hear that worked and happy modeling! :slight_smile:

John