Public bug reported:
I share my debug on the arm64 issue.
1) deal.ii fails to use ld=GOLD on Ubuntu, while it succeeds in Debian,
so the arm64 link failure is just a problem hidden in Debian because
gold is correctly used.
this is what is done in the check to test if cxx and flags are usable:
cat main.cpp
int main () { return 0; }
/usr/bin/c++ -DDEAL_II_HAVE_USABLE_FLAGS_DEBUG -pedantic -fPIC -Wall -Wextra
-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 -std=c++17 -g -O2
-fdebug-prefix-map=/deal.ii-9.1.1=. -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wno-nonnull-compare
-Wno-address -Wno-unused-local-typedefs -O0 -ggdb -Wa,--compress-debug-sections
-rdynamic main.cpp -o cmTC_10815
-Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/openmpi:/usr/lib/x86_64-linux-gnu/openmpi/lib:/usr/lib/x86_64-linux-gnu/hdf5/openmpi/lib/lib
-rdynamic -fuse-ld=gold -Wl,-Bsymbolic-functions -Wl,-z,relro -pthread
-pthread -ggdb /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 -pthread
/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_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_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_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.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_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/hdf5/openmpi/libhdf5.so
/usr/lib/x86_64-linux-gnu/libtbb.so /usr/lib/x86_64-linux-gnu/libz.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 -ldl
/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 -lrt
/usr/lib/x86_64-linux-gnu/libparpack.so /usr/lib/x86_64-linux-gnu/libarpack.so
/usr/lib/x86_64-linux-gnu/libassimp.so /usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so
/usr/lib/x86_64-linux-gnu/hdf5/openmpi/lib/lib/libhdf5_hl.so
/usr/lib/x86_64-linux-gnu/hdf5/openmpi/lib/lib/libhdf5.so
/usr/lib/x86_64-linux-gnu/libmuparser.so
/usr/lib/x86_64-linux-gnu/libnetcdf_c++.so
/usr/lib/x86_64-linux-gnu/libnetcdf.so /usr/lib/x86_64-linux-gnu/libTKBO.so
/usr/lib/x86_64-linux-gnu/libTKBool.so /usr/lib/x86_64-linux-gnu/libTKBRep.so
/usr/lib/x86_64-linux-gnu/libTKernel.so /usr/lib/x86_64-linux-gnu/libTKFeat.so
/usr/lib/x86_64-linux-gnu/libTKFillet.so /usr/lib/x86_64-linux-gnu/libTKG2d.so
/usr/lib/x86_64-linux-gnu/libTKG3d.so
/usr/lib/x86_64-linux-gnu/libTKGeomAlgo.so
/usr/lib/x86_64-linux-gnu/libTKGeomBase.so
/usr/lib/x86_64-linux-gnu/libTKHLR.so /usr/lib/x86_64-linux-gnu/libTKIGES.so
/usr/lib/x86_64-linux-gnu/libTKMath.so /usr/lib/x86_64-linux-gnu/libTKMesh.so
/usr/lib/x86_64-linux-gnu/libTKOffset.so /usr/lib/x86_64-linux-gnu/libTKPrim.so
/usr/lib/x86_64-linux-gnu/libTKShHealing.so
/usr/lib/x86_64-linux-gnu/libTKSTEP.so
/usr/lib/x86_64-linux-gnu/libTKSTEPAttr.so
/usr/lib/x86_64-linux-gnu/libTKSTEPBase.so
/usr/lib/x86_64-linux-gnu/libTKSTEP209.so /usr/lib/x86_64-linux-gnu/libTKSTL.so
/usr/lib/x86_64-linux-gnu/libTKTopAlgo.so
/usr/lib/x86_64-linux-gnu/libTKXSBase.so /usr/lib/x86_64-linux-gnu/libp4est.so
/usr/lib/x86_64-linux-gnu/libsc.so
/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
-lgfortran -lquadmath -lm -lc -lgcc_s -lgcc
/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
/usr/lib/x86_64-linux-gnu/libslepc.so /usr/lib/x86_64-linux-gnu/libpetsc.so
/usr/lib/x86_64-linux-gnu/libsundials_idas.so
/usr/lib/x86_64-linux-gnu/libsundials_arkode.so
/usr/lib/x86_64-linux-gnu/libsundials_kinsol.so
/usr/lib/x86_64-linux-gnu/libsundials_nvecserial.so
/usr/lib/x86_64-linux-gnu/libsundials_nvecparallel.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so: error: undefined reference
to 'opal_class_init_epoch'
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so: error: undefined reference
to 'opal_list_item_t_class'
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so: error: undefined reference
to 'opal_class_initialize'
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so: error: undefined reference
to 'opal_uses_threads'
collect2: error: ld returned 1 exit status
So I presume as soon as openmpi is built with gcc-9 asneeded flag Debian will
have the same failure.
** Affects: deal.ii (Ubuntu)
Importance: Undecided
Assignee: Graham Inggs (ginggs)
Status: New
** Changed in: deal.ii (Ubuntu)
Assignee: (unassigned) => Graham Inggs (ginggs)
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https://bugs.launchpad.net/bugs/1841577
Title:
deal.ii FTBFS on arm64, bug in openmpi?
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