[petsc-users] error building petsc with gcc

[Bakytzhan Kallemov]

Hello,

We are getting an error when linking our code.
This is our compiler:

kallemov at cori03:~/svn_treb/EBAMRINS/execBCG> CC --version
g++ (GCC) 7.3.0 20180125 (Cray Inc.)
Copyright (C) 2017 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

We are missing an external function __isnormal. Do you have any ideas?

Baky (and Mark Adams)


/bin/csh -f -c "CC  -march=native -std=c++11 -Wno-unused-but-set-variable
-Wno-long-long -Wno-sign-compare -Wno-deprecated -ftemplate-depth-99
-Wno-unused-local-typedefs -Wno-literal-suffix -Wno-variadic-macros
-fopenmp -O3 -march=native -std=c++11 -Wno-unused-but-set-variable
-Wno-long-long -Wno-sign-compare -Wno-deprecated -ftemplate-depth-99
-Wno-unused-local-typedefs -Wno-literal-suffix -Wno-variadic-macros
-fopenmp
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/viscousDriver.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/HairIF.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBCrankNicolson.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/AMRINSUtils.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/CotanIF.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/TrigIF.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/ArteryIF.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/HairyIF.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBCPPlotter.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/RampIF.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBAMRNoSubcycle.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBPetscSolver.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBIBC.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBGradDivFilter.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/TrebDirichletPoissonEBBC.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBPetscAMRSolver.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/NoFlowAdvectBC.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBCompositeCCProjector.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/copyWithGhost.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBLevelCCProjector.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBPetscLinearSolverPoisson.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/TrebNeumannPoissonEBBC.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBCompositeMACProjector.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBLevelMACProjector.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBPetscCompGridPois.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/InflowOutflowAdvectBC.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/InflowOutflowPoissonDomainBC.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBIBCFactory.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/TrebEBPetscLinearSolverPoisson.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/copyOver.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/extrapolateData.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/RobinPoissonEBBC.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/SVD.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/InflowOutflowIBC.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/NoFlowVortex.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/lsStencil.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/Choose.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/PoiseuilleInflowBCValue.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/util.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBPetscGridConductivity.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBPetscMap.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBPetscGridPoisson.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBAMRNoSubcycleF.o
o/3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC/EBGradDivFilterF.o
 -L../../../Chombo/lib
-lebamrtimedependent3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC
-lebamrelliptic3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC
-lebamrtools3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC
-lworkshop3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC
-lebtools3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC
-lamrtimedependent3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC
-lamrelliptic3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC
-lamrtools3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC
-lboxtools3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC
-lbasetools3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC
-L/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/lib       -lhdf5 -lz
 -L/global/homes/m/madams/petsc_install/petsc-cori-knl-opt64-gcc-omp/lib
-Wl,-rpath,/global/homes/m/madams/petsc_install/petsc-cori-knl-opt64-gcc-omp/lib
-L/global/homes/m/madams/petsc_install/petsc-cori-knl-opt64-gcc-omp/lib
-lpetsc -lsuperlu_dist -lHYPRE -lparmetis -lmetis -lstdc++ -ldl
 -lgfortran -lm -lgomp  -o
viscousDriver3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC.ex |&  awk -f
../../../Chombo/lib/mk/tempnam.awk"
/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/lib/libhdf5.a(H5PL.o): In
function `H5PL_load':
H5PL.c:(.text+0x7a0): warning: Using 'dlopen' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/global/homes/m/madams/petsc_install/petsc-cori-knl-opt64-gcc-omp/lib/libpetsc.a(send.o):
In function `PetscOpenSocket':
/global/u2/m/madams/petsc_install/petsc/src/sys/classes/viewer/impls/socket/send.c:107:
warning: Using 'gethostbyname' in statically linked applications requires
at runtime the shared libraries from the glibc version used for linking
/global/homes/m/madams/petsc_install/petsc-cori-knl-opt64-gcc-omp/lib/libpetsc.a(mathinf.o):
In function `PetscIsNormalReal':
/global/u2/m/madams/petsc_install/petsc/src/sys/utils/mathinf.c:23:
undefined reference to `__isnormal'
/usr/bin/ld: link errors found, deleting executable
`viscousDriver3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC.ex'
collect2: error: ld returned 1 exit status
../../../Chombo/lib/mk/Make.rules:412: recipe for target
'viscousDriver3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC.ex' failed
gmake[1]: ***
[viscousDriver3d.Linux.64.CC.ftn.OPTHIGH.MPI.OPENMPCC.PETSC.ex] Error 1
../../../Chombo/lib/mk/Make.rules:325: recipe for target 'all-example'
failed
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