[petsc-users] error building petsc with gcc

Fri Aug 24 11:43:11 CDT 2018

  Is the application specifically linking against -lm and all the other libraries that PETSc links against?

> On Aug 24, 2018, at 12:32 AM, Mark Adams <mfadams at lbl.gov> wrote:
> 
> 
> 
> On Thu, Aug 23, 2018 at 7:23 PM Smith, Barry F. <bsmith at mcs.anl.gov> wrote:
> 
>   Some mixup between an Intel build and a gcc build?
> 
> I was careful about this. I reconfigured and am getting missing LAPACK methods on PETSc tests. (This __isnormal error came from building the application, which has its own build system and that might have LAPACK in it.) I reconfigured and download blas and PETSc tests are working. 
> 
> Baky: try it again.
> 
> Thanks,
> Mark
>  
> 
> 
> > On Aug 23, 2018, at 4:15 PM, Bakytzhan Kallemov <bkallemov at lbl.gov> wrote:
> > 
> > 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
> > 
> 