<div dir="ltr"><br><br><div class="gmail_quote"><div dir="ltr">On Thu, Aug 23, 2018 at 7:23 PM Smith, Barry F. <<a href="mailto:bsmith@mcs.anl.gov" target="_blank">bsmith@mcs.anl.gov</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><br>
  Some mixup between an Intel build and a gcc build?<br></blockquote><div><br></div><div>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. </div><div><br></div><div>Baky: try it again.</div><div><br></div><div>Thanks,</div><div>Mark</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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> On Aug 23, 2018, at 4:15 PM, Bakytzhan Kallemov <<a href="mailto:bkallemov@lbl.gov" target="_blank">bkallemov@lbl.gov</a>> wrote:<br>
> <br>
> Hello,<br>
> <br>
> We are getting an error when linking our code. <br>
> This is our compiler:<br>
> <br>
> kallemov@cori03:~/svn_treb/EBAMRINS/execBCG> CC --version<br>
> g++ (GCC) 7.3.0 20180125 (Cray Inc.)<br>
> Copyright (C) 2017 Free Software Foundation, Inc.<br>
> This is free software; see the source for copying conditions.  There is NO<br>
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.<br>
> <br>
> We are missing an external function __isnormal. Do you have any ideas?<br>
> <br>
> Baky (and Mark Adams)<br>
> <br>
> <br>
> /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 -<a href="http://lebamrelliptic3d.Linux.64.CC" target="_blank">lebamrelliptic3d.Linux.64.CC</a>.ftn.OPTHIGH.MPI.OPENMPCC.PETSC -<a href="http://lebamrtools3d.Linux.64.CC" target="_blank">lebamrtools3d.Linux.64.CC</a>.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 -<a href="http://lamrelliptic3d.Linux.64.CC" target="_blank">lamrelliptic3d.Linux.64.CC</a>.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/<a href="http://1.10.1.1/GNU/5.1/lib" rel="noreferrer" target="_blank">1.10.1.1/GNU/5.1/lib</a>       -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 <a href="http://viscousDriver3d.Linux.64.CC" target="_blank">viscousDriver3d.Linux.64.CC</a>.ftn.OPTHIGH.MPI.OPENMPCC.PETSC.ex |&  awk -f ../../../Chombo/lib/mk/tempnam.awk"<br>
> /opt/cray/pe/hdf5-parallel/<a href="http://1.10.1.1/GNU/5.1/lib/libhdf5.a(H5PL.o)" rel="noreferrer" target="_blank">1.10.1.1/GNU/5.1/lib/libhdf5.a(H5PL.o)</a>: In function `H5PL_load':<br>
> H5PL.c:(.text+0x7a0): warning: Using 'dlopen' in statically linked applications requires at runtime the shared libraries from the glibc version used for linking<br>
> /global/homes/m/madams/petsc_install/petsc-cori-knl-opt64-gcc-omp/lib/libpetsc.a(send.o): In function `PetscOpenSocket':<br>
> /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<br>
> /global/homes/m/madams/petsc_install/petsc-cori-knl-opt64-gcc-omp/lib/libpetsc.a(mathinf.o): In function `PetscIsNormalReal':<br>
> /global/u2/m/madams/petsc_install/petsc/src/sys/utils/mathinf.c:23: undefined reference to `__isnormal'<br>
> /usr/bin/ld: link errors found, deleting executable `<a href="http://viscousDriver3d.Linux.64.CC" target="_blank">viscousDriver3d.Linux.64.CC</a>.ftn.OPTHIGH.MPI.OPENMPCC.PETSC.ex'<br>
> collect2: error: ld returned 1 exit status<br>
> ../../../Chombo/lib/mk/Make.rules:412: recipe for target '<a href="http://viscousDriver3d.Linux.64.CC" target="_blank">viscousDriver3d.Linux.64.CC</a>.ftn.OPTHIGH.MPI.OPENMPCC.PETSC.ex' failed<br>
> gmake[1]: *** [<a href="http://viscousDriver3d.Linux.64.CC" target="_blank">viscousDriver3d.Linux.64.CC</a>.ftn.OPTHIGH.MPI.OPENMPCC.PETSC.ex] Error 1<br>
> ../../../Chombo/lib/mk/Make.rules:325: recipe for target 'all-example' failed<br>
> <br>
<br>
</blockquote></div></div>