`--with-fortran-lib` "No such file or directory"

tomchudley

Hello all,

I am attempting to compile an installation of ISSM with a Python interface on MacOS (I already have a working MATLAB interface).

I can successfully ./configure.sh the install, but when running make I eventually receive the following error:

[...]
  CXXLD    libISSMCore.la
/bin/sh: -L/opt/homebrew/lib/gcc/current: No such file or directory
make[3]: *** [libISSMCore.la] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

The -L/opt/homebrew/lib/gcc/current pointed towards is user-specified via the --with-fortran-lib option within configure.sh:

        --with-fortran-lib="-L/opt/homebrew/lib/gcc/current -lgfortran"

This was installed via homebrew, and definitely exists - in fact, I use exactly the same line within my MATLAB installation, which compiles perfectly!

I wonder if anyone has pointers as to what is going on, or any gremlins that might differ when compiling for Python?

Cheers.

justinquinn

tomchudley Hi, yeah there should be no difference here. Did you by any chance just update macOS? Sometimes this causes some issues with the Command Line Tools. You might try reinstalling them with sudo rm -rf /Library/Developer/CommandLineTools; xcode-select --install.

tomchudley

justinquinn Thanks Justin! There have been no updates to MacOS in between the installs. I thought you might be on to something here as I had to switch from Command Line Tools to full xcode last week for some licensing-related admin. However, I confirmed with xcode-select --print-path that I'm pointing to CommandLineTools and even reinstalled them to make sure. No luck unfortunately, still receiving the same error after running autoreconf -ivf; ./configure.sh; make...

mathieumorlighem

can you type make V=1 and send us the output here?

tomchudley

mathieumorlighem Sure thing - full error message as follows:

/bin/sh ../../libtool  --tag=CXX   --mode=link /opt/homebrew/bin/g++-14 -g -O2 -fPIC -std=c++11 -D_DO_NOT_LOAD_GLOBALS_ -Wno-deprecated-register -Wno-return-type  -g -O2 -fPIC -std=c++11 -D_DO_NOT_LOAD_GLOBALS_ -Wno-deprecated-register -Wno-return-type -avoid-version    -Wl,-ld_classic -o libISSMCore.la -rpath /Users/tom/ISSM-python/ISSM/lib ./bamg/libISSMCore_la-BamgGeom.lo ./bamg/libISSMCore_la-BamgMesh.lo ./bamg/libISSMCore_la-BamgOpts.lo ./bamg/libISSMCore_la-CrackedEdge.lo ./bamg/libISSMCore_la-Curve.lo ./bamg/libISSMCore_la-Edge.lo ./bamg/libISSMCore_la-GeomEdge.lo ./bamg/libISSMCore_la-GeomSubDomain.lo ./bamg/libISSMCore_la-GeomVertex.lo ./bamg/libISSMCore_la-Geometry.lo ./bamg/libISSMCore_la-ListofIntersectionTriangles.lo ./bamg/libISSMCore_la-EigenMetric.lo ./bamg/libISSMCore_la-Metric.lo ./bamg/libISSMCore_la-BamgQuadtree.lo ./bamg/libISSMCore_la-SetOfE4.lo ./bamg/libISSMCore_la-SubDomain.lo ./bamg/libISSMCore_la-AdjacentTriangle.lo ./bamg/libISSMCore_la-Triangle.lo ./bamg/libISSMCore_la-BamgVertex.lo ./bamg/libISSMCore_la-VertexOnEdge.lo ./bamg/libISSMCore_la-VertexOnGeom.lo ./bamg/libISSMCore_la-VertexOnVertex.lo ./bamg/libISSMCore_la-Mesh.lo ./shared/Bamg/libISSMCore_la-BigPrimeNumber.lo ./modules/Bamgx/libISSMCore_la-Bamgx.lo ./modules/BamgConvertMeshx/libISSMCore_la-BamgConvertMeshx.lo ./modules/BamgTriangulatex/libISSMCore_la-BamgTriangulatex.lo   ./classes/libISSMCore_la-AmrBamg.lo ./datastructures/libISSMCore_la-DataSet.lo ./classes/gauss/libISSMCore_la-GaussSeg.lo ./classes/gauss/libISSMCore_la-GaussTria.lo ./classes/gauss/libISSMCore_la-GaussTetra.lo ./classes/gauss/libISSMCore_la-GaussPenta.lo ./classes/libISSMCore_la-IoModel.lo ./classes/libISSMCore_la-FemModel.lo ./classes/Loads/libISSMCore_la-Friction.lo ./classes/Constraints/libISSMCore_la-SpcTransient.lo ./classes/libISSMCore_la-DependentObject.lo ./classes/libISSMCore_la-Contours.lo ./classes/libISSMCore_la-Vertices.lo ./classes/libISSMCore_la-Nodes.lo ./classes/libISSMCore_la-Numberedcostfunction.lo ./classes/libISSMCore_la-Misfit.lo ./classes/libISSMCore_la-Cfsurfacesquare.lo ./classes/libISSMCore_la-Cfsurfacesquaretransient.lo ./classes/libISSMCore_la-Cfdragcoeffabsgrad.lo ./classes/libISSMCore_la-Cfdragcoeffabsgradtransient.lo ./classes/libISSMCore_la-Cfrheologybbarabsgrad.lo ./classes/libISSMCore_la-Cfrheologybbarabsgradtransient.lo ./classes/libISSMCore_la-Cfsurfacelogvel.lo ./classes/libISSMCore_la-Cflevelsetmisfit.lo ./classes/libISSMCore_la-Regionaloutput.lo ./classes/libISSMCore_la-Nodalvalue.lo ./classes/libISSMCore_la-Node.lo ./classes/libISSMCore_la-Vertex.lo ./classes/libISSMCore_la-Hook.lo ./classes/libISSMCore_la-Radar.lo ./classes/libISSMCore_la-BarystaticContributions.lo ./classes/ExternalResults/libISSMCore_la-Results.lo ./classes/Elements/libISSMCore_la-Element.lo ./classes/Elements/libISSMCore_la-Elements.lo ./classes/Elements/libISSMCore_la-ElementHook.lo ./classes/Elements/libISSMCore_la-Seg.lo ./classes/Elements/libISSMCore_la-SegRef.lo ./classes/Elements/libISSMCore_la-Tria.lo ./classes/Elements/libISSMCore_la-TriaRef.lo ./classes/Elements/libISSMCore_la-Tetra.lo ./classes/Elements/libISSMCore_la-TetraRef.lo ./classes/Elements/libISSMCore_la-Penta.lo ./classes/Elements/libISSMCore_la-PentaRef.lo ./classes/Materials/libISSMCore_la-Materials.lo ./classes/Materials/libISSMCore_la-Matice.lo ./classes/Materials/libISSMCore_la-Matlitho.lo ./classes/Materials/libISSMCore_la-Matestar.lo ./classes/Constraints/libISSMCore_la-Constraints.lo ./classes/Constraints/libISSMCore_la-SpcStatic.lo ./classes/Constraints/libISSMCore_la-SpcDynamic.lo ./classes/Loads/libISSMCore_la-Channel.lo ./classes/Loads/libISSMCore_la-Loads.lo ./classes/Loads/libISSMCore_la-Penpair.lo ./classes/Loads/libISSMCore_la-Pengrid.lo ./classes/Loads/libISSMCore_la-Moulin.lo ./classes/Loads/libISSMCore_la-Numericalflux.lo ./classes/Loads/libISSMCore_la-Neumannflux.lo ./classes/matrix/libISSMCore_la-ElementMatrix.lo ./classes/matrix/libISSMCore_la-ElementVector.lo ./classes/Params/libISSMCore_la-Parameters.lo ./classes/Params/libISSMCore_la-BoolParam.lo ./classes/Params/libISSMCore_la-ControlParam.lo ./classes/Params/libISSMCore_la-IntParam.lo ./classes/Params/libISSMCore_la-IntVecParam.lo ./classes/Params/libISSMCore_la-IntMatParam.lo ./classes/Params/libISSMCore_la-DoubleParam.lo ./classes/Params/libISSMCore_la-FileParam.lo ./classes/Params/libISSMCore_la-StringArrayParam.lo ./classes/Params/libISSMCore_la-DoubleMatParam.lo ./classes/Params/libISSMCore_la-DoubleTransientMatParam.lo ./classes/Params/libISSMCore_la-DoubleMatArrayParam.lo ./classes/Params/libISSMCore_la-DoubleVecParam.lo ./classes/Params/libISSMCore_la-StringParam.lo ./classes/Params/libISSMCore_la-MatrixParam.lo ./classes/Params/libISSMCore_la-VectorParam.lo ./classes/Params/libISSMCore_la-TransientParam.lo ./classes/Params/libISSMCore_la-TransientArrayParam.lo ./classes/Params/libISSMCore_la-TransientGriddedFieldParam.lo ./classes/Params/libISSMCore_la-DataSetParam.lo ./classes/libISSMCore_la-Profiler.lo ./shared/Matrix/libISSMCore_la-MatrixUtils.lo ./shared/io/Disk/libISSMCore_la-pfopen.lo ./shared/io/Disk/libISSMCore_la-pfclose.lo ./shared/io/Disk/libISSMCore_la-WriteLockFile.lo ./shared/io/Print/libISSMCore_la-PrintfFunction.lo ./shared/io/Comm/libISSMCore_la-IssmComm.lo ./shared/io/Marshalling/libISSMCore_la-IoCodeConversions.lo ./shared/io/Marshalling/libISSMCore_la-Marshalling.lo ./shared/LatLong/libISSMCore_la-Ll2xyx.lo ./shared/LatLong/libISSMCore_la-Xy2llx.lo ./shared/FSanalyticals/libISSMCore_la-fsanalyticals.lo ./shared/Enum/libISSMCore_la-EnumToStringx.lo ./shared/Enum/libISSMCore_la-StringToEnumx.lo ./shared/Numerics/libISSMCore_la-Verbosity.lo ./shared/Numerics/libISSMCore_la-GaussPoints.lo ./shared/Numerics/libISSMCore_la-cross.lo ./shared/Numerics/libISSMCore_la-cubic.lo ./shared/Numerics/libISSMCore_la-NewtonSolveDnorm.lo ./shared/Numerics/libISSMCore_la-ODE1.lo ./shared/Numerics/libISSMCore_la-extrema.lo ./shared/Numerics/libISSMCore_la-legendre.lo ./shared/Numerics/libISSMCore_la-XZvectorsToCoordinateSystem.lo ./shared/Numerics/libISSMCore_la-Normals.lo ./shared/Numerics/libISSMCore_la-Interpolation.lo ./shared/Exceptions/libISSMCore_la-Exceptions.lo ./shared/Sorting/libISSMCore_la-binary_search.lo ./shared/Elements/libISSMCore_la-Cuffey.lo ./shared/Elements/libISSMCore_la-BuddJacka.lo ./shared/Elements/libISSMCore_la-CuffeyTemperate.lo ./shared/Elements/libISSMCore_la-StressIntensityIntegralWeight.lo ./shared/Elements/libISSMCore_la-Paterson.lo ./shared/Elements/libISSMCore_la-Arrhenius.lo ./shared/Elements/libISSMCore_la-NyeCO2.lo ./shared/Elements/libISSMCore_la-NyeH2O.lo ./shared/Elements/libISSMCore_la-LliboutryDuval.lo ./shared/Elements/libISSMCore_la-PrintArrays.lo ./shared/Elements/libISSMCore_la-PddSurfaceMassBalance.lo ./shared/Elements/libISSMCore_la-PddSurfaceMassBalanceSicopolis.lo ./shared/Elements/libISSMCore_la-ComputeDelta18oTemperaturePrecipitation.lo ./shared/Elements/libISSMCore_la-ComputeMungsmTemperaturePrecipitation.lo ./shared/Elements/libISSMCore_la-ComputeD18OTemperaturePrecipitationFromPD.lo ./shared/Elements/libISSMCore_la-DrainageFunctionWaterfraction.lo ./shared/Elements/libISSMCore_la-EstarComponents.lo ./shared/Random/libISSMCore_la-random.lo ./shared/Random/libISSMCore_la-randomgenerator.lo ./shared/String/libISSMCore_la-DescriptorIndex.lo ./toolkits/issm/libISSMCore_la-IssmToolkitUtils.lo ./toolkits/issm/libISSMCore_la-IssmSolver.lo ./toolkits/mpi/libISSMCore_la-issmmpi.lo ./toolkits/mpi/commops/libISSMCore_la-DetermineLocalSize.lo ./toolkits/mpi/commops/libISSMCore_la-DetermineGlobalSize.lo ./toolkits/mpi/commops/libISSMCore_la-DetermineRowRankFromLocalSize.lo ./toolkits/mpi/commops/libISSMCore_la-GetOwnershipBoundariesFromRange.lo ./toolkits/libISSMCore_la-ToolkitOptions.lo ./modules/MmeToInputFromIdx/libISSMCore_la-MmeToInputFromIdx.lo ./modules/MmeToInputx/libISSMCore_la-MmeToInputx.lo ./modules/ModelProcessorx/libISSMCore_la-ModelProcessorx.lo ./modules/ModelProcessorx/libISSMCore_la-ElementsAndVerticesPartitioning.lo ./modules/ModelProcessorx/libISSMCore_la-EdgesPartitioning.lo ./modules/ModelProcessorx/libISSMCore_la-FacesPartitioning.lo ./modules/ModelProcessorx/libISSMCore_la-CreateParameters.lo ./modules/ModelProcessorx/Autodiff/libISSMCore_la-CreateParametersAutodiff.lo ./modules/ModelProcessorx/libISSMCore_la-CreateFaces.lo ./modules/ModelProcessorx/libISSMCore_la-CreateEdges.lo ./modules/ModelProcessorx/libISSMCore_la-CreateSingleNodeToElementConnectivity.lo ./modules/ModelProcessorx/libISSMCore_la-CreateNumberNodeToElementConnectivity.lo ./modules/ModelProcessorx/libISSMCore_la-CreateElementsVerticesAndMaterials.lo ./modules/ModelProcessorx/libISSMCore_la-CreateNodes.lo ./modules/ParseToolkitsOptionsx/libISSMCore_la-ParseToolkitsOptionsx.lo ./modules/NodesDofx/libISSMCore_la-NodesDofx.lo ./modules/NodalValuex/libISSMCore_la-NodalValuex.lo ./modules/VertexCoordinatesx/libISSMCore_la-VertexCoordinatesx.lo ./modules/ElementCoordinatesx/libISSMCore_la-ElementCoordinatesx.lo ./modules/OutputResultsx/libISSMCore_la-OutputResultsx.lo ./modules/InputDepthAverageAtBasex/libISSMCore_la-InputDepthAverageAtBasex.lo ./modules/InputDuplicatex/libISSMCore_la-InputDuplicatex.lo ./modules/InputExtrudex/libISSMCore_la-InputExtrudex.lo ./modules/SurfaceAreax/libISSMCore_la-SurfaceAreax.lo ./modules/AllocateSystemMatricesx/libISSMCore_la-AllocateSystemMatricesx.lo ./modules/CreateJacobianMatrixx/libISSMCore_la-CreateJacobianMatrixx.lo ./modules/SystemMatricesx/libISSMCore_la-SystemMatricesx.lo ./modules/CreateNodalConstraintsx/libISSMCore_la-CreateNodalConstraintsx.lo ./modules/UpdateDynamicConstraintsx/libISSMCore_la-UpdateDynamicConstraintsx.lo ./modules/IoModelToConstraintsx/libISSMCore_la-IoModelToConstraintsx.lo ./modules/SetActiveNodesLSMx/libISSMCore_la-SetActiveNodesLSMx.lo ./modules/InputUpdateFromConstantx/libISSMCore_la-InputUpdateFromConstantx.lo ./modules/InputUpdateFromSolutionx/libISSMCore_la-InputUpdateFromSolutionx.lo ./modules/GeothermalFluxx/libISSMCore_la-GeothermalFluxx.lo ./modules/GetSolutionFromInputsx/libISSMCore_la-GetSolutionFromInputsx.lo ./modules/GetVectorFromInputsx/libISSMCore_la-GetVectorFromInputsx.lo ./modules/InputUpdateFromVectorx/libISSMCore_la-InputUpdateFromVectorx.lo ./modules/FloatingiceMeltingRatex/libISSMCore_la-FloatingiceMeltingRatex.lo ./modules/FloatingiceMeltingRatePicox/libISSMCore_la-FloatingiceMeltingRatePicox.lo ./modules/FrontalForcingsx/libISSMCore_la-FrontalForcingsx.lo ./modules/ConfigureObjectsx/libISSMCore_la-ConfigureObjectsx.lo ./modules/SpcNodesx/libISSMCore_la-SpcNodesx.lo ./modules/SurfaceMassBalancex/libISSMCore_la-SurfaceMassBalancex.lo ./modules/SurfaceMassBalancex/libISSMCore_la-Gembx.lo ./modules/Reducevectorgtofx/libISSMCore_la-Reducevectorgtofx.lo ./modules/Reduceloadx/libISSMCore_la-Reduceloadx.lo ./modules/ConstraintsStatex/libISSMCore_la-ConstraintsStatex.lo ./modules/ResetConstraintsx/libISSMCore_la-ResetConstraintsx.lo ./modules/ResetFSBasalBoundaryConditionx/libISSMCore_la-ResetFSBasalBoundaryConditionx.lo ./modules/Solverx/libISSMCore_la-Solverx.lo ./modules/StochasticForcingx/libISSMCore_la-StochasticForcingx.lo ./modules/Mergesolutionfromftogx/libISSMCore_la-Mergesolutionfromftogx.lo ./modules/UpdateMmesx/libISSMCore_la-UpdateMmesx.lo ./cores/libISSMCore_la-ProcessArguments.lo ./cores/libISSMCore_la-ResetBoundaryConditions.lo ./cores/libISSMCore_la-WrapperCorePointerFromSolutionEnum.lo ./cores/libISSMCore_la-WrapperPreCorePointerFromSolutionEnum.lo ./cores/libISSMCore_la-CorePointerFromSolutionEnum.lo ./cores/libISSMCore_la-ad_core.lo ./main/libISSMCore_la-EnvironmentInit.lo ./main/libISSMCore_la-EnvironmentFinalize.lo ./analyses/libISSMCore_la-EnumToAnalysis.lo ./solutionsequences/libISSMCore_la-solutionsequence_la.lo ./solutionsequences/libISSMCore_la-solutionsequence_la_theta.lo ./solutionsequences/libISSMCore_la-solutionsequence_linear.lo ./solutionsequences/libISSMCore_la-solutionsequence_nonlinear.lo ./solutionsequences/libISSMCore_la-solutionsequence_newton.lo ./solutionsequences/libISSMCore_la-solutionsequence_fct.lo ./solutionsequences/libISSMCore_la-solutionsequence_schurcg.lo ./solutionsequences/libISSMCore_la-solutionsequence_sampling.lo ./solutionsequences/libISSMCore_la-convergence.lo ./classes/Options/libISSMCore_la-Options.lo ./classes/libISSMCore_la-RiftStruct.lo ./modules/ModelProcessorx/Transient/libISSMCore_la-UpdateElementsTransient.lo ./modules/ModelProcessorx/Transient/libISSMCore_la-UpdateParametersTransient.lo ./cores/libISSMCore_la-transient_core.lo ./cores/libISSMCore_la-steadystate_core.lo ./cores/libISSMCore_la-masstransport_core.lo ./cores/libISSMCore_la-mmemasstransport_core.lo ./cores/libISSMCore_la-oceantransport_core.lo ./cores/libISSMCore_la-depthaverage_core.lo ./cores/libISSMCore_la-extrudefrombase_core.lo ./cores/libISSMCore_la-extrudefromtop_core.lo ./cores/libISSMCore_la-thermal_core.lo ./cores/libISSMCore_la-smb_core.lo ./cores/libISSMCore_la-bmb_core.lo ./cores/libISSMCore_la-debris_core.lo ./solutionsequences/libISSMCore_la-solutionsequence_thermal_nonlinear.lo ./modules/ControlInputSetGradientx/libISSMCore_la-ControlInputSetGradientx.lo ./modules/GetVectorFromControlInputsx/libISSMCore_la-GetVectorFromControlInputsx.lo ./modules/SetControlInputsFromVectorx/libISSMCore_la-SetControlInputsFromVectorx.lo ./modules/ModelProcessorx/Control/libISSMCore_la-CreateParametersControl.lo ./modules/ModelProcessorx/Control/libISSMCore_la-UpdateElementsAndMaterialsControl.lo ./modules/SurfaceAbsVelMisfitx/libISSMCore_la-SurfaceAbsVelMisfitx.lo ./modules/SurfaceRelVelMisfitx/libISSMCore_la-SurfaceRelVelMisfitx.lo ./modules/SurfaceLogVelMisfitx/libISSMCore_la-SurfaceLogVelMisfitx.lo ./modules/SurfaceLogVxVyMisfitx/libISSMCore_la-SurfaceLogVxVyMisfitx.lo ./modules/SurfaceAverageVelMisfitx/libISSMCore_la-SurfaceAverageVelMisfitx.lo ./modules/ThicknessAbsMisfitx/libISSMCore_la-ThicknessAbsMisfitx.lo ./modules/Gradjx/libISSMCore_la-Gradjx.lo ./modules/DragCoefficientAbsGradientx/libISSMCore_la-DragCoefficientAbsGradientx.lo ./modules/ThicknessAlongGradientx/libISSMCore_la-ThicknessAlongGradientx.lo ./modules/ThicknessAcrossGradientx/libISSMCore_la-ThicknessAcrossGradientx.lo ./modules/RheologyBbarAbsGradientx/libISSMCore_la-RheologyBbarAbsGradientx.lo ./modules/RheologyBAbsGradientx/libISSMCore_la-RheologyBAbsGradientx.lo ./shared/Numerics/libISSMCore_la-BrentSearch.lo ./cores/libISSMCore_la-control_core.lo ./cores/libISSMCore_la-controltao_core.lo ./cores/libISSMCore_la-controlm1qn3_core.lo ./cores/libISSMCore_la-controladm1qn3_core.lo ./cores/libISSMCore_la-controlvalidation_core.lo ./cores/libISSMCore_la-adjointstressbalance_core.lo ./cores/libISSMCore_la-adjointbalancethickness_core.lo ./cores/libISSMCore_la-adjointbalancethickness2_core.lo ./cores/libISSMCore_la-AdjointCorePointerFromSolutionEnum.lo ./solutionsequences/libISSMCore_la-solutionsequence_adjoint_linear.lo ./cores/libISSMCore_la-hydrology_core.lo ./solutionsequences/libISSMCore_la-solutionsequence_hydro_nonlinear.lo ./solutionsequences/libISSMCore_la-solutionsequence_shakti_nonlinear.lo ./solutionsequences/libISSMCore_la-solutionsequence_glads_nonlinear.lo ./cores/libISSMCore_la-stressbalance_core.lo ./solutionsequences/libISSMCore_la-solutionsequence_stokescoupling_nonlinear.lo ./cores/libISSMCore_la-balancethickness_core.lo ./cores/libISSMCore_la-balancethickness2_core.lo ./cores/libISSMCore_la-balancevelocity_core.lo ./cores/libISSMCore_la-dummy_core.lo ./cores/libISSMCore_la-surfaceslope_core.lo ./cores/libISSMCore_la-bedslope_core.lo ./cores/libISSMCore_la-damage_core.lo ./cores/libISSMCore_la-levelsetfunctionslope_core.lo ./cores/libISSMCore_la-movingfront_core.lo ./cores/libISSMCore_la-groundingline_core.lo ./modules/GroundinglineMigrationx/libISSMCore_la-GroundinglineMigrationx.lo ./classes/Loads/libISSMCore_la-Riftfront.lo ./modules/ConstraintsStatex/libISSMCore_la-RiftConstraintsState.lo ./modules/ModelProcessorx/libISSMCore_la-CreateOutputDefinitions.lo ./modules/OutputDefinitionsResponsex/libISSMCore_la-OutputDefinitionsResponsex.lo ./modules/InterpFromMeshToMesh2dx/libISSMCore_la-InterpFromMeshToMesh2dx.lo ./classes/Inputs/libISSMCore_la-Inputs.lo ./classes/Inputs/libISSMCore_la-BoolInput.lo ./classes/Inputs/libISSMCore_la-DoubleInput.lo ./classes/Inputs/libISSMCore_la-IntInput.lo ./classes/Inputs/libISSMCore_la-ElementInput.lo ./classes/Inputs/libISSMCore_la-SegInput.lo ./classes/Inputs/libISSMCore_la-TriaInput.lo ./classes/Inputs/libISSMCore_la-PentaInput.lo ./classes/Inputs/libISSMCore_la-DatasetInput.lo ./classes/Inputs/libISSMCore_la-ControlInput.lo ./classes/Inputs/libISSMCore_la-TransientInput.lo ./classes/Inputs/libISSMCore_la-TransientFileInput.lo ./classes/Inputs/libISSMCore_la-ArrayInput.lo ./classes/Inputs/libISSMCore_la-IntArrayInput.lo     ./toolkits/petsc/patches/libISSMCore_la-VecToMPISerial.lo ./toolkits/petsc/patches/libISSMCore_la-MatToMPISerial.lo ./toolkits/petsc/patches/libISSMCore_la-NewVec.lo ./toolkits/petsc/patches/libISSMCore_la-PetscOptionsDetermineSolverType.lo ./toolkits/petsc/patches/libISSMCore_la-NewMat.lo ./toolkits/petsc/patches/libISSMCore_la-VecFree.lo ./toolkits/petsc/patches/libISSMCore_la-KSPFree.lo ./toolkits/petsc/patches/libISSMCore_la-MatFree.lo ./toolkits/petsc/patches/libISSMCore_la-ISSMToPetscMatrixType.lo ./toolkits/petsc/patches/libISSMCore_la-ISSMToPetscInsertMode.lo ./toolkits/petsc/patches/libISSMCore_la-ISSMToPetscNormMode.lo ./toolkits/petsc/objects/libISSMCore_la-PetscMat.lo ./toolkits/petsc/objects/libISSMCore_la-PetscVec.lo ./toolkits/petsc/objects/libISSMCore_la-PetscSolver.lo ./toolkits/mumps/libISSMCore_la-MumpsSolve.lo   ./analyses/libISSMCore_la-AdjointBalancethicknessAnalysis.lo ./analyses/libISSMCore_la-AdjointBalancethickness2Analysis.lo ./analyses/libISSMCore_la-AdjointHorizAnalysis.lo ./analyses/libISSMCore_la-AgeAnalysis.lo ./analyses/libISSMCore_la-BalancethicknessAnalysis.lo ./analyses/libISSMCore_la-Balancethickness2Analysis.lo ./analyses/libISSMCore_la-BalancethicknessSoftAnalysis.lo ./analyses/libISSMCore_la-BalancevelocityAnalysis.lo ./analyses/libISSMCore_la-L2ProjectionBaseAnalysis.lo ./analyses/libISSMCore_la-DamageEvolutionAnalysis.lo ./modules/Damagex/libISSMCore_la-Damagex.lo ./analyses/libISSMCore_la-DebrisAnalysis.lo ./analyses/libISSMCore_la-StressbalanceAnalysis.lo ./analyses/libISSMCore_la-UzawaPressureAnalysis.lo ./analyses/libISSMCore_la-StressbalanceSIAAnalysis.lo ./analyses/libISSMCore_la-StressbalanceVerticalAnalysis.lo ./analyses/libISSMCore_la-EnthalpyAnalysis.lo ./analyses/libISSMCore_la-GLheightadvectionAnalysis.lo ./analyses/libISSMCore_la-HydrologyShreveAnalysis.lo ./analyses/libISSMCore_la-HydrologyTwsAnalysis.lo ./analyses/libISSMCore_la-HydrologyShaktiAnalysis.lo ./analyses/libISSMCore_la-HydrologyPismAnalysis.lo ./analyses/libISSMCore_la-HydrologyGlaDSAnalysis.lo ./analyses/libISSMCore_la-HydrologyDCInefficientAnalysis.lo ./analyses/libISSMCore_la-HydrologyDCEfficientAnalysis.lo ./analyses/libISSMCore_la-HydrologyArmapwAnalysis.lo ./analyses/libISSMCore_la-L2ProjectionEPLAnalysis.lo ./analyses/libISSMCore_la-MeltingAnalysis.lo ./analyses/libISSMCore_la-MasstransportAnalysis.lo ./analyses/libISSMCore_la-MmemasstransportAnalysis.lo ./analyses/libISSMCore_la-OceantransportAnalysis.lo ./analyses/libISSMCore_la-SmbAnalysis.lo ./analyses/libISSMCore_la-FreeSurfaceBaseAnalysis.lo ./analyses/libISSMCore_la-FreeSurfaceTopAnalysis.lo ./analyses/libISSMCore_la-ExtrudeFromBaseAnalysis.lo ./analyses/libISSMCore_la-ExtrudeFromTopAnalysis.lo ./analyses/libISSMCore_la-DepthAverageAnalysis.lo ./analyses/libISSMCore_la-ThermalAnalysis.lo ./analyses/libISSMCore_la-SmoothAnalysis.lo ./analyses/libISSMCore_la-LevelsetAnalysis.lo ./modules/Calvingx/libISSMCore_la-Calvingx.lo ./modules/KillIcebergsx/libISSMCore_la-KillIcebergsx.lo ./analyses/libISSMCore_la-ExtrapolationAnalysis.lo  ./cores/libISSMCore_la-esa_core.lo ./analyses/libISSMCore_la-EsaAnalysis.lo  ./cores/libISSMCore_la-sampling_core.lo ./analyses/libISSMCore_la-SamplingAnalysis.lo   ./modules/MeshPartitionx/libISSMCore_la-MeshPartitionx.lo ./toolkits/metis/patches/libISSMCore_la-METIS_PartMeshNodalPatch.lo   ./classes/kriging/libISSMCore_la-Observations.lo ./classes/kriging/libISSMCore_la-GaussianVariogram.lo ./classes/kriging/libISSMCore_la-ExponentialVariogram.lo ./classes/kriging/libISSMCore_la-SphericalVariogram.lo ./classes/kriging/libISSMCore_la-PowerVariogram.lo ./classes/kriging/libISSMCore_la-Quadtree.lo ./classes/kriging/libISSMCore_la-Covertree.lo ./classes/kriging/libISSMCore_la-Observation.lo ./modules/Krigingx/libISSMCore_la-pKrigingx.lo  -L/Users/tom/ISSM-python/ISSM/externalpackages/chaco/install/lib -lchacominusblas  -L/Users/tom/ISSM-python/ISSM/externalpackages/petsc/install/lib -lpetsc -L/Users/tom/ISSM-python/ISSM/externalpackages/petsc/install/lib -ldmumps -lcmumps -lmumps_common -lpord -lzmumps -L/Users/tom/ISSM-python/ISSM/externalpackages/petsc/install/lib -lscalapack -L/Users/tom/ISSM-python/ISSM/externalpackages/petsc/install/lib -lflapack -lfblas -L/Users/tom/ISSM-python/ISSM/externalpackages/petsc/install/lib -lparmetis -L/Users/tom/ISSM-python/ISSM/externalpackages/petsc/install/lib -lmetis   -L/Users/tom/ISSM-python/ISSM/externalpackages/m1qn3/install -lm1qn3 -lddot              -L/Users/tom/ISSM-python/ISSM/externalpackages/petsc/install/lib -lmpi -lmpifo>          -L/opt/homebrew/lib/gcc/current -lgfortran  
/bin/sh: -L/opt/homebrew/lib/gcc/current: No such file or directory
make[3]: *** [libISSMCore.la] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all] Error 2

justinquinn

tomchudley Any way you have Conda activated? If so, deactivate it.

Also, even though a Homebrew installed copy of gcc will in fact be a wrapper around clang, it look like it's running /opt/homebrew/bin/g++-14 as the linker. You might try brew unlink gcc, brew unlink g++, and similar commands to ensure that it is not picked up before the vanilla clang included with the Command Line Tools. If it's still acting up, you might remove gcc via Homebrew entirely, unless you absolutely need it elsewhere.

Another possible culprit is if you have autotools (i.e. libtool, autom4ke) installed via Homebrew.

mathieumorlighem

I see this at this end:

.... -L/Users/tom/ISSM-python/ISSM/externalpackages/petsc/install/lib -lmpi -lmpifo>

I am a bit worried about this >, where is it coming from? Could you send us your configure.sh ?

justinquinn

mathieumorlighem Yep, I noticed the same and thought it might be because of one of the things I mentioned. That should be lmpifort, but that > is getting inserted somewhere. It could be as simple as a typo or unclosed quotes in the configuration, like you mentioned.

tomchudley

Thanks so much both - you're absolutely right. I had overwritten --with-mpi-libflags="-L$ISSM_DIR/externalpackages/petsc/install/include/ -lmpich -lmpi -lmpifort -lmpicxx" \ to become --with-mpi-libflags="-L$ISSM_DIR/externalpackages/petsc/install/include/ -lmpich -lmpi -lmpifor>" \, and was so fixated on the --with-fortran-lib message that I completely failed to notice! It compiles successfully. Really appreciate your help.