Error when updating ISSM

ASand

When attempting to update ISSM, I am running into this error (figure attached).

libddot.a is not portable
libm1qn3.a is not portable

justinquinn

ASand
Could you please route the entire configure and compile output to a file and attach it here please?

ASand

Here's the configure.sh script:
./configure \
--prefix="${ISSM_DIR}" \
--with-numthreads=2 \
--with-mpi-include="${ISSM_DIR}/externalpackages/petsc/install/include" \
--with-mpi-libflags="-L${ISSM_DIR}/externalpackages/petsc/install/lib -lmpi -lmpicxx -lmpifort" \
--with-metis-dir="${ISSM_DIR}/externalpackages/petsc/install" \
--with-blas-lapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
--with-scalapack-dir="${ISSM_DIR}/externalpackages/petsc/install" \
--with-mumps-dir="${ISSM_DIR}/externalpackages/petsc/install" \
--with-petsc-dir="${ISSM_DIR}/externalpackages/petsc/install" \
--with-chaco-dir="${ISSM_DIR}/externalpackages/chaco/install" \
--with-m1qn3-dir="${ISSM_DIR}/externalpackages/m1qn3/install" \
--with-semic-dir="${ISSM_DIR}/externalpackages/semic/install"

justinquinn

ASand
Thanks, I'd like to see the full output when you run make; make install to see if there are any other obvious errors in there.

ASand

Making install in src
make[1]: Entering directory '/home/anjali.sandip/issm-project/trunk-jpl/src'
Making install in c
make[2]: Entering directory '/home/anjali.sandip/issm-project/trunk-jpl/src/c'
CXX main/issm-issm.o
CXX bamg/libISSMCore_la-BamgGeom.lo
CXX bamg/libISSMCore_la-BamgMesh.lo
CXX bamg/libISSMCore_la-BamgOpts.lo
CXX bamg/libISSMCore_la-CrackedEdge.lo
CXX bamg/libISSMCore_la-Curve.lo
CXX bamg/libISSMCore_la-Edge.lo
CXX bamg/libISSMCore_la-GeomEdge.lo
CXX bamg/libISSMCore_la-GeomSubDomain.lo
CXX bamg/libISSMCore_la-GeomVertex.lo
CXX bamg/libISSMCore_la-Geometry.lo
CXX bamg/libISSMCore_la-ListofIntersectionTriangles.lo
CXX bamg/libISSMCore_la-EigenMetric.lo
CXX bamg/libISSMCore_la-Metric.lo
CXX bamg/libISSMCore_la-BamgQuadtree.lo
CXX bamg/libISSMCore_la-SetOfE4.lo
CXX bamg/libISSMCore_la-SubDomain.lo
CXX bamg/libISSMCore_la-AdjacentTriangle.lo
CXX bamg/libISSMCore_la-Triangle.lo
CXX bamg/libISSMCore_la-BamgVertex.lo
CXX bamg/libISSMCore_la-VertexOnEdge.lo
CXX bamg/libISSMCore_la-VertexOnGeom.lo
CXX bamg/libISSMCore_la-VertexOnVertex.lo
CXX bamg/libISSMCore_la-Mesh.lo
CXX modules/Bamgx/libISSMCore_la-Bamgx.lo
CXX modules/BamgConvertMeshx/libISSMCore_la-BamgConvertMeshx.lo
CXX modules/BamgTriangulatex/libISSMCore_la-BamgTriangulatex.lo
CXX classes/libISSMCore_la-AmrBamg.lo
CXX datastructures/libISSMCore_la-DataSet.lo
CXX classes/gauss/libISSMCore_la-GaussSeg.lo
CXX classes/gauss/libISSMCore_la-GaussTria.lo
CXX classes/gauss/libISSMCore_la-GaussTetra.lo
CXX classes/gauss/libISSMCore_la-GaussPenta.lo
CXX classes/libISSMCore_la-IoModel.lo
CXX classes/libISSMCore_la-FemModel.lo
CXX classes/Loads/libISSMCore_la-Friction.lo
CXX classes/Constraints/libISSMCore_la-SpcTransient.lo
CXX classes/libISSMCore_la-DependentObject.lo
CXX classes/libISSMCore_la-Contours.lo
CXX classes/libISSMCore_la-Vertices.lo
CXX classes/libISSMCore_la-Nodes.lo
CXX classes/libISSMCore_la-Numberedcostfunction.lo
CXX classes/libISSMCore_la-Misfit.lo
CXX classes/libISSMCore_la-Cfsurfacesquare.lo
CXX classes/libISSMCore_la-Cfsurfacesquaretransient.lo
CXX classes/libISSMCore_la-Cfdragcoeffabsgrad.lo
CXX classes/libISSMCore_la-Cfrheologybbarabsgrad.lo
CXX classes/libISSMCore_la-Cfsurfacelogvel.lo
CXX classes/libISSMCore_la-Cflevelsetmisfit.lo
CXX classes/libISSMCore_la-Regionaloutput.lo
CXX classes/libISSMCore_la-Nodalvalue.lo
CXX classes/libISSMCore_la-Node.lo
CXX classes/libISSMCore_la-Vertex.lo
CXX classes/libISSMCore_la-Hook.lo
CXX classes/libISSMCore_la-Radar.lo
CXX classes/libISSMCore_la-BarystaticContributions.lo
CXX classes/ExternalResults/libISSMCore_la-Results.lo
CXX classes/Elements/libISSMCore_la-Element.lo
CXX classes/Elements/libISSMCore_la-Elements.lo
CXX classes/Elements/libISSMCore_la-ElementHook.lo
CXX classes/Elements/libISSMCore_la-Seg.lo
CXX classes/Elements/libISSMCore_la-SegRef.lo
CXX classes/Elements/libISSMCore_la-Tria.lo
CXX classes/Elements/libISSMCore_la-TriaRef.lo
CXX classes/Elements/libISSMCore_la-Tetra.lo
CXX classes/Elements/libISSMCore_la-TetraRef.lo
CXX classes/Elements/libISSMCore_la-Penta.lo
CXX classes/Elements/libISSMCore_la-PentaRef.lo
CXX classes/Materials/libISSMCore_la-Materials.lo
CXX classes/Materials/libISSMCore_la-Matice.lo
CXX classes/Materials/libISSMCore_la-Matlitho.lo
CXX classes/Materials/libISSMCore_la-Matestar.lo
CXX classes/Constraints/libISSMCore_la-Constraints.lo
CXX classes/Constraints/libISSMCore_la-SpcStatic.lo
CXX classes/Constraints/libISSMCore_la-SpcDynamic.lo
CXX classes/Loads/libISSMCore_la-Channel.lo
CXX classes/Loads/libISSMCore_la-Loads.lo
CXX classes/Loads/libISSMCore_la-Penpair.lo
CXX classes/Loads/libISSMCore_la-Pengrid.lo
CXX classes/Loads/libISSMCore_la-Moulin.lo
CXX classes/Loads/libISSMCore_la-Numericalflux.lo
CXX classes/Loads/libISSMCore_la-Neumannflux.lo
CXX classes/matrix/libISSMCore_la-ElementMatrix.lo
CXX classes/matrix/libISSMCore_la-ElementVector.lo
CXX classes/Params/libISSMCore_la-Parameters.lo
CXX classes/Params/libISSMCore_la-BoolParam.lo
CXX classes/Params/libISSMCore_la-ControlParam.lo
CXX classes/Params/libISSMCore_la-IntParam.lo
CXX classes/Params/libISSMCore_la-IntVecParam.lo
CXX classes/Params/libISSMCore_la-IntMatParam.lo
CXX classes/Params/libISSMCore_la-DoubleParam.lo
CXX classes/Params/libISSMCore_la-FileParam.lo
CXX classes/Params/libISSMCore_la-StringArrayParam.lo
CXX classes/Params/libISSMCore_la-DoubleMatParam.lo
CXX classes/Params/libISSMCore_la-DoubleTransientMatParam.lo
CXX classes/Params/libISSMCore_la-DoubleMatArrayParam.lo
CXX classes/Params/libISSMCore_la-DoubleVecParam.lo
CXX classes/Params/libISSMCore_la-StringParam.lo
CXX classes/Params/libISSMCore_la-MatrixParam.lo
CXX classes/Params/libISSMCore_la-VectorParam.lo
CXX classes/Params/libISSMCore_la-TransientParam.lo
CXX classes/Params/libISSMCore_la-TransientArrayParam.lo
CXX classes/Params/libISSMCore_la-DataSetParam.lo
CXX classes/libISSMCore_la-Profiler.lo
CXX shared/Matrix/libISSMCore_la-MatrixUtils.lo
CXX shared/io/Disk/libISSMCore_la-pfopen.lo
CXX shared/io/Disk/libISSMCore_la-pfclose.lo
CXX shared/io/Disk/libISSMCore_la-WriteLockFile.lo
CXX shared/io/Print/libISSMCore_la-PrintfFunction.lo
CXX shared/io/Comm/libISSMCore_la-IssmComm.lo
CXX shared/io/Marshalling/libISSMCore_la-IoCodeConversions.lo
CXX shared/io/Marshalling/libISSMCore_la-Marshalling.lo
CXX shared/LatLong/libISSMCore_la-Ll2xyx.lo
CXX shared/LatLong/libISSMCore_la-Xy2llx.lo
CXX shared/FSanalyticals/libISSMCore_la-fsanalyticals.lo
CXX shared/Enum/libISSMCore_la-EnumToStringx.lo
CXX shared/Enum/libISSMCore_la-StringToEnumx.lo
CXX shared/Numerics/libISSMCore_la-Verbosity.lo
CXX shared/Numerics/libISSMCore_la-GaussPoints.lo
CXX shared/Numerics/libISSMCore_la-cross.lo
CXX shared/Numerics/libISSMCore_la-cubic.lo
CXX shared/Numerics/libISSMCore_la-NewtonSolveDnorm.lo
CXX shared/Numerics/libISSMCore_la-ODE1.lo
CXX shared/Numerics/libISSMCore_la-extrema.lo
CXX shared/Numerics/libISSMCore_la-legendre.lo
CXX shared/Numerics/libISSMCore_la-XZvectorsToCoordinateSystem.lo
CXX shared/Exceptions/libISSMCore_la-Exceptions.lo
CXX shared/Sorting/libISSMCore_la-binary_search.lo
CXX shared/Elements/libISSMCore_la-Cuffey.lo
CXX shared/Elements/libISSMCore_la-BuddJacka.lo
CXX shared/Elements/libISSMCore_la-CuffeyTemperate.lo
CXX shared/Elements/libISSMCore_la-StressIntensityIntegralWeight.lo
CXX shared/Elements/libISSMCore_la-Paterson.lo
CXX shared/Elements/libISSMCore_la-Arrhenius.lo
CXX shared/Elements/libISSMCore_la-NyeCO2.lo
CXX shared/Elements/libISSMCore_la-NyeH2O.lo
CXX shared/Elements/libISSMCore_la-LliboutryDuval.lo
CXX shared/Elements/libISSMCore_la-PrintArrays.lo
CXX shared/Elements/libISSMCore_la-PddSurfaceMassBalance.lo
CXX shared/Elements/libISSMCore_la-PddSurfaceMassBalanceSicopolis.lo
CXX shared/Elements/libISSMCore_la-ComputeDelta18oTemperaturePrecipitation.lo
CXX shared/Elements/libISSMCore_la-ComputeMungsmTemperaturePrecipitation.lo
CXX shared/Elements/libISSMCore_la-ComputeD18OTemperaturePrecipitationFromPD.lo
CXX shared/Elements/libISSMCore_la-DrainageFunctionWaterfraction.lo
CXX shared/Elements/libISSMCore_la-EstarComponents.lo
CXX shared/Random/libISSMCore_la-random.lo
CXX shared/String/libISSMCore_la-DescriptorIndex.lo
CXX toolkits/issm/libISSMCore_la-IssmToolkitUtils.lo
CXX toolkits/issm/libISSMCore_la-IssmSolver.lo
CXX toolkits/mpi/libISSMCore_la-issmmpi.lo
CXX toolkits/mpi/commops/libISSMCore_la-DetermineLocalSize.lo
CXX toolkits/mpi/commops/libISSMCore_la-DetermineGlobalSize.lo
CXX toolkits/mpi/commops/libISSMCore_la-DetermineRowRankFromLocalSize.lo
CXX toolkits/mpi/commops/libISSMCore_la-GetOwnershipBoundariesFromRange.lo
CXX toolkits/libISSMCore_la-ToolkitOptions.lo
CXX modules/MmeToInputFromIdx/libISSMCore_la-MmeToInputFromIdx.lo
CXX modules/ModelProcessorx/libISSMCore_la-ModelProcessorx.lo
CXX modules/ModelProcessorx/libISSMCore_la-ElementsAndVerticesPartitioning.lo
CXX modules/ModelProcessorx/libISSMCore_la-NodesPartitioning.lo
CXX modules/ModelProcessorx/libISSMCore_la-EdgesPartitioning.lo
CXX modules/ModelProcessorx/libISSMCore_la-FacesPartitioning.lo
CXX modules/ModelProcessorx/libISSMCore_la-CreateParameters.lo
CXX modules/ModelProcessorx/Autodiff/libISSMCore_la-CreateParametersAutodiff.lo
CXX modules/ModelProcessorx/libISSMCore_la-CreateFaces.lo
CXX modules/ModelProcessorx/libISSMCore_la-CreateEdges.lo
CXX modules/ModelProcessorx/libISSMCore_la-CreateSingleNodeToElementConnectivity.lo
CXX modules/ModelProcessorx/libISSMCore_la-CreateNumberNodeToElementConnectivity.lo
CXX modules/ModelProcessorx/libISSMCore_la-CreateElementsVerticesAndMaterials.lo
CXX modules/ModelProcessorx/libISSMCore_la-CreateNodes.lo
CXX modules/ParseToolkitsOptionsx/libISSMCore_la-ParseToolkitsOptionsx.lo
CXX modules/NodesDofx/libISSMCore_la-NodesDofx.lo
CXX modules/NodalValuex/libISSMCore_la-NodalValuex.lo
CXX modules/VertexCoordinatesx/libISSMCore_la-VertexCoordinatesx.lo
CXX modules/ElementCoordinatesx/libISSMCore_la-ElementCoordinatesx.lo
CXX modules/OutputResultsx/libISSMCore_la-OutputResultsx.lo
CXX modules/InputDepthAverageAtBasex/libISSMCore_la-InputDepthAverageAtBasex.lo
CXX modules/InputDuplicatex/libISSMCore_la-InputDuplicatex.lo
CXX modules/InputExtrudex/libISSMCore_la-InputExtrudex.lo
CXX modules/SurfaceAreax/libISSMCore_la-SurfaceAreax.lo
CXX modules/AllocateSystemMatricesx/libISSMCore_la-AllocateSystemMatricesx.lo
CXX modules/CreateJacobianMatrixx/libISSMCore_la-CreateJacobianMatrixx.lo
CXX modules/SystemMatricesx/libISSMCore_la-SystemMatricesx.lo
CXX modules/CreateNodalConstraintsx/libISSMCore_la-CreateNodalConstraintsx.lo
CXX modules/UpdateDynamicConstraintsx/libISSMCore_la-UpdateDynamicConstraintsx.lo
CXX modules/IoModelToConstraintsx/libISSMCore_la-IoModelToConstraintsx.lo
CXX modules/SetActiveNodesLSMx/libISSMCore_la-SetActiveNodesLSMx.lo
CXX modules/InputUpdateFromConstantx/libISSMCore_la-InputUpdateFromConstantx.lo
CXX modules/InputUpdateFromSolutionx/libISSMCore_la-InputUpdateFromSolutionx.lo
CXX modules/GeothermalFluxx/libISSMCore_la-GeothermalFluxx.lo
CXX modules/GetSolutionFromInputsx/libISSMCore_la-GetSolutionFromInputsx.lo
CXX modules/GetVectorFromInputsx/libISSMCore_la-GetVectorFromInputsx.lo
CXX modules/InputUpdateFromVectorx/libISSMCore_la-InputUpdateFromVectorx.lo
CXX modules/FloatingiceMeltingRatex/libISSMCore_la-FloatingiceMeltingRatex.lo
CXX modules/FloatingiceMeltingRatePicox/libISSMCore_la-FloatingiceMeltingRatePicox.lo
CXX modules/FrontalForcingsx/libISSMCore_la-FrontalForcingsx.lo
CXX modules/ConfigureObjectsx/libISSMCore_la-ConfigureObjectsx.lo
CXX modules/SpcNodesx/libISSMCore_la-SpcNodesx.lo
CXX modules/SurfaceMassBalancex/libISSMCore_la-SurfaceMassBalancex.lo
CXX modules/SurfaceMassBalancex/libISSMCore_la-Gembx.lo
CXX modules/Reducevectorgtofx/libISSMCore_la-Reducevectorgtofx.lo
CXX modules/Reduceloadx/libISSMCore_la-Reduceloadx.lo
CXX modules/ConstraintsStatex/libISSMCore_la-ConstraintsStatex.lo
CXX modules/ResetConstraintsx/libISSMCore_la-ResetConstraintsx.lo
CXX modules/ResetFSBasalBoundaryConditionx/libISSMCore_la-ResetFSBasalBoundaryConditionx.lo
CXX modules/Solverx/libISSMCore_la-Solverx.lo
CXX modules/StochasticForcingx/libISSMCore_la-StochasticForcingx.lo
CXX modules/Mergesolutionfromftogx/libISSMCore_la-Mergesolutionfromftogx.lo
CXX cores/libISSMCore_la-ProcessArguments.lo
CXX cores/libISSMCore_la-ResetBoundaryConditions.lo
CXX cores/libISSMCore_la-WrapperCorePointerFromSolutionEnum.lo
CXX cores/libISSMCore_la-WrapperPreCorePointerFromSolutionEnum.lo
CXX cores/libISSMCore_la-CorePointerFromSolutionEnum.lo
CXX cores/libISSMCore_la-ad_core.lo
CXX cores/libISSMCore_la-adgradient_core.lo
CXX main/libISSMCore_la-EnvironmentInit.lo
CXX main/libISSMCore_la-EnvironmentFinalize.lo
CXX analyses/libISSMCore_la-EnumToAnalysis.lo
CXX solutionsequences/libISSMCore_la-solutionsequence_la.lo
CXX solutionsequences/libISSMCore_la-solutionsequence_la_theta.lo
CXX solutionsequences/libISSMCore_la-solutionsequence_linear.lo
CXX solutionsequences/libISSMCore_la-solutionsequence_nonlinear.lo
CXX solutionsequences/libISSMCore_la-solutionsequence_newton.lo
CXX solutionsequences/libISSMCore_la-solutionsequence_fct.lo
CXX solutionsequences/libISSMCore_la-solutionsequence_schurcg.lo
CXX solutionsequences/libISSMCore_la-solutionsequence_sampling.lo
CXX solutionsequences/libISSMCore_la-convergence.lo
CXX classes/Options/libISSMCore_la-Options.lo
CXX classes/Options/libISSMCore_la-OptionUtilities.lo
CXX classes/libISSMCore_la-RiftStruct.lo
CXX modules/ModelProcessorx/Transient/libISSMCore_la-UpdateElementsTransient.lo
CXX modules/ModelProcessorx/Transient/libISSMCore_la-UpdateParametersTransient.lo
CXX cores/libISSMCore_la-transient_core.lo
CXX cores/libISSMCore_la-steadystate_core.lo
CXX cores/libISSMCore_la-masstransport_core.lo
CXX cores/libISSMCore_la-oceantransport_core.lo
CXX cores/libISSMCore_la-depthaverage_core.lo
CXX cores/libISSMCore_la-extrudefrombase_core.lo
CXX cores/libISSMCore_la-extrudefromtop_core.lo
CXX cores/libISSMCore_la-thermal_core.lo
CXX cores/libISSMCore_la-smb_core.lo
CXX cores/libISSMCore_la-bmb_core.lo
CXX cores/libISSMCore_la-debris_core.lo
CXX solutionsequences/libISSMCore_la-solutionsequence_thermal_nonlinear.lo
CXX modules/ControlInputSetGradientx/libISSMCore_la-ControlInputSetGradientx.lo
CXX modules/GetVectorFromControlInputsx/libISSMCore_la-GetVectorFromControlInputsx.lo
CXX modules/SetControlInputsFromVectorx/libISSMCore_la-SetControlInputsFromVectorx.lo
CXX modules/ModelProcessorx/Control/libISSMCore_la-CreateParametersControl.lo
CXX modules/ModelProcessorx/Control/libISSMCore_la-UpdateElementsAndMaterialsControl.lo
CXX modules/SurfaceAbsVelMisfitx/libISSMCore_la-SurfaceAbsVelMisfitx.lo
CXX modules/SurfaceRelVelMisfitx/libISSMCore_la-SurfaceRelVelMisfitx.lo
CXX modules/SurfaceLogVelMisfitx/libISSMCore_la-SurfaceLogVelMisfitx.lo
CXX modules/SurfaceLogVxVyMisfitx/libISSMCore_la-SurfaceLogVxVyMisfitx.lo
CXX modules/SurfaceAverageVelMisfitx/libISSMCore_la-SurfaceAverageVelMisfitx.lo
CXX modules/ThicknessAbsMisfitx/libISSMCore_la-ThicknessAbsMisfitx.lo
CXX modules/Gradjx/libISSMCore_la-Gradjx.lo
CXX modules/DragCoefficientAbsGradientx/libISSMCore_la-DragCoefficientAbsGradientx.lo
CXX modules/ThicknessAlongGradientx/libISSMCore_la-ThicknessAlongGradientx.lo
CXX modules/ThicknessAcrossGradientx/libISSMCore_la-ThicknessAcrossGradientx.lo
CXX modules/RheologyBbarAbsGradientx/libISSMCore_la-RheologyBbarAbsGradientx.lo
CXX modules/RheologyBAbsGradientx/libISSMCore_la-RheologyBAbsGradientx.lo
CXX shared/Numerics/libISSMCore_la-BrentSearch.lo
CXX cores/libISSMCore_la-control_core.lo
CXX cores/libISSMCore_la-controltao_core.lo
CXX cores/libISSMCore_la-controlm1qn3_core.lo
CXX cores/libISSMCore_la-controladm1qn3_core.lo
CXX cores/libISSMCore_la-controlvalidation_core.lo
CXX cores/libISSMCore_la-adjointstressbalance_core.lo
CXX cores/libISSMCore_la-adjointbalancethickness_core.lo
CXX cores/libISSMCore_la-adjointbalancethickness2_core.lo
CXX cores/libISSMCore_la-AdjointCorePointerFromSolutionEnum.lo
CXX solutionsequences/libISSMCore_la-solutionsequence_adjoint_linear.lo
CXX cores/libISSMCore_la-hydrology_core.lo
CXX solutionsequences/libISSMCore_la-solutionsequence_hydro_nonlinear.lo
CXX solutionsequences/libISSMCore_la-solutionsequence_shakti_nonlinear.lo
CXX solutionsequences/libISSMCore_la-solutionsequence_glads_nonlinear.lo
CXX cores/libISSMCore_la-stressbalance_core.lo
CXX solutionsequences/libISSMCore_la-solutionsequence_stokescoupling_nonlinear.lo
CXX cores/libISSMCore_la-balancethickness_core.lo
CXX cores/libISSMCore_la-balancethickness2_core.lo
CXX cores/libISSMCore_la-balancevelocity_core.lo
CXX cores/libISSMCore_la-surfaceslope_core.lo
CXX cores/libISSMCore_la-bedslope_core.lo
CXX cores/libISSMCore_la-damage_core.lo
CXX cores/libISSMCore_la-levelsetfunctionslope_core.lo
CXX cores/libISSMCore_la-movingfront_core.lo
CXX cores/libISSMCore_la-groundingline_core.lo
CXX modules/GroundinglineMigrationx/libISSMCore_la-GroundinglineMigrationx.lo
CXX classes/Loads/libISSMCore_la-Riftfront.lo
CXX modules/ConstraintsStatex/libISSMCore_la-RiftConstraintsState.lo
CXX modules/ModelProcessorx/libISSMCore_la-CreateOutputDefinitions.lo
CXX modules/OutputDefinitionsResponsex/libISSMCore_la-OutputDefinitionsResponsex.lo
CXX modules/InterpFromMeshToMesh2dx/libISSMCore_la-InterpFromMeshToMesh2dx.lo
CXX classes/Inputs/libISSMCore_la-Inputs.lo
CXX classes/Inputs/libISSMCore_la-BoolInput.lo
CXX classes/Inputs/libISSMCore_la-DoubleInput.lo
CXX classes/Inputs/libISSMCore_la-IntInput.lo
CXX classes/Inputs/libISSMCore_la-ElementInput.lo
CXX classes/Inputs/libISSMCore_la-SegInput.lo
CXX classes/Inputs/libISSMCore_la-TriaInput.lo
CXX classes/Inputs/libISSMCore_la-PentaInput.lo
CXX classes/Inputs/libISSMCore_la-DatasetInput.lo
CXX classes/Inputs/libISSMCore_la-ControlInput.lo
CXX classes/Inputs/libISSMCore_la-TransientInput.lo
CXX classes/Inputs/libISSMCore_la-ArrayInput.lo
CXX classes/Inputs/libISSMCore_la-IntArrayInput.lo
CXX toolkits/petsc/patches/libISSMCore_la-VecToMPISerial.lo
CXX toolkits/petsc/patches/libISSMCore_la-MatToMPISerial.lo
CXX toolkits/petsc/patches/libISSMCore_la-NewVec.lo
CXX toolkits/petsc/patches/libISSMCore_la-PetscOptionsDetermineSolverType.lo
CXX toolkits/petsc/patches/libISSMCore_la-NewMat.lo
CXX toolkits/petsc/patches/libISSMCore_la-VecFree.lo
CXX toolkits/petsc/patches/libISSMCore_la-KSPFree.lo
CXX toolkits/petsc/patches/libISSMCore_la-MatFree.lo
CXX toolkits/petsc/patches/libISSMCore_la-MatMultPatch.lo
CXX toolkits/petsc/patches/libISSMCore_la-ISSMToPetscMatrixType.lo
CXX toolkits/petsc/patches/libISSMCore_la-ISSMToPetscInsertMode.lo
CXX toolkits/petsc/patches/libISSMCore_la-ISSMToPetscNormMode.lo
CXX toolkits/petsc/objects/libISSMCore_la-PetscMat.lo
CXX toolkits/petsc/objects/libISSMCore_la-PetscVec.lo
CXX toolkits/petsc/objects/libISSMCore_la-PetscSolver.lo
CXX toolkits/mumps/libISSMCore_la-MumpsSolve.lo
CXX analyses/libISSMCore_la-AdjointBalancethicknessAnalysis.lo
CXX analyses/libISSMCore_la-AdjointBalancethickness2Analysis.lo
CXX analyses/libISSMCore_la-AdjointHorizAnalysis.lo
CXX analyses/libISSMCore_la-AgeAnalysis.lo
CXX analyses/libISSMCore_la-BalancethicknessAnalysis.lo
CXX analyses/libISSMCore_la-Balancethickness2Analysis.lo
CXX analyses/libISSMCore_la-BalancethicknessSoftAnalysis.lo
CXX analyses/libISSMCore_la-BalancevelocityAnalysis.lo
CXX analyses/libISSMCore_la-L2ProjectionBaseAnalysis.lo
CXX analyses/libISSMCore_la-DamageEvolutionAnalysis.lo
CXX modules/Damagex/libISSMCore_la-Damagex.lo
CXX analyses/libISSMCore_la-DebrisAnalysis.lo
CXX analyses/libISSMCore_la-StressbalanceAnalysis.lo
CXX analyses/libISSMCore_la-UzawaPressureAnalysis.lo
CXX analyses/libISSMCore_la-StressbalanceSIAAnalysis.lo
CXX analyses/libISSMCore_la-StressbalanceVerticalAnalysis.lo
CXX analyses/libISSMCore_la-EnthalpyAnalysis.lo
CXX analyses/libISSMCore_la-GLheightadvectionAnalysis.lo
CXX analyses/libISSMCore_la-HydrologyShreveAnalysis.lo
CXX analyses/libISSMCore_la-HydrologyTwsAnalysis.lo
CXX analyses/libISSMCore_la-HydrologyShaktiAnalysis.lo
CXX analyses/libISSMCore_la-HydrologyPismAnalysis.lo
CXX analyses/libISSMCore_la-HydrologyGlaDSAnalysis.lo
CXX analyses/libISSMCore_la-HydrologyDCInefficientAnalysis.lo
CXX analyses/libISSMCore_la-HydrologyDCEfficientAnalysis.lo
CXX analyses/libISSMCore_la-HydrologyArmapwAnalysis.lo
CXX analyses/libISSMCore_la-L2ProjectionEPLAnalysis.lo
CXX analyses/libISSMCore_la-MeltingAnalysis.lo
CXX analyses/libISSMCore_la-MasstransportAnalysis.lo
CXX analyses/libISSMCore_la-OceantransportAnalysis.lo
CXX analyses/libISSMCore_la-SmbAnalysis.lo
CXX analyses/libISSMCore_la-FreeSurfaceBaseAnalysis.lo
CXX analyses/libISSMCore_la-FreeSurfaceTopAnalysis.lo
CXX analyses/libISSMCore_la-ExtrudeFromBaseAnalysis.lo
CXX analyses/libISSMCore_la-ExtrudeFromTopAnalysis.lo
CXX analyses/libISSMCore_la-DepthAverageAnalysis.lo
CXX analyses/libISSMCore_la-ThermalAnalysis.lo
CXX analyses/libISSMCore_la-SmoothAnalysis.lo
CXX analyses/libISSMCore_la-LevelsetAnalysis.lo
CXX modules/Calvingx/libISSMCore_la-Calvingx.lo
CXX modules/KillIcebergsx/libISSMCore_la-KillIcebergsx.lo
CXX analyses/libISSMCore_la-ExtrapolationAnalysis.lo
CXX cores/libISSMCore_la-love_core.lo
CXX analyses/libISSMCore_la-LoveAnalysis.lo
CXX cores/libISSMCore_la-esa_core.lo
CXX analyses/libISSMCore_la-EsaAnalysis.lo
CXX cores/libISSMCore_la-sampling_core.lo
CXX analyses/libISSMCore_la-SamplingAnalysis.lo
CXX cores/libISSMCore_la-sealevelchange_core.lo
CXX analyses/libISSMCore_la-SealevelchangeAnalysis.lo
CXX classes/libISSMCore_la-GrdLoads.lo
CXX classes/libISSMCore_la-SealevelGeometry.lo
CXX modules/GiaDeflectionCorex/libISSMCore_la-GiaDeflectionCorex.lo
CXX toolkits/metis/patches/libISSMCore_la-METIS_PartMeshNodalPatch.lo
CXX classes/kriging/libISSMCore_la-Observations.lo
CXX classes/kriging/libISSMCore_la-GaussianVariogram.lo
CXX classes/kriging/libISSMCore_la-ExponentialVariogram.lo
CXX classes/kriging/libISSMCore_la-SphericalVariogram.lo
CXX classes/kriging/libISSMCore_la-PowerVariogram.lo
CXX classes/kriging/libISSMCore_la-Quadtree.lo
CXX classes/kriging/libISSMCore_la-Covertree.lo
CXX classes/kriging/libISSMCore_la-Observation.lo
CXX modules/Krigingx/libISSMCore_la-pKrigingx.lo
CXX shared/String/ApiPrintf.lo
CXX shared/Threads/libISSMModules_la-LaunchThread.lo
CXX shared/Threads/libISSMModules_la-PartitionRange.lo
CXX shared/Exp/libISSMModules_la-exp.lo
CXX shared/Triangle/libISSMModules_la-GridInsideHole.lo
CXX shared/Triangle/libISSMModules_la-TriangleUtils.lo
CXX modules/Trianglex/libISSMModules_la-Trianglex.lo
CXX modules/ProcessRiftsx/libISSMModules_la-ProcessRiftsx.lo
CXX modules/PointCloudFindNeighborsx/libISSMModules_la-PointCloudFindNeighborsx.lo
CXX modules/PointCloudFindNeighborsx/libISSMModules_la-PointCloudFindNeighborsxt.lo
CXX modules/InterpFromGridToMeshx/libISSMModules_la-InterpFromGridToMeshx.lo
CXX modules/InterpFromMesh2dx/libISSMModules_la-InterpFromMesh2dx.lo
CXX modules/InterpFromMesh2dx/libISSMModules_la-InterpFromMesh2dxt.lo
CXX modules/InterpFromMeshToMesh3dx/libISSMModules_la-InterpFromMeshToMesh3dx.lo
CXX modules/InterpFromMeshToGridx/libISSMModules_la-InterpFromMeshToGridx.lo
CXX modules/MeshProfileIntersectionx/libISSMModules_la-MeshProfileIntersectionx.lo
CXX modules/ContourToMeshx/libISSMModules_la-ContourToMeshx.lo
CXX modules/ContourToMeshx/libISSMModules_la-ContourToMeshxt.lo
CXX modules/ExpToLevelSetx/libISSMModules_la-ExpToLevelSetx.lo
CXX modules/ExpToLevelSetx/libISSMModules_la-ExpToLevelSetxt.lo
CXX modules/ContourToNodesx/libISSMModules_la-ContourToNodesx.lo
CXX modules/DistanceToMaskBoundaryx/libISSMModules_la-DistanceToMaskBoundaryx.lo
CXX modules/DistanceToMaskBoundaryx/libISSMModules_la-DistanceToMaskBoundaryxt.lo
CXX modules/NodeConnectivityx/libISSMModules_la-NodeConnectivityx.lo
CXX modules/ElementConnectivityx/libISSMModules_la-ElementConnectivityx.lo
CXX modules/PropagateFlagsFromConnectivityx/libISSMModules_la-PropagateFlagsFromConnectivityx.lo
CXX modules/Chacox/libISSMModules_la-Chacox.lo
CXX modules/Chacox/libISSMModules_la-input_parse.lo
CXX modules/Chacox/libISSMModules_la-user_params.lo
CXX modules/Krigingx/libISSMModules_la-Krigingx.lo
CXX modules/Krigingx/libISSMModules_la-pKrigingx.lo
CXX main/issm_slc-issm_slc.o
CXX main/kriging-kriging.o
CXXLD libISSMCore.la
CXXLD libISSMOverload.la

*** Warning: Linking the shared library libISSMCore.la against the
*** static library /home/anjali.sandip/issm-project/trunk-jpl/externalpackages/m1qn3/install/libm1qn3.a is not portable!

*** Warning: Linking the shared library libISSMCore.la against the
*** static library /home/anjali.sandip/issm-project/trunk-jpl/externalpackages/m1qn3/install/libddot.a is not portable!
/usr/bin/grep: /cm/local/apps/gcc/9.2.0/lib/../lib64/libstdc++.la: No such file or directory
/usr/bin/sed: can't read /cm/local/apps/gcc/9.2.0/lib/../lib64/libstdc++.la: No such file or directory
libtool: error: '/cm/local/apps/gcc/9.2.0/lib/../lib64/libstdc++.la' is not a valid libtool archive
make[2]: *** [Makefile:4770: libISSMCore.la] Error 1
make[2]: Leaving directory '/home/anjali.sandip/issm-project/trunk-jpl/src/c'
make[1]: *** [Makefile:470: install-recursive] Error 1
make[1]: Leaving directory '/home/anjali.sandip/issm-project/trunk-jpl/src'
make: *** [Makefile:591: install-recursive] Error 1

justinquinn

ASand
Hmmm, I wonder if it might help to explicitly get mpicc and other compilers explicitly. Can you try running,

export CC=${ISSM_DIR}/externalpackages/petsc/install/bin/mpicc
export CXX=${ISSM_DIR}/externalpackages/petsc/install/bin/mpicxx
export FC=${ISSM_DIR}/externalpackages/petsc/install/bin/mpifort

then running make; make install again?

ASand

Here's what I attempted:
cd $ISSM_DIR
svn update
autoreconf -ivf
./configure.sh
export CC=${ISSM_DIR}/externalpackages/petsc/install/bin/mpicc
export CXX=${ISSM_DIR}/externalpackages/petsc/install/bin/mpicxx
export FC=${ISSM_DIR}/externalpackages/petsc/install/bin/mpifort
make -j4 install

And this is error I get:
*** Warning: Linking the shared library libISSMCore.la against the
*** static library .../trunk-jpl/externalpackages/m1qn3/install/libm1qn3.a is not portable!

*** Warning: Linking the shared library libISSMCore.la against the
*** static library .../externalpackages/m1qn3/install/libddot.a is not portable!
/usr/bin/grep: /cm/local/apps/gcc/9.2.0/lib/../lib64/libstdc++.la: No such file or directory
/usr/bin/sed: can't read /cm/local/apps/gcc/9.2.0/lib/../lib64/libstdc++.la: No such file or directory
libtool: error: '/cm/local/apps/gcc/9.2.0/lib/../lib64/libstdc++.la' is not a valid libtool archive
make[2]: *** [Makefile:4770: libISSMCore.la] Error 1
make[2]: Leaving directory
make[1]: *** [Makefile:470: install-recursive] Error 1
make[1]: Leaving directory
make: *** [Makefile:591: install-recursive] Error 1

justinquinn

ASand
Okay, in a new terminal, try,

cd $ISSM_DIR
source $ISSM_DIR/etc/environment.sh
make clean
autoreconf -ivf
make -j4

Because this is an update and recompile, I think there may be an issue with artifacts from a previous build that are being obscured here. The two warnings are normal and not causing any issues, by the way.

ASand

Thank you, I attempted the above. I continue to receive the same error message. I am not sure what I am missing here...

justinquinn

ASand
Do you have a more recent version of gcc available to you that you can try to use to compile?

harryzou

"justinquinn"#p1832 Sorry I am replying on behave of @ASand , the current gcc compiler we are using is gcc8.5.0. Should we update it into a more recent version?

justinquinn

harryzou Hi, yes, please: try a newer version to see if it will clear the error. You may or may not need to recompile autotools (and possibly petsc) as well using the newer version.

harryzou

I reload a gcc 9.5.0 module, recompiled cmake, petsc, and autotools. After that, it worked. Thank you.

justinquinn

harryzou Awesome, glad to hear it worked 🙂