Invalid MEX-file: Missing dependent shared libraries...

skime

Hello, I've problem in running ISSM on Ubuntu 16.04, MATLAB 2017a. After compiling externalpackages and ISSM I've such error:

>> addpath(genpath('/usr/local/issm/trunk/src/m')) addpath /usr/local/issm/trunk/bin/ /usr/local/issm/trunk/lib/ >> issmversion Invalid MEX-file '/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64': Missing dependent shared libraries: 'libpetsc.so.3.6' required by '/usr/local/issm/trunk/lib/libISSMMatlab.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' 'libparmetis.so' required by '/usr/local/issm/trunk/lib/libISSMMatlab.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' 'libmetis.so' required by '/usr/local/issm/trunk/lib/libISSMMatlab.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' 'libpetsc.so.3.6' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' 'libmetis.so' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'blacs_gridexit_' required by '/usr/local/issm/trunk/lib/libISSMMatlab.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'blacs_gridinfo_' required by '/usr/local/issm/trunk/lib/libISSMMatlab.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'blacs_gridinit_' required by '/usr/local/issm/trunk/lib/libISSMMatlab.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'descinit_' required by '/usr/local/issm/trunk/lib/libISSMMatlab.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'metis_nodend_' required by '/usr/local/issm/trunk/lib/libISSMMatlab.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'metis_setdefaultoptions_' required by '/usr/local/issm/trunk/lib/libISSMMatlab.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'numroc_' required by '/usr/local/issm/trunk/lib/libISSMMatlab.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'ParMETIS_V3_NodeND' required by '/usr/local/issm/trunk/lib/libISSMMatlab.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'pdgetrf_' required by '/usr/local/issm/trunk/lib/libISSMMatlab.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'pdgetrs_' required by '/usr/local/issm/trunk/lib/libISSMMatlab.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'pdpotrf_' required by '/usr/local/issm/trunk/lib/libISSMMatlab.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'pdpotrs_' required by '/usr/local/issm/trunk/lib/libISSMMatlab.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'dmumps_c' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'ISCreateGeneral' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'KSPCreate' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'KSPDestroy' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'KSPGetIterationNumber' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'KSPGetPC' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'KSPSetFromOptions' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'KSPSetInitialGuessNonzero' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'KSPSetOperators' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'KSPSolve' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'KSPView' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatAssemblyBegin' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatAssemblyEnd' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatConvert' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatCreate' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatCreateAIJ' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatCreateDense' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatDestroy' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatDuplicate' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatGetInfo' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatGetLocalSize' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatGetOwnershipRange' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatGetRow' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatGetSize' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatGetType' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatGetValues' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatMPIAIJSetPreallocation' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatMult' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatNorm' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatRestoreRow' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatSetFromOptions' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatSetSizes' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatSetValues' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatTranspose' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'MatView' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'METIS_PartMeshNodal' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'METIS_SetDefaultOptions' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PCFactorSetMatSolverPackage' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PCFieldSplitSetIS' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PETSC_COMM_WORLD' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PetscFinalize' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PetscGetFlops' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PetscInitialize' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PetscMemoryGetCurrentUsage' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PetscOptionsClear' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PetscOptionsGetString' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PetscOptionsSetFromOptions' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PetscOptionsSetValue' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PetscOptionsView' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PetscStrlen' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PetscTokenCreate' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PetscTokenDestroy' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PetscTokenFind' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'PETSC_VIEWER_STDOUT_' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'TaoCreate' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'TaoDestroy' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'TaoGetGradientVector' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'TaoGetSolutionStatus' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'TaoGetSolutionVector' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'TaoSetFromOptions' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'TaoSetInitialVector' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'TaoSetMaximumFunctionEvaluations' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'TaoSetMaximumIterations' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'TaoSetMonitor' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'TaoSetObjectiveAndGradientRoutine' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'TaoSetTolerances' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'TaoSetType' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'TaoSetVariableBounds' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'TaoSolve' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'TaoView' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecAssemblyBegin' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecAssemblyEnd' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecAXPBY' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecAXPBYPCZ' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecAXPY' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecAYPX' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecCopy' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecCreate' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecDestroy' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecDot' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecDuplicate' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecGetArray' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecGetLocalSize' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecGetOwnershipRange' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecGetSize' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecGetValues' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecMax' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecNorm' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecPointwiseDivide' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecPointwiseMult' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecRestoreArray' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecScale' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecSet' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecSetFromOptions' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecSetSizes' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecSetValues' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecShift' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecView' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol 'VecZeroEntries' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol '_Z9ApiPrintfPKc' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol '_ZN14ToolkitOptions14toolkitoptionsE' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol '_ZN8IssmComm4commE' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64' Missing symbol '_ZN8IssmComm8parallelE' required by '/usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64'. Error in IssmConfig (line 14) value = IssmConfig_matlab(string); Error in issmversion (line 13)

disp();

My configure.sh:

#!/bin/sh

./configure \
	--prefix=$ISSM_DIR\
	--with-matlab-dir=/usr/local/MATLAB/R2017a \
	--with-triangle-dir=$ISSM_DIR/externalpackages/triangle/install \
	--with-mpi-include=$ISSM_DIR/externalpackages/mpich/install/include  \
	--with-mpi-libflags="-L$ISSM_DIR/externalpackages/mpich/install/lib -lmpich" \
	--with-petsc-dir=$ISSM_DIR/externalpackages/petsc/install \
	--with-metis-dir=$ISSM_DIR/externalpackages/petsc/install \
	--with-mumps-dir=$ISSM_DIR/externalpackages/petsc/install \
	--with-blas-lapack-dir=$ISSM_DIR/externalpackages/petsc/install \
	--with-math77-dir=$ISSM_DIR/externalpackages/math77/install \
	--with-fortran-lib="-L/usr/lib/gcc/x86_64-linux-gnu/4.9 -lgfortran" \
	--with-Gia \
	--with-numthreads=4 \
	--disable-static \
	--enable-development \
	--enable-debugging \

ldd of IssmConfig_matlab.mexa64:

ldd /usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64
	linux-vdso.so.1 =>  (0x00007ffcfd4fe000)
	libISSMMatlab.so.0 => /usr/local/issm/trunk/lib/libISSMMatlab.so.0 (0x00007febdeb8b000)
	libISSMCore.so.0 => /usr/local/issm/trunk/lib/libISSMCore.so.0 (0x00007febde312000)
	libISSMApi.so.0 => /usr/local/issm/trunk/lib/libISSMApi.so.0 (0x00007febde110000)
	libmex.so => not found
	libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007febddd6d000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007febdd9a3000)
	libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007febdd78c000)
	libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007febdd45a000)
	libmpich.so.10 => /usr/local/issm/trunk/externalpackages/mpich/install/lib/libmpich.so.10 (0x00007febdcfdf000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007febdcdc2000)
	libpetsc.so.3.6 => /usr/local/issm/trunk/externalpackages/petsc/install/lib/libpetsc.so.3.6 (0x00007febdbc33000)
	libparmetis.so => /usr/local/issm/trunk/externalpackages/petsc/install/lib/libparmetis.so (0x00007febdb9f4000)
	libmetis.so => /usr/local/issm/trunk/externalpackages/petsc/install/lib/libmetis.so (0x00007febdb783000)
	libmx.so => not found
	libmex.so => not found
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007febdb479000)
	/lib64/ld-linux-x86-64.so.2 (0x00005580d788e000)
	libmex.so => not found
	libquadmath.so.0 => /usr/lib/x86_64-linux-gnu/libquadmath.so.0 (0x00007febdb238000)
	libmpl.so.1 => /usr/local/issm/trunk/externalpackages/mpich/install/lib/libmpl.so.1 (0x00007febdb032000)
	librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007febdae2a000)
	libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007febdac25000)

Do you have any ideas what should I do? Petsc 3.6 libraries are compiled/installed, why they are missing in IssmConfig_matlab.mexa64?

mathieumorlighem

Hi, what happens in from MATLAB you do:

>> !ldd /usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64

skime

>> !ldd /usr/local/issm/trunk/lib/libISSMCore.so.0->/usr/local/issm/trunk/lib/IssmConfig_matlab.mexa64
ldd: /usr/local/issm/trunk/lib/libISSMCore.so.0-: No such file or directory

>> !ldd /usr/local/issm/trunk/lib/libISSMCore.so.0
	linux-vdso.so.1 =>  (0x00007ffe9ef69000)
	libpetsc.so.3.6 => not found
	libmetis.so => not found
	libmpich.so.10 => /usr/local/issm/trunk/externalpackages/mpich/install/lib/libmpich.so.10 (0x00007f9f7d70f000)
	libgfortran.so.3 => /usr/local/MATLAB/R2017a/sys/os/glnxa64/libgfortran.so.3 (0x00007f9f7d3f1000)
	libstdc++.so.6 => /usr/local/MATLAB/R2017a/sys/os/glnxa64/libstdc++.so.6 (0x00007f9f7d0de000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f9f7cdd5000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f9f7ca0b000)
	libgcc_s.so.1 => /usr/local/MATLAB/R2017a/sys/os/glnxa64/libgcc_s.so.1 (0x00007f9f7c7f4000)
	libmpl.so.1 => /usr/local/issm/trunk/externalpackages/mpich/install/lib/libmpl.so.1 (0x00007f9f7c5ef000)
	librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f9f7c3e7000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f9f7c1c9000)
	/lib64/ld-linux-x86-64.so.2 (0x0000556c39f20000)
	libquadmath.so.0 => /usr/local/MATLAB/R2017a/sys/os/glnxa64/libquadmath.so.0 (0x00007f9f7bf8c000)

Ok... so broken links in this file. How to repair it? Recompile with other settings?

mathieumorlighem

Hi,

it is hard to figure out what's going on with just this. What did you do exactly? Did you have a version that was working before? If yes what did you change? If you installed a new version of PETSc, did you reconfigure (by running ./configure.sh) after you recompiled PETSc? Did you run make install in trunk?

Thanks

Mathieu

glperez

Hey,

This looks like an environment issue.

What does your LD_LIBRARY_PATH contain?


echo $LD_LIBRARY_PATH

If the directory where Matlab has its libraries is not there, then you will likely have this problem.

-Gil

skime

This system is fresh. I've installed Ubuntu 16.04. Installed MATLAB. Then compiled all libraries in the sequence that is required. Configured ISSM by the instruction (configure.sh is higher in posts). Compiled it... And there is the error in MATLAB. Yes I ran "make, make install" in trunk directory.

(I have doubt about one point in instruction, after installing each package should I run the command: $ source $ISSM_DIR/etc/environment.sh?)

Then I tried reinstalling MATLAB, removed "trunk", and the procedure again with compilers gcc, g++, gfortran 4.9.x versions - the same.

echo of $LD_LIBRARY_PATH

echo $LD_LIBRARY_PATH


:/usr/local/issm/trunk/externalpackages/mpich/install/lib:/usr/local/issm/trunk/externalpackages/petsc/install/lib

Compilers on the system:

dpkg --list | grep compiler


ii  clang                                       1.8-33ubuntu3.1                            amd64        C, C++ and Objective-C compiler (LLVM based)
ii  clang-3.8                                   1.8-2ubuntu4                               amd64        C, C++ and Objective-C compiler (LLVM based)
ii  g++                                         4.3.1-1ubuntu1                             amd64        GNU C++ compiler
ii  g++-4.7                                     4.7.4-3ubuntu12                              amd64        GNU C++ compiler
ii  g++-4.9                                     4.9.4-2ubuntu1~16.04                         amd64        GNU C++ compiler
ii  g++-5                                       5.4.1-2ubuntu1~16.04                         amd64        GNU C++ compiler
ii  gcc                                         4.3.1-1ubuntu1                             amd64        GNU C compiler
ii  gcc-4.7                                     4.7.4-3ubuntu12                              amd64        GNU C compiler
ii  gcc-4.9                                     4.9.4-2ubuntu1~16.04                         amd64        GNU C compiler
ii  gcc-5                                       5.4.1-2ubuntu1~16.04                         amd64        GNU C compiler
ii  gfortran                                    4.3.1-1ubuntu1                             amd64        GNU Fortran 95 compiler
ii  gfortran-4.9                                4.9.4-2ubuntu1~16.04                         amd64        GNU Fortran compiler
ii  gfortran-5                                  5.4.1-2ubuntu1~16.04                         amd64        GNU Fortran compiler
ii  hardening-includes                          2.7ubuntu2                                   all          Makefile for enabling compiler flags for security hardening
ii  libllvm3.8                            1.8-2ubuntu4                               amd64        Modular compiler and toolchain technologies, runtime library
ii  libllvm4.0                            1.0-1ubuntu1~16.04.2                       amd64        Modular compiler and toolchain technologies, runtime library
ii  libxkbcommon0                         0.5.0-1ubuntu2                               amd64        library interface to the XKB compiler - shared library
ii  llvm-3.8                                    1.8-2ubuntu4                               amd64        Modular compiler and toolchain technologies
ii  llvm-3.8-dev                                1.8-2ubuntu4                               amd64        Modular compiler and toolchain technologies, libraries and headers
ii  llvm-3.8-runtime                            1.8-2ubuntu4                               amd64        Modular compiler and toolchain technologies, IR interpreter

glperez

Right. So your LD_LIBRARY_PATH is missing Matlab stuff.

There are a number of solutions, but since you are on Ubuntu I recommend using the Software Center to install the Matlab extension.

Here's the link:

https://apps.ubuntu.com/cat/applications/matlab-support/

This won't install Matlab. Instead it will create symbolic links to all the required libraries and the Matlab executable so that they are found in standard locations. This should resolve the issue you are having and makes Matlab easier to use in a Linux environment.

Of course, you could always just modify the variable yourself by appending the Matlab library path.

Let us know if this works for you!

-Gil

skime

Thank you for your advice. I've installed MATLAB support you provided but it didn't change anything. Then I reconfigured and recompiled ISSM - same error.

I set environmental variable "LD_LIBRARY_PATH" to "/usr/local/MATLAB/R2017a/bin/glnxa64:/usr/local/MATLAB/R2017a/sys/os/glnxa64" in .bashrc but it also didn't work.

Do you have any other suggestions?

skime

Okay, I resolved the problem. Reinstalled/recompilled MATLAB and ISSM on other paths... I had some error with libpetsc.so.3.6 but I moved the library file to /usr/lib/x86_64-linux-gnu/ and MATLAB stopped complaining. Thank you!

mathieumorlighem

Hi,

it is still a bit funny that MATLAB could find mpich but not PETSc. I think Gil got confused, you are not supposed to have anything MATLAB related in LD_LIBRARY_PATH outside of MATLAB. The problem is that somehow, MATLAB changes the library path and seems to be removing PETSc. Would you mind doing one last experiment? Could you do the following in MATLAB:

>> getenv('LD_LIBRARY_PATH')
>> getenv('LD_RUN_PATH')

and tell us what you get? I want to see what MATLAB is doing to your path.

Thanks

Mathieu

skime

Argh, its too late - I've uninstalled MATLAB that was doing this error. The issue could be connected to that firstly I've compiled ISSM and then installed MATLAB (?)