[aspect-devel] Installation on cluster CentOS

Tue Sep 25 01:17:18 PDT 2018

Hi all,

I just moved to a new lab, and I am trying to install ASPECT on the 
cluster here. So far, it works on my new computer + the test computer, 
so I'm quite happy... But the installation on the cluster is more 
complicated.

I am stucked with the installation of deal_ii.

The cluster is on CentOS, and uses modules. So far, I asked the staff to 
provide most of the required librairies, and I think we got almost all 
of them.

I am using candi to do the installation, and simply following the 
instructions.

I am using gcc 8.1.0, and we have lapack compiled with gcc8.1.0. cmake 
is 3.9.6. I have tried to use hdf5 and petsc from the modules, but the 
system did not recognize the HDF5_DIR and PETSC_DIR, so I compiled them 
through candi.

I got all installed (parmetis, p4est, slepc, hdf5, trilinos), but the 
compilation of deal_ii end up with an error (highlighted below). And I 
looked at the log file 
//home/LPGN/lasbleis-m/bin/tmp/build/deal.II-v9.0.0/CMakeFiles/CMakeOutput.log/, 
but there is absolutely no error in the log file... So I'm a little bit 
puzzled. /
/

Any idea that could help me? /
/

(attached file: log file. And below, last lines I got while running 
candi.sh)

Best,

Marine

/
/

/[more things here] ......../

/-- Include 
/home/LPGN/lasbleis-m/bin/tmp/unpack/deal.II-v9.0.0/cmake/setup_cpack.cmake//
//-- //
//-- Include 
/home/LPGN/lasbleis-m/bin/tmp/unpack/deal.II-v9.0.0/cmake/setup_custom_targets.cmake//
//-- //
//-- Include 
/home/LPGN/lasbleis-m/bin/tmp/unpack/deal.II-v9.0.0/cmake/setup_finalize.cmake//
//CMake Error at cmake/setup_finalize.cmake:95 (MESSAGE)://
////
//
//*  Configuration error: Cannot compile a test program with the final 
set of*/*/
/**/    compiler and linker flags:/*/
//      CXX flags (DEBUG): -pedantic -fPIC -Wall -Wextra -Wpointer-arith 
-Wwrite-strings -Wsynth -Wsign-compare -Wswitch -Woverloaded-virtual 
-Wno-placement-new -Wno-deprecated-declarations -Wno-literal-suffix 
-fopenmp-simd -std=c++17 -Wno-parentheses -Wno-unused-local-typedefs -Og 
-ggdb -Wa,--compress-debug-sections//
//      LD flags  (DEBUG): -Wl,--as-needed -rdynamic -fuse-ld=gold -ggdb//
//      LIBRARIES (DEBUG): 
/usr/lib64/libz.so;rt;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libmuelu-adapters.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libmuelu-interface.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libmuelu.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libteko.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libstratimikos.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libstratimikosbelos.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libstratimikosaztecoo.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libstratimikosamesos.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libstratimikosml.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libstratimikosifpack.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libifpack2-adapters.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libifpack2.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libanasazitpetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libModeLaplace.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libanasaziepetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libanasazi.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libamesos2.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libbelostpetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libbelosepetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libbelos.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libml.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libifpack.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libzoltan2.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libpamgen_extras.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libpamgen.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libamesos.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libgaleri-xpetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libgaleri-epetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libaztecoo.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libisorropia.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libxpetra-sup.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libxpetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libthyratpetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libthyraepetraext.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libthyraepetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libthyracore.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libepetraext.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libtpetraext.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libtpetrainout.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libtpetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libkokkostsqr.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libtpetrakernels.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libtpetraclassiclinalg.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libtpetraclassicnodeapi.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libtpetraclassic.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libtriutils.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libzoltan.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libepetra.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libsacado.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/librtop.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libteuchoskokkoscomm.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libteuchoskokkoscompat.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libteuchosremainder.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libteuchosnumerics.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libteuchoscomm.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libteuchosparameterlist.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libteuchoscore.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libkokkosalgorithms.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libkokkoscontainers.so;/home/LPGN/lasbleis-m/bin/trilinos-release-12-10-1/lib/libkokkoscore.so;/home/LPGN/lasbleis-m/bin/hdf5-1.10.1/lib/libhdf5_hl.so;/home/LPGN/lasbleis-m/bin/hdf5-1.10.1/lib/libhdf5.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKBO.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKBool.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKBRep.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKernel.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKFeat.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKFillet.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKG2d.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKG3d.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKGeomAlgo.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKGeomBase.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKHLR.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKIGES.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKMath.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKMesh.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKOffset.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKPrim.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKShHealing.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKSTEP.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKSTEPAttr.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKSTEPBase.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKSTEP209.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKSTL.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKTopAlgo.so;/home/LPGN/lasbleis-m/bin/oce-OCE-0.18.2/lib/libTKXSBase.so;mpi_usempif08;mpi_usempi_ignore_tkr;mpi_mpifh;mpi;c;gcc_s;gcc;/home/LPGN/lasbleis-m/bin/slepc-3.7.3/lib/libslepc.so;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libpetsc.so;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libcmumps.a;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libdmumps.a;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libsmumps.a;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libzmumps.a;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libmumps_common.a;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libpord.a;/home/LPGN/lasbleis-m/bin/parmetis-4.0.3/lib/libparmetis.so;/home/LPGN/lasbleis-m/bin/parmetis-4.0.3/lib/libmetis.so;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libHYPRE.a;/home/LPGN/lasbleis-m/bin/petsc-3.7.6/lib/libscalapack.a;/trinity/shared/apps/cv-standard/lapack/3.8.0_gcc81/lib64/liblapack.a;/trinity/shared/apps/cv-standard/lapack/3.8.0_gcc81/lib64/libblas.a;/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/lib/libmpi_usempif08.so;/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/lib/libmpi_usempi_ignore_tkr.so;/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/lib/libmpi_mpifh.so;gfortran;quadmath;/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/lib/libmpi_cxx.so;m;/trinity/shared/apps/cv-standard/openmpi/psm2/gcc81/3.1.0/lib/libmpi.so;pthread;dl;/home/LPGN/lasbleis-m/bin/p4est-2.0/DEBUG/lib/libp4est.so;/home/LPGN/lasbleis-m/bin/p4est-2.0/DEBUG/lib/libsc.so//
////
//
////
//
//Call Stack (most recent call first)://
//  cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)//
//  CMakeLists.txt:132 (VERBOSE_INCLUDE)//
//
//
//-- Configuring incomplete, errors occurred!//
//See also 
"/home/LPGN/lasbleis-m/bin/tmp/build/deal.II-v9.0.0/CMakeFiles/CMakeOutput.log".//
//Failure with exit status: 1//
//Exit message: There was a problem configuring dealii v9.0.0./

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