Dear all,
I installed the Deal.II on a cluster.
The first thing I found is that, the /dealii-9.2.0/cmake/configure/configure_1_mpi.cmake automatically set the DEAL_II_WITH_MPI argument as "off", therefore the MPI_FOUND module cannot run. I switched it on and cmake can find the MPI library.
The second thing I found is very strange. Cmake gives the message "Could not find a sufficient PETSC installation: PETSC is compiled against a different MPI library than the one deal.II picked up." The PETSc library is integrated in the cluster's public library, I can add it by the command "module add". Does this message mean that I need to compile a new version of PETSc different from the one in the public library?
Thanks!
Best
**************************************************************************************************
-- Include /home/yjin6/DEALII/dealii-9.2.0/cmake/configure/configure_3_petsc.cmake
-- Found PETSC_LIBRARY
-- Found PETSC_INCLUDE_DIR_ARCH
-- Found PETSC_INCLUDE_DIR_COMMON
-- Found PETSC_PETSCVARIABLES
-- Found PETSC_LIBRARY_mkl_scalapack_lp64
-- Found PETSC_LIBRARY_mkl_blacs_intelmpi_lp64
-- Found PETSC_LIBRARY_mkl_intel_lp64
-- Found PETSC_LIBRARY_mkl_sequential
-- Found PETSC_LIBRARY_mkl_core
-- Found PETSC_LIBRARY_umfpack
-- Found PETSC_LIBRARY_klu
-- Found PETSC_LIBRARY_cholmod
-- Found PETSC_LIBRARY_btf
-- Found PETSC_LIBRARY_ccolamd
-- Found PETSC_LIBRARY_colamd
-- Found PETSC_LIBRARY_camd
-- Found PETSC_LIBRARY_amd
-- Found PETSC_LIBRARY_suitesparseconfig
-- Found PETSC_LIBRARY_HYPRE
-- Found PETSC_LIBRARY_fftw3xc_intel_pic
-- Found PETSC_LIBRARY_fftw3x_cdft_lp64_pic
-- Found PETSC_LIBRARY_mkl_cdft_core
-- Found PETSC_LIBRARY_mkl_blacs_intelmpi_lp64
-- Found PETSC_LIBRARY_mkl_intel_lp64
-- Found PETSC_LIBRARY_mkl_sequential
-- Found PETSC_LIBRARY_mkl_core
-- Found PETSC_LIBRARY_mkl_intel_lp64
-- Found PETSC_LIBRARY_mkl_sequential
-- Found PETSC_LIBRARY_mkl_core
-- Found PETSC_LIBRARY_parmetis
-- Found PETSC_LIBRARY_metis
-- Performing Test PETSC_LIBRARY_dl
-- Performing Test PETSC_LIBRARY_dl - Success
-- Found PETSC_LIBRARY_iomp5
-- Performing Test PETSC_LIBRARY_pthread
-- Performing Test PETSC_LIBRARY_pthread - Success
-- Performing Test PETSC_LIBRARY_rt
-- Performing Test PETSC_LIBRARY_rt - Success
-- Found PETSC_LIBRARY_mpifort
-- Found PETSC_LIBRARY_mpi
-- Found PETSC_LIBRARY_ifport
-- Found PETSC_LIBRARY_ifcoremt_pic
-- Found PETSC_LIBRARY_imf
-- Found PETSC_LIBRARY_svml
-- Performing Test PETSC_LIBRARY_m
-- Performing Test PETSC_LIBRARY_m - Success
-- Found PETSC_LIBRARY_ipgo
-- Found PETSC_LIBRARY_irc
-- Found PETSC_LIBRARY_irc_s
-- Found PETSC_LIBRARY_iomp5
-- PETSC_VERSION: 3.10.2.0
-- PETSC_LIBRARIES: /project/cacds/apps/easybuild/software/PETSc/3.10.2-intel-2017b/lib/libpetsc.a;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_scalapack_lp64.so;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_intel_lp64.so;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_sequential.so;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_core.so;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/UMFPACK/Lib/libumfpack.a;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/KLU/Lib/libklu.a;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/CHOLMOD/Lib/libcholmod.a;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/BTF/Lib/libbtf.a;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/CCOLAMD/Lib/libccolamd.a;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/COLAMD/Lib/libcolamd.a;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/CAMD/Lib/libcamd.a;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/UMFPACK/Lib/libamd.a;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/SuiteSparse_config/libsuitesparseconfig.a;/project/cacds/apps/easybuild/software/Hypre/2.14.0-intel-2017b/lib/libHYPRE.a;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libfftw3xc_intel_pic.a;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libfftw3x_cdft_lp64_pic.a;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_cdft_core.so;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_intel_lp64.so;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_sequential.so;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_core.so;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_intel_lp64.so;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_sequential.so;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/lib/intel64/libmkl_core.so;/project/cacds/apps/easybuild/software/ParMETIS/4.0.3-intel-2017b/lib/libparmetis.a;/project/cacds/apps/easybuild/software/ParMETIS/4.0.3-intel-2017b/lib/libmetis.a;dl;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/lib/intel64/libiomp5.so;pthread;rt;/project/cacds/apps/intelmpi/2019.0.117/intel64/lib/libmpifort.so;/project/cacds/apps/intelmpi/2019.0.117/intel64/lib/release/libmpi.so;/project/cacds/apps/easybuild/software/ifort/2017.8.262-GCC-6.4.0-2.28/compilers_and_libraries_2017.8.262/linux/compiler/lib/intel64/libifport.so;/project/cacds/apps/easybuild/software/ifort/2017.8.262-GCC-6.4.0-2.28/compilers_and_libraries_2017.8.262/linux/compiler/lib/intel64/libifcoremt_pic.a;/project/cacds/apps/easybuild/software/ifort/2017.8.262-GCC-6.4.0-2.28/compilers_and_libraries_2017.8.262/linux/compiler/lib/intel64/libimf.so;/project/cacds/apps/easybuild/software/ifort/2017.8.262-GCC-6.4.0-2.28/compilers_and_libraries_2017.8.262/linux/compiler/lib/intel64/libsvml.so;m;/project/cacds/apps/easybuild/software/ifort/2017.8.262-GCC-6.4.0-2.28/compilers_and_libraries_2017.8.262/linux/compiler/lib/intel64/libipgo.a;/project/cacds/apps/easybuild/software/ifort/2017.8.262-GCC-6.4.0-2.28/compilers_and_libraries_2017.8.262/linux/compiler/lib/intel64/libirc.so;/project/cacds/apps/easybuild/software/ifort/2017.8.262-GCC-6.4.0-2.28/compilers_and_libraries_2017.8.262/linux/compiler/lib/intel64/libirc_s.a;dl;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/lib/intel64/libiomp5.so;pthread;rt
-- PETSC_INCLUDE_DIRS: /project/cacds/apps/easybuild/software/PETSc/3.10.2-intel-2017b/include;/project/cacds/apps/easybuild/software/PETSc/3.10.2-intel-2017b/include;/project/cacds/apps/easybuild/software/PETSc/3.10.2-intel-2017b/include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/UMFPACK/Include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/KLU/Include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/CHOLMOD/Include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/BTF/Include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/CCOLAMD/Include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/COLAMD/Include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/CAMD/Include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/AMD/Include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/SuiteSparse_config;/project/cacds/apps/easybuild/software/Hypre/2.14.0-intel-2017b/include;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/include/fftw;/project/cacds/apps/easybuild/software/ParMETIS/4.0.3-intel-2017b/include;/project/cacds/apps/easybuild/software/METIS/5.1.0-GCCcore-6.4.0/include;/project/cacds/apps/easybuild/software/Boost/1.66.0-intel-2017b/include
-- PETSC_USER_INCLUDE_DIRS: /project/cacds/apps/easybuild/software/PETSc/3.10.2-intel-2017b/include;/project/cacds/apps/easybuild/software/PETSc/3.10.2-intel-2017b/include;/project/cacds/apps/easybuild/software/PETSc/3.10.2-intel-2017b/include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/UMFPACK/Include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/KLU/Include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/CHOLMOD/Include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/BTF/Include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/CCOLAMD/Include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/COLAMD/Include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/CAMD/Include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/AMD/Include;/project/cacds/apps/easybuild/software/SuiteSparse/5.1.2-intel-2017b-METIS-5.1.0/SuiteSparse_config;/project/cacds/apps/easybuild/software/Hypre/2.14.0-intel-2017b/include;/project/cacds/apps/easybuild/software/imkl/2017.4.239-iimpi-2017b/mkl/include/fftw;/project/cacds/apps/easybuild/software/ParMETIS/4.0.3-intel-2017b/include;/project/cacds/apps/easybuild/software/METIS/5.1.0-GCCcore-6.4.0/include;/project/cacds/apps/easybuild/software/Boost/1.66.0-intel-2017b/include
-- Found PETSC
-- Could not find a sufficient PETSC installation: PETSC is compiled against a different MPI library than the one deal.II picked up.
-- DEAL_II_WITH_PETSC has unmet external dependencies.
--
Yuesu Jin,
Ph.D student,
University of Houston,
College of Natural Sciences and Mathematics,
Department of Earth and Atmospheric Sciences,
Houston, Texas 77204-5008