The petsc -3.7.6 problem in candi

installation
#1

Our system CC environment are following
CC = /home/ncku/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpicc
CXX = /home/ncku/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpicxx
FC = /home/ncku/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpif90
FF = /home/ncku/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/bin/mpif77

when I run the candi during install dealii v9.0.1

the erro massage appeared

– Include /home/ncku/PinRong/bin/tmp/unpack/deal.II-v9.0.1/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_cmumps
– Found PETSC_LIBRARY_dmumps
– Found PETSC_LIBRARY_smumps
– Found PETSC_LIBRARY_zmumps
– Found PETSC_LIBRARY_mumps_common
– Found PETSC_LIBRARY_pord
– Found PETSC_LIBRARY_parmetis
– Found PETSC_LIBRARY_metis
– Found PETSC_LIBRARY_scalapack
– Found PETSC_LIBRARY_HYPRE
– Found PETSC_LIBRARY_mpicxx
– Performing Test PETSC_LIBRARY_m
– Performing Test PETSC_LIBRARY_m - Success
– Found PETSC_LIBRARY_lapack
– Found PETSC_LIBRARY_blas
– Found PETSC_LIBRARY_hwloc
– Performing Test PETSC_LIBRARY_gfortran
– Performing Test PETSC_LIBRARY_gfortran - Success
– Performing Test PETSC_LIBRARY_quadmath
– Performing Test PETSC_LIBRARY_quadmath - Success
– Found PETSC_LIBRARY_mpicxx
– Performing Test PETSC_LIBRARY_dl
– Performing Test PETSC_LIBRARY_dl - Success
– Found PETSC_LIBRARY_mpifort
– Found PETSC_LIBRARY_mpi
– Performing Test PETSC_LIBRARY_rt
– Performing Test PETSC_LIBRARY_rt - Success
– Performing Test PETSC_LIBRARY_pthread
– Performing Test PETSC_LIBRARY_pthread - Success
– PETSC_VERSION: 3.7.6.0
– PETSC_LIBRARIES: /home/ncku/PinRong/bin/petsc-3.7.6/lib/libpetsc.so;/home/ncku/PinRong/bin/petsc-3.7.6/lib/libcmumps.a;/home/ncku/PinRong/bin/petsc-3.7.6/lib/libdmumps.a;/home/ncku/PinRong/bin/petsc-3.7.6/lib/libsmumps.a;/home/ncku/PinRong/bin/petsc-3.7.6/lib/libzmumps.a;/home/ncku/PinRong/bin/petsc-3.7.6/lib/libmumps_common.a;/home/ncku/PinRong/bin/petsc-3.7.6/lib/libpord.a;/home/ncku/PinRong/bin/parmetis-4.0.3/lib/libparmetis.so;/home/ncku/PinRong/bin/parmetis-4.0.3/lib/libmetis.so;/home/ncku/PinRong/bin/petsc-3.7.6/lib/libscalapack.a;/home/ncku/PinRong/bin/petsc-3.7.6/lib/libHYPRE.a;/home/ncku/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/lib/libmpicxx.so;m;/usr/lib/liblapack.so;/usr/lib/libblas.so;/usr/lib/x86_64-linux-gnu/libhwloc.so;m;gfortran;m;gfortran;m;quadmath;/home/ncku/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/lib/libmpicxx.so;m;dl;/home/ncku/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/lib/libmpifort.so;/home/ncku/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/lib/debug_mt/libmpi.so;rt;pthread;dl
– PETSC_INCLUDE_DIRS: /home/ncku/PinRong/bin/petsc-3.7.6/include;/home/ncku/PinRong/bin/petsc-3.7.6/include;/home/ncku/PinRong/bin/petsc-3.7.6/include;/home/ncku/PinRong/bin/parmetis-4.0.3/include
– PETSC_USER_INCLUDE_DIRS: /home/ncku/PinRong/bin/petsc-3.7.6/include;/home/ncku/PinRong/bin/petsc-3.7.6/include;/home/ncku/PinRong/bin/petsc-3.7.6/include;/home/ncku/PinRong/bin/parmetis-4.0.3/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.
CMake Error at cmake/configure/configure_3_petsc.cmake:122 (MESSAGE):

Could not find the petsc library!
Could not find a sufficient PETSC installation:
PETSC has to be compiled against the same MPI library as deal.II but the link line of PETSC contains:
/home/ncku/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/lib/debug_mt/libmpi.so
which is not listed in MPI_LIBRARIES:
MPI_LIBRARIES = “/home/ncku/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/lib/libmpicxx.so /home/ncku/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/lib/libmpifort.so /home/ncku/intel/compilers_and_libraries_2019.1.144/linux/mpi/intel64/lib/release/libmpi.so /usr/lib/x86_64-linux-gnu/librt.so /usr/lib/x86_64-linux-gnu/libpthread.so /usr/lib/x86_64-linux-gnu/libdl.so”

Please ensure that the petsc library version 3.3.0 or newer is installed on
your computer and is configured with the same mpi options as deal.II

If the library is not at a default location, either provide some hints

for the autodetection:

PETSc installed with --prefix=<…> to a destination:

  $ PETSC_DIR="..." cmake <...>
  $ cmake -DPETSC_DIR="..." <...>

PETSc compiled in source tree:

  $ PETSC_DIR="..."  PETSC_ARCH="..." cmake <...>
  $ cmake -DPETSC_DIR="..." -DPETSC_ARCH="..." <...>

or set the relevant variables by hand in ccmake.

Call Stack (most recent call first):
/home/ncku/PinRong/bin/tmp/build/deal.II-v9.0.1/CMakeFiles/CMakeTmp/evaluate_expression.tmp:1 (FEATURE_PETSC_ERROR_MESSAGE)
cmake/macros/macro_evaluate_expression.cmake:30 (INCLUDE)
cmake/macros/macro_configure_feature.cmake:267 (EVALUATE_EXPRESSION)
cmake/configure/configure_3_petsc.cmake:141 (CONFIGURE_FEATURE)
cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
CMakeLists.txt:124 (VERBOSE_INCLUDE)

– Configuring incomplete, errors occurred!
See also “/home/ncku/PinRong/bin/tmp/build/deal.II-v9.0.1/CMakeFiles/CMakeOutput.log”.
Failure with exit status: 1
Exit message: There was a problem configuring dealii v9.0.1.

The first

I found the Petsc-3.7.6 wasn’t completely installed

and I checked the released version of Petsc from the host web, the 3.7.6 isn’t available to download now

Then second ,

I re-installed the latest version

the command

./configure --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-fblaslapack --download-scalapack --download-mumps --download-hypre

and set environment with

export PETSC_DIR=/home/ncku/PinRong/bin/petsc
export PETSC_ARCH=/home/ncku/PinRong/bin/petsc/arch-linux2-c-debug >

then log out and run the candi
still the same erro

Third,
I installed dealii by hand
but it couldn’t configure with petsc p4est trillions

how do I change the option in the candi.sh or candi.cfg? and let the installation smooth

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#2

You typically don’t need PETSc to run ASPECT, so the easiest option is to go into candi.cfg, find the line that contains “once:petsc” and comment it out. Then rerun candi as before.

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#3

thanks for reply

I found that need to command out the program related to the petsc and slepc not only in candi.cfg but also in dealii.package

I compile dealii and aspect successfully

thanks a lot

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