Dear dealii community,
I am trying to install dealii v9.2.0 with candi on stampede2 by following
instruction shown in here
<https://github.com/geodynamics/aspect/wiki/Compiling-and-Running-ASPECT-on-TACC-Stampede2>.
I encounter errors when installing dealii and trilinos.
My modules are:
1) git/2.24.1 3) xalt/2.8 5) gcc/7.1.0 7) python/2.7.13 9)
autotools/1.1
2) cmake/3.16.1 4) TACC 6) impi/17.0.3 8) mkl/17.0.4
By using the latest version of candi, I only change DEAL_CONFOPTS to
DEAL_CONFOPTS="-D DEAL_II_FORCE_BUNDLED_THREADS=ON"
and MKL setting to:
MKL=ON
MKL_DIR=$MKLROOT/lib/intel64
However, I got an error when installing trilinos:
CMake Error at
cmake/tribits/core/package_arch/TribitsAdjustPackageEnables.cmake:1098
(MESSAGE):
***
*** ERROR: Setting Trilinos_ENABLE_Amesos2=OFF which was 'ON' because
Amesos2 has a required library dependence on disabled package Tpetra!
***
It seems that it happened when installing trilinos with MKL (see here
<https://community.geodynamics.org/t/trilinos-installation-with-candi-and-mkl-fails/1294/7>)
though it seems to be resolved. I noted that in the post they use "intel"
however, to use MKL, I have to use gcc in stampede2. I also tried to
install the older version of trilinos (v12-10-1) by slightly modifying
"trilinos.package" but it did not work neither.
Out of curiosity, I skip trilinos and install the rest of packages
including dealii. However, I got an error when installing dealii:
-- A library with LAPACK API found.
-- Performing Test mpifort_LIBRARY
-- Performing Test mpifort_LIBRARY - Success
-- Performing Test mpi_LIBRARY
-- Performing Test mpi_LIBRARY - Success
-- Performing Test mpigi_LIBRARY
-- Performing Test mpigi_LIBRARY - Success
-- Performing Test dl_LIBRARY
-- Performing Test dl_LIBRARY - Success
-- Performing Test pthread_LIBRARY
-- Performing Test pthread_LIBRARY - Success
-- Performing Test gfortran_LIBRARY
-- Performing Test gfortran_LIBRARY - Success
-- Performing Test m_LIBRARY
-- Performing Test m_LIBRARY - Success
-- Performing Test gcc_s_LIBRARY
-- Performing Test gcc_s_LIBRARY - Success
-- Performing Test gcc_LIBRARY
-- Performing Test gcc_LIBRARY - Success
-- Performing Test quadmath_LIBRARY
-- Performing Test quadmath_LIBRARY - Success
-- Performing Test c_LIBRARY
-- Performing Test c_LIBRARY - Success
-- LAPACK_LIBRARIES: *** Required variable "_lapack_libraries" empty ***
-- LAPACK_LINKER_FLAGS:
-- LAPACK_INCLUDE_DIRS:
-- LAPACK_USER_INCLUDE_DIRS:
-- Could NOT find LAPACK
-- DEAL_II_WITH_LAPACK has unmet external dependencies.
CMake Error at cmake/macros/macro_configure_feature.cmake:112 (MESSAGE):
Could not find the lapack library!
Please ensure that a suitable lapack library is installed on your
computer.
If the library is not at a default location, either provide some hints for
autodetection,
$ LAPACK_DIR="..." cmake <...>
$ cmake -DLAPACK_DIR="..." <...>
or set the relevant variables by hand in ccmake.
It seems also happened before (see here
<https://github.com/dealii/dealii/issues/7373> and here
<https://groups.google.com/u/1/g/dealii/c/Ui7cvZOO22E>). I tried different
setting in MKL and DEAL_CONFOPTS that are mentioned in the posts but none
of them work for me. (To link Lapack in stampede2, I referent to here
<https://portal.tacc.utexas.edu/tutorials/blaslapack>.)
i.e.
-
DEAL_CONFOPTS="-DLAPACK_DIR=${TACC_MKL_DIR}/lib/intel64_lin/libmkl_intel_lp64.so;${TACC_MKL_DIR}/lib/intel64_lin/libmkl_core.so"
- DEAL_CONFOPTS="-DLAPACK_DIR=${TACC_MKL_DIR}"
or in MKL section
-
- LAPACK_DIR=${TACC_MKL_LIB}
-
LAPACK_LIBRARIES="${TACC_MKL_DIR}/lib/intel64_lin/libmkl_intel_lp64.so;${TACC_MKL_DIR}/lib/intel64_lin/libmkl_core.so"
-
DLAPACK_LIBRARIES="${TACC_MKL_DIR}/lib/intel64_lin/libmkl_intel_lp64.so;${TACC_MKL_DIR}/lib/intel64_lin/libmkl_core.so"
Any suggestion or comment will be greatly appreciated!
Best,
Jau-Uei Chen
--
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-- Include
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-- Include
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-- Include
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-- Include
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-- Include
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-- Include
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-- Include
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-- Include
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--
-- Include
/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/deal.II-v9.2.0/cmake/setup_cached_variables.cmake
-- Prepending ${CUDA_NVCC_FLAGS} to ${DEAL_II_CUDA_FLAGS}
-- The CXX compiler identification is GNU 7.1.0
-- The C compiler identification is GNU 7.1.0
-- Check for working CXX compiler:
/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpicxx
-- Check for working CXX compiler:
/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpicxx --
works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler:
/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpicc
-- Check for working C compiler:
/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpicc --
works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- The Fortran compiler identification is GNU 7.1.0
-- Check for working Fortran compiler:
/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpif90
-- Check for working Fortran compiler:
/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpif90 --
works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether
/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpif90
supports Fortran 90
-- Checking whether
/opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpif90
supports Fortran 90 -- yes
--
-- Include
/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/deal.II-v9.2.0/cmake/setup_deal_ii.cmake
--
-- Include
/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/deal.II-v9.2.0/cmake/setup_compiler_flags.cmake
--
-- Include
/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/deal.II-v9.2.0/cmake/setup_compiler_flags_gnu.cmake
--
-- Include
/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/deal.II-v9.2.0/bundled/setup_bundled.cmake
--
-- Include
/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/deal.II-v9.2.0/cmake/checks/check_01_cpu_features.cmake
--
-- Include
/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/deal.II-v9.2.0/cmake/checks/check_01_cxx_features.cmake
-- Using C++ version flag "-std=c++17"
-- DEAL_II_WITH_CXX14 successfully set up
-- DEAL_II_WITH_CXX17 successfully set up
--
-- Include
/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/deal.II-v9.2.0/cmake/checks/check_02_compiler_features.cmake
--
-- Include
/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/deal.II-v9.2.0/cmake/checks/check_02_system_features.cmake
--
-- Include
/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/deal.II-v9.2.0/cmake/checks/check_03_compiler_bugs.cmake
--
-- Include
/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/deal.II-v9.2.0/cmake/configure/configure_1_cuda.cmake
-- DEAL_II_WITH_CUDA is set to off.
--
-- Include
/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/deal.II-v9.2.0/cmake/configure/configure_1_lapack.cmake
-- A library with LAPACK API found.
-- Performing Test mpifort_LIBRARY
-- Performing Test mpifort_LIBRARY - Success
-- Performing Test mpi_LIBRARY
-- Performing Test mpi_LIBRARY - Success
-- Performing Test mpigi_LIBRARY
-- Performing Test mpigi_LIBRARY - Success
-- Performing Test dl_LIBRARY
-- Performing Test dl_LIBRARY - Success
-- Performing Test pthread_LIBRARY
-- Performing Test pthread_LIBRARY - Success
-- Performing Test gfortran_LIBRARY
-- Performing Test gfortran_LIBRARY - Success
-- Performing Test m_LIBRARY
-- Performing Test m_LIBRARY - Success
-- Performing Test gcc_s_LIBRARY
-- Performing Test gcc_s_LIBRARY - Success
-- Performing Test gcc_LIBRARY
-- Performing Test gcc_LIBRARY - Success
-- Performing Test quadmath_LIBRARY
-- Performing Test quadmath_LIBRARY - Success
-- Performing Test c_LIBRARY
-- Performing Test c_LIBRARY - Success
-- LAPACK_LIBRARIES: *** Required variable "_lapack_libraries" empty ***
-- LAPACK_LINKER_FLAGS:
-- LAPACK_INCLUDE_DIRS:
-- LAPACK_USER_INCLUDE_DIRS:
-- Could NOT find LAPACK
-- DEAL_II_WITH_LAPACK has unmet external dependencies.
CMake Error at cmake/macros/macro_configure_feature.cmake:112 (MESSAGE):
Could not find the lapack library!
Please ensure that a suitable lapack library is installed on your computer.
If the library is not at a default location, either provide some hints for
autodetection,
$ LAPACK_DIR="..." cmake <...>
$ cmake -DLAPACK_DIR="..." <...>
or set the relevant variables by hand in ccmake.
Call Stack (most recent call first):
cmake/macros/macro_configure_feature.cmake:269 (FEATURE_ERROR_MESSAGE)
cmake/configure/configure_1_lapack.cmake:116 (CONFIGURE_FEATURE)
cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
CMakeLists.txt:124 (VERBOSE_INCLUDE)
-- Configuring incomplete, errors occurred!
See also
"/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/build/deal.II-v9.2.0/CMakeFiles/CMakeOutput.log".
Configuring Trilinos build directory
--
PROJECT_SOURCE_DIR='/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/Trilinos-trilinos-release-12-18-1'
--
PROJECT_BINARY_DIR='/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/build/trilinos-release-12-18-1'
--
Trilinos_TRIBITS_DIR='/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/Trilinos-trilinos-release-12-18-1/cmake/tribits'
-- TriBITS_VERSION_STRING='0.9 (Dev)'
-- CMAKE_VERSION='3.16.1'
-- CMAKE_GENERATOR='Unix Makefiles'
-- CMAKE_HOST_SYSTEM_NAME='Linux'
-- Trilinos_HOSTNAME='login2.stampede2.tacc.utexas.edu'
-- PYTHON_EXECUTABLE='/opt/apps/gcc7_1/python/2.7.13/bin/python'
Setting up major user options ...
CMake Warning (dev) at cmake/tribits/core/utils/AdvancedSet.cmake:57 (SET):
implicitly converting 'FILENAME' to 'STRING' type.
Call Stack (most recent call first):
cmake/tribits/core/package_arch/TribitsGlobalMacros.cmake:751 (ADVANCED_SET)
cmake/tribits/core/package_arch/TribitsProjectImpl.cmake:128
(TRIBITS_DEFINE_GLOBAL_OPTIONS_AND_DEFINE_EXTRA_REPOS)
cmake/tribits/core/package_arch/TribitsProject.cmake:93 (TRIBITS_PROJECT_IMPL)
CMakeLists.txt:90 (TRIBITS_PROJECT)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Setting Trilinos_ENABLE_TriKota=OFF because
'/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/Trilinos-trilinos-release-12-18-1/packages/TriKota/Dakota'
does not exist!
NOTE: Skipping generation of TrilinosRepoVersion.txt because project source is
not a git repo!
Reading list of native packages from
/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/Trilinos-trilinos-release-12-18-1/PackagesList.cmake
-- Trilinos_NUM_PACKAGES='62'
Reading list of native TPLs from
/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/unpack/Trilinos-trilinos-release-12-18-1/TPLsList.cmake
-- Trilinos_NUM_TPLS='112'
Processing Project, Repository, and Package dependency files and building
internal dependencies graph ...
-- Trilinos_NUM_SE_PACKAGES='165'
-- Tentatively enabling TPL 'DLlib'
Explicitly enabled packages on input (by user): Teuchos Sacado Epetra Zoltan
EpetraExt AztecOO Amesos Ifpack ML Belos Amesos2 Stratimikos MueLu ROL 14
Explicitly enabled SE packages on input (by user): Teuchos Sacado Epetra
Zoltan EpetraExt AztecOO Amesos Ifpack ML Belos Amesos2 Stratimikos MueLu ROL 14
Explicitly disabled packages on input (by user or by default): Tpetra Claps
Trios Ifpack2 TriKota NewPackage 6
Explicitly disabled SE packages on input (by user or by default):
KokkosExample Tpetra Claps ShyLU_NodeBasker ShyLU_NodeFastILU SEACASExotec2
SEACASSlice Trioscommsplitter Triossupport Triosnnti Triosnssi Triosprograms
Triosexamples Triostests Triosnetcdf-service Trios Ifpack2 TriKota STKExp
ShyLU_DDCore PanzerExprEval NewPackage 22
Explicitly enabled TPLs on input (by user): MPI ParMETIS SuperLUDist DLlib 4
Explicitly disabled TPLs on input (by user or by default): TBB Boost 2
Disabling all packages that have a required dependency on disabled TPLs and
optional package TPL support based on TPL_ENABLE_<TPL>=OFF ...
-- Setting Trilinos_ENABLE_MiniTensor=OFF because MiniTensor has a required
library dependence on disabled TPL Boost
-- Setting Trilinos_ENABLE_STKUtil=OFF because STKUtil has a required library
dependence on disabled TPL Boost
Disabling subpackages for hard disables of parent packages due to
Trilinos_ENABLE_<PARENT_PACKAGE>=OFF ...
-- Setting subpackage enable Trilinos_ENABLE_TpetraClassic=OFF because parent
package Trilinos_ENABLE_Tpetra=OFF
-- Setting subpackage enable Trilinos_ENABLE_TpetraTSQR=OFF because parent
package Trilinos_ENABLE_Tpetra=OFF
-- Setting subpackage enable Trilinos_ENABLE_TpetraCore=OFF because parent
package Trilinos_ENABLE_Tpetra=OFF
Disabling forward required SE packages and optional intra-package support that
have a dependancy on disabled SE packages Trilinos_ENABLE_<TRIBITS_PACKAGE>=OFF
...
-- Setting ROL_ENABLE_MiniTensor=OFF because ROL has an optional library
dependence on disabled package MiniTensor
-- Setting Trilinos_ENABLE_PanzerCore=OFF because PanzerCore has a required
library dependence on disabled package TpetraCore
-- Setting Trilinos_ENABLE_ThyraTpetraAdapters=OFF because ThyraTpetraAdapters
has a required library dependence on disabled package Tpetra
-- Setting Trilinos_ENABLE_Zoltan2=OFF because Zoltan2 has a required library
dependence on disabled package Tpetra
CMake Error at
cmake/tribits/core/package_arch/TribitsAdjustPackageEnables.cmake:1098
(MESSAGE):
***
*** ERROR: Setting Trilinos_ENABLE_Amesos2=OFF which was 'ON' because
Amesos2 has a required library dependence on disabled package Tpetra!
***
Call Stack (most recent call first):
cmake/tribits/core/package_arch/TribitsAdjustPackageEnables.cmake:1181
(TRIBITS_PRIVATE_PRINT_DISABLE)
cmake/tribits/core/package_arch/TribitsAdjustPackageEnables.cmake:1204
(TRIBITS_PRIVATE_PRINT_DISABLE_REQUIRED_PACKAGE_ENABLE)
cmake/tribits/core/package_arch/TribitsAdjustPackageEnables.cmake:1396
(TRIBITS_PRIVATE_DISABLE_REQUIRED_PACKAGE_ENABLES)
cmake/tribits/core/package_arch/TribitsAdjustPackageEnables.cmake:2320
(TRIBITS_DISABLE_FORWARD_REQUIRED_DEP_PACKAGES)
cmake/tribits/core/package_arch/TribitsGlobalMacros.cmake:1782
(TRIBITS_ADJUST_PACKAGE_ENABLES)
cmake/tribits/core/package_arch/TribitsProjectImpl.cmake:171
(TRIBITS_ADJUST_AND_PRINT_PACKAGE_DEPENDENCIES)
cmake/tribits/core/package_arch/TribitsProject.cmake:93 (TRIBITS_PROJECT_IMPL)
CMakeLists.txt:90 (TRIBITS_PROJECT)
-- Configuring incomplete, errors occurred!
See also
"/work/04833/tg841328/stampede2/deal_II_9.2/candi/install/tmp/build/trilinos-release-12-18-1/CMakeFiles/CMakeOutput.log".
