Fatal Error while compiling Cardinal #911
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BlondArrow72
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Replies: 3 comments
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Hi Fletcher! Can you try the following and attach here the
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I ran those commands and emailed you the out.txt file |
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Sent from Mailspring (https://getmailspring.com/), the best free email app for work
On Jun 18 2024, at 2:29 pm, April Novak ***@***.***> wrote:
Hi Fletcher! Can you try the following and attach here the out.txt? This will have all the console output for me to take a look at.
conda activate moose
cd cardinal
rm -rf build/ install/
export ENABLE_NEK=false
export HDF5_ROOT=$CONDA_PREFIX
export LD_LIBRARY_PATH=$CONDA_PREFIX/lib:$LD_LIBRARY_PATH
make -j2 >> out.txt 2>&1
—
Reply to this email directly, view it on GitHub (#911 (comment)), or unsubscribe (https://github.com/notifications/unsubscribe-auth/A5ZBXHNQFJLFCOCEYIT5PTLZICKDVAVCNFSM6AAAAABJQXQGQWVHI2DSMVQWIX3LMV43SRDJONRXK43TNFXW4Q3PNVWWK3TUHM4TQMJQGUYTK).
You are receiving this because you authored the thread.
Cardinal is using HDF5 from /home/fbsmith/miniforge/envs/moose
Cardinal is using MOOSE from /home/fbsmith/cardinal/contrib/moose
Cardinal is using OpenMC from /home/fbsmith/cardinal/contrib/openmc
Cardinal is compiled with the following MOOSE modules
FLUID_PROPERTIES
HEAT_TRANSFER
NAVIER_STOKES
REACTOR
SOLID_PROPERTIES
STOCHASTIC_TOOLS
THERMAL_HYDRAULICS
Linking libpng: -L/home/fbsmith/miniforge/envs/moose/lib -lpng16
Skipping Nek build because ENABLE_NEK is not set to 'yes'
Skipping MOAB build because ENABLE_DAGMC is not set to 'yes'
Skipping DagMC build because ENABLE_DAGMC is not set to 'yes'
mkdir -p /home/fbsmith/cardinal/build/openmc
cd /home/fbsmith/cardinal/build/openmc && \
cmake -L \
-DCMAKE_BUILD_TYPE=Release \
-DOPENMC_USE_LIBMESH=ON \
-DOPENMC_USE_MPI=ON \
-DOPENMC_USE_DAGMC=no \
-DDAGMC_DIR=/home/fbsmith/cardinal/contrib/DAGMC \
-DCMAKE_C_COMPILER="mpicc" \
-DCMAKE_CXX_COMPILER="mpicxx;-std=gnu++17" \
-DCMAKE_Fortran_COMPILER="mpifort" \
-DCMAKE_PREFIX_PATH=/home/fbsmith/miniforge/envs/moose/libmesh \
-DCMAKE_INSTALL_PREFIX=/home/fbsmith/cardinal/install \
-DCMAKE_INSTALL_LIBDIR=/home/fbsmith/cardinal/install/lib \
-DCMAKE_CXX_STANDARD=17 \
-DCMAKE_INSTALL_MESSAGE=LAZY \
/home/fbsmith/cardinal/contrib/openmc
-- The C compiler identification is GNU 10.4.0
-- The CXX compiler identification is GNU 10.4.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /home/fbsmith/miniforge/envs/moose/bin/mpicc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /home/fbsmith/miniforge/envs/moose/bin/mpicxx - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Found MPI_C: /home/fbsmith/miniforge/envs/moose/bin/mpicc (found version "4.0")
-- Found MPI_CXX: /home/fbsmith/miniforge/envs/moose/bin/mpicxx (found version "4.0")
-- Found MPI: TRUE (found version "4.0")
CMake Warning (dev) at /home/fbsmith/miniforge/envs/moose/share/cmake-3.25/Modules/FindPackageHandleStandardArgs.cmake:438 (message):
The package name passed to `find_package_handle_standard_args` (PkgConfig)
does not match the name of the calling package (LIBMESH). This can lead to
problems in calling code that expects `find_package` result variables
(e.g., `_FOUND`) to follow a certain pattern.
Call Stack (most recent call first):
/home/fbsmith/miniforge/envs/moose/share/cmake-3.25/Modules/FindPkgConfig.cmake:99 (find_package_handle_standard_args)
cmake/Modules/FindLIBMESH.cmake:17 (include)
CMakeLists.txt:145 (find_package)
This warning is for project developers. Use -Wno-dev to suppress it.
…-- Found PkgConfig: /home/fbsmith/miniforge/envs/moose/bin/pkg-config (found version "0.29.2")
-- Checking for module 'libmesh>=1.7.0'
-- Found libmesh, version 1.8.0-pre
-- Found ZLIB: /home/fbsmith/miniforge/envs/moose/lib/libz.so (found version "1.2.13")
-- Found PNG: /home/fbsmith/miniforge/envs/moose/lib/libpng.so (found version "1.6.43")
Linking Library /home/fbsmith/cardinal/contrib/moose/modules/heat_transfer/lib/libheat_transfer-opt.la...
-- HDF5 C compiler wrapper is unable to compile a minimal HDF5 program.
-- Found HDF5: /home/fbsmith/miniforge/envs/moose/lib/libhdf5.so (found version "1.12.1") found components: C HL
-- HDF5 Libraries: /home/fbsmith/miniforge/envs/moose/lib/libhdf5.so
-- Using parallel HDF5
-- OpenMC C++ flags: -DH5Oget_info_by_idx_vers=1;-DH5O_info_t_vers=1
-- OpenMC Linker flags:
-- Found Git: /usr/bin/git (found version "2.43.0")
-- Submodule update
-- Found pugixml: /home/fbsmith/miniforge/envs/moose/lib/cmake/pugixml (version 1.11)
-- Found fmt: /usr/local/lib/cmake/fmt (version 8.0.1)
-- Performing Test arch_native_supported
-- Performing Test arch_native_supported - Success
-- Found xtensor: /usr/local/share/cmake/xtensor (version 0.25.0)
-- Found gsl-lite: /usr/local/lib/cmake/gsl-lite (version 0.36.1)
-- Did not find Catch2, will use submodule instead
-- Performing Test HAVE_FLAG__ffile_prefix_map__home_fbsmith_cardinal_contrib_openmc_vendor_Catch2__
Creating Unity Directory /home/fbsmith/cardinal/build/unity_src
Rebuilding symlinks in /home/fbsmith/cardinal/build/header_symlinks
Creating Unity /home/fbsmith/cardinal/build/unity_src/actions_Unity.C
Creating Unity /home/fbsmith/cardinal/build/unity_src/parser_Unity.C
Creating Unity /home/fbsmith/cardinal/build/unity_src/timesteppers_Unity.C
Creating Unity /home/fbsmith/cardinal/build/unity_src/userobjects_Unity.C
Creating Unity /home/fbsmith/cardinal/build/unity_src/postprocessors_Unity.C
Creating Unity /home/fbsmith/cardinal/build/unity_src/utils_Unity.C
-- Performing Test HAVE_FLAG__ffile_prefix_map__home_fbsmith_cardinal_contrib_openmc_vendor_Catch2__ - Success
-- Configuring done
Creating Unity /home/fbsmith/cardinal/build/unity_src/base_Unity.C
Creating Unity /home/fbsmith/cardinal/build/unity_src/auxkernels_Unity.C
Creating Unity /home/fbsmith/cardinal/build/unity_src/meshgenerators_Unity.C
Creating Unity /home/fbsmith/cardinal/build/unity_src/transfers_Unity.C
Creating Unity /home/fbsmith/cardinal/build/unity_src/mesh_Unity.C
Creating Unity /home/fbsmith/cardinal/build/unity_src/controls_Unity.C
Linking Library /home/fbsmith/cardinal/contrib/moose/modules/solid_properties/lib/libsolid_properties-opt.la...
-- Generating done
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_Fortran_COMPILER
-- Build files have been written to: /home/fbsmith/cardinal/build/openmc
-- Cache values
BUILD_TESTING:BOOL=ON
CATCH_CONFIG_ANDROID_LOGWRITE:BOOL=OFF
CATCH_CONFIG_BAZEL_SUPPORT:BOOL=OFF
CATCH_CONFIG_COLOUR_WIN32:BOOL=OFF
CATCH_CONFIG_CONSOLE_WIDTH:STRING=80
CATCH_CONFIG_COUNTER:BOOL=OFF
CATCH_CONFIG_CPP11_TO_STRING:BOOL=OFF
CATCH_CONFIG_CPP17_BYTE:BOOL=OFF
CATCH_CONFIG_CPP17_OPTIONAL:BOOL=OFF
CATCH_CONFIG_CPP17_STRING_VIEW:BOOL=OFF
CATCH_CONFIG_CPP17_UNCAUGHT_EXCEPTIONS:BOOL=OFF
CATCH_CONFIG_CPP17_VARIANT:BOOL=OFF
CATCH_CONFIG_DEFAULT_REPORTER:STRING=console
CATCH_CONFIG_DISABLE:BOOL=OFF
CATCH_CONFIG_DISABLE_EXCEPTIONS:BOOL=OFF
CATCH_CONFIG_DISABLE_EXCEPTIONS_CUSTOM_HANDLER:BOOL=OFF
CATCH_CONFIG_DISABLE_STRINGIFICATION:BOOL=OFF
CATCH_CONFIG_ENABLE_ALL_STRINGMAKERS:BOOL=OFF
CATCH_CONFIG_ENABLE_OPTIONAL_STRINGMAKER:BOOL=OFF
CATCH_CONFIG_ENABLE_PAIR_STRINGMAKER:BOOL=OFF
CATCH_CONFIG_ENABLE_TUPLE_STRINGMAKER:BOOL=OFF
CATCH_CONFIG_ENABLE_VARIANT_STRINGMAKER:BOOL=OFF
CATCH_CONFIG_EXPERIMENTAL_REDIRECT:BOOL=OFF
CATCH_CONFIG_FAST_COMPILE:BOOL=OFF
CATCH_CONFIG_GETENV:BOOL=OFF
CATCH_CONFIG_GLOBAL_NEXTAFTER:BOOL=OFF
CATCH_CONFIG_NOSTDOUT:BOOL=OFF
CATCH_CONFIG_NO_ANDROID_LOGWRITE:BOOL=OFF
CATCH_CONFIG_NO_BAZEL_SUPPORT:BOOL=OFF
CATCH_CONFIG_NO_COLOUR_WIN32:BOOL=OFF
CATCH_CONFIG_NO_COUNTER:BOOL=OFF
CATCH_CONFIG_NO_CPP11_TO_STRING:BOOL=OFF
CATCH_CONFIG_NO_CPP17_BYTE:BOOL=OFF
CATCH_CONFIG_NO_CPP17_OPTIONAL:BOOL=OFF
CATCH_CONFIG_NO_CPP17_STRING_VIEW:BOOL=OFF
CATCH_CONFIG_NO_CPP17_UNCAUGHT_EXCEPTIONS:BOOL=OFF
CATCH_CONFIG_NO_CPP17_VARIANT:BOOL=OFF
CATCH_CONFIG_NO_GETENV:BOOL=OFF
CATCH_CONFIG_NO_GLOBAL_NEXTAFTER:BOOL=OFF
CATCH_CONFIG_NO_POSIX_SIGNALS:BOOL=OFF
CATCH_CONFIG_NO_USE_ASYNC:BOOL=OFF
CATCH_CONFIG_NO_WCHAR:BOOL=OFF
CATCH_CONFIG_NO_WINDOWS_SEH:BOOL=OFF
CATCH_CONFIG_POSIX_SIGNALS:BOOL=OFF
CATCH_CONFIG_PREFIX_ALL:BOOL=OFF
CATCH_CONFIG_USE_ASYNC:BOOL=OFF
CATCH_CONFIG_WCHAR:BOOL=OFF
CATCH_CONFIG_WINDOWS_CRTDBG:BOOL=OFF
CATCH_CONFIG_WINDOWS_SEH:BOOL=OFF
CATCH_DEVELOPMENT_BUILD:BOOL=OFF
CATCH_INSTALL_DOCS:BOOL=ON
CATCH_INSTALL_EXTRAS:BOOL=ON
CMAKE_BUILD_TYPE:STRING=Release
CMAKE_INSTALL_PREFIX:PATH=/home/fbsmith/cardinal/install
Catch2_DIR:PATH=Catch2_DIR-NOTFOUND
GIT_SUBMODULE:BOOL=ON
OPENMC_BUILD_TESTS:BOOL=ON
OPENMC_ENABLE_COVERAGE:BOOL=OFF
OPENMC_ENABLE_PROFILE:BOOL=OFF
OPENMC_USE_DAGMC:BOOL=no
OPENMC_USE_LIBMESH:BOOL=ON
OPENMC_USE_MCPL:BOOL=OFF
OPENMC_USE_MPI:BOOL=ON
OPENMC_USE_NCRYSTAL:BOOL=OFF
OPENMC_USE_OPENMP:BOOL=ON
OPENMC_USE_UWUW:BOOL=OFF
TBB_DIR:PATH=/home/fbsmith/miniforge/envs/moose/lib/cmake/TBB
fmt_DIR:PATH=/usr/local/lib/cmake/fmt
gsl-lite_DIR:PATH=/usr/local/lib/cmake/gsl-lite
pugixml_DIR:PATH=/home/fbsmith/miniforge/envs/moose/lib/cmake/pugixml
xsimd_DIR:PATH=xsimd_DIR-NOTFOUND
xtensor_DIR:PATH=/usr/local/share/cmake/xtensor
xtl_DIR:PATH=/usr/local/share/cmake/xtl
Linking Library /home/fbsmith/cardinal/contrib/moose/modules/navier_stokes/lib/libnavier_stokes-opt.la...
Creating Unity /home/fbsmith/cardinal/build/unity_src/ics_Unity.C
make VERBOSE=1 -C /home/fbsmith/cardinal/build/openmc install
make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule.
make[1]: Entering directory '/home/fbsmith/cardinal/build/openmc'
/home/fbsmith/miniforge/envs/moose/bin/cmake -S/home/fbsmith/cardinal/contrib/openmc -B/home/fbsmith/cardinal/build/openmc --check-build-system CMakeFiles/Makefile.cmake 0
/home/fbsmith/miniforge/envs/moose/bin/cmake -E cmake_progress_start /home/fbsmith/cardinal/build/openmc/CMakeFiles /home/fbsmith/cardinal/build/openmc//CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/home/fbsmith/cardinal/build/openmc'
make -f CMakeFiles/libopenmc.dir/build.make CMakeFiles/libopenmc.dir/depend
make[3]: Entering directory '/home/fbsmith/cardinal/build/openmc'
cd /home/fbsmith/cardinal/build/openmc && /home/fbsmith/miniforge/envs/moose/bin/cmake -E cmake_depends "Unix Makefiles" /home/fbsmith/cardinal/contrib/openmc /home/fbsmith/cardinal/contrib/openmc /home/fbsmith/cardinal/build/openmc /home/fbsmith/cardinal/build/openmc /home/fbsmith/cardinal/build/openmc/CMakeFiles/libopenmc.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/home/fbsmith/cardinal/build/openmc'
make -f CMakeFiles/libopenmc.dir/build.make CMakeFiles/libopenmc.dir/build
make[3]: Entering directory '/home/fbsmith/cardinal/build/openmc'
[ 1%] Building CXX object CMakeFiles/libopenmc.dir/src/bank.cpp.o
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[ 4%] Building CXX object CMakeFiles/libopenmc.dir/src/distribution.cpp.o
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[ 4%] Building CXX object CMakeFiles/libopenmc.dir/src/distribution_angle.cpp.o
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[ 5%] Building CXX object CMakeFiles/libopenmc.dir/src/distribution_energy.cpp.o
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[ 5%] Building CXX object CMakeFiles/libopenmc.dir/src/distribution_multi.cpp.o
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[ 6%] Building CXX object CMakeFiles/libopenmc.dir/src/distribution_spatial.cpp.o
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[ 6%] Building CXX object CMakeFiles/libopenmc.dir/src/eigenvalue.cpp.o
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[ 7%] Building CXX object CMakeFiles/libopenmc.dir/src/event.cpp.o
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[ 8%] Building CXX object CMakeFiles/libopenmc.dir/src/file_utils.cpp.o
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[ 8%] Building CXX object CMakeFiles/libopenmc.dir/src/finalize.cpp.o
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[ 9%] Building CXX object CMakeFiles/libopenmc.dir/src/geometry.cpp.o
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[ 9%] Building CXX object CMakeFiles/libopenmc.dir/src/geometry_aux.cpp.o
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[ 10%] Building CXX object CMakeFiles/libopenmc.dir/src/hdf5_interface.cpp.o
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[ 10%] Building CXX object CMakeFiles/libopenmc.dir/src/initialize.cpp.o
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[ 11%] Building CXX object CMakeFiles/libopenmc.dir/src/lattice.cpp.o
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[ 11%] Building CXX object CMakeFiles/libopenmc.dir/src/material.cpp.o
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[ 12%] Building CXX object CMakeFiles/libopenmc.dir/src/math_functions.cpp.o
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[ 12%] Building CXX object CMakeFiles/libopenmc.dir/src/mcpl_interface.cpp.o
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[ 12%] Building CXX object CMakeFiles/libopenmc.dir/src/mesh.cpp.o
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[ 13%] Building CXX object CMakeFiles/libopenmc.dir/src/message_passing.cpp.o
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[ 13%] Building CXX object CMakeFiles/libopenmc.dir/src/mgxs.cpp.o
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[ 14%] Building CXX object CMakeFiles/libopenmc.dir/src/mgxs_interface.cpp.o
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[ 14%] Building CXX object CMakeFiles/libopenmc.dir/src/ncrystal_interface.cpp.o
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[ 15%] Building CXX object CMakeFiles/libopenmc.dir/src/nuclide.cpp.o
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[ 15%] Building CXX object CMakeFiles/libopenmc.dir/src/output.cpp.o
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/home/fbsmith/miniforge/envs/moose/bin/mpicxx -std=gnu++17 -DBUILD_TYPE=Release -DCOMPILER_ID=GNU -DCOMPILER_VERSION=10.4.0 -DGIT_SHA1=\"a7d6939c11a2d905d0aab3c57a97cd82e7018b3a\" -DGSL_THROW_ON_CONTRACT_VIOLATION -DLIBMESH -DOPENMC_MPI -DPHDF5 -DUSE_LIBPNG -Dgsl_CONFIG_ALLOWS_NONSTRICT_SPAN_COMPARISON=1 -Dgsl_CONFIG_DEFAULTS_VERSION=1 -Dlibopenmc_EXPORTS -I/home/fbsmith/cardinal/contrib/openmc/include -I/home/fbsmith/cardinal/build/openmc/include -isystem /usr/local/include -isystem /home/fbsmith/miniforge/envs/moose/libmesh/include -isystem /home/fbsmith/miniforge/envs/moose/libmesh-vtk/include/vtk-9.2 -O2 -felide-constructors -fstrict-aliasing -Wdisabled-optimization -funroll-loops -ftrapping-math -fopenmp -DMETHOD=opt -DWASP_ENABLED -I/home/fbsmith/miniforge/envs/moose/wasp/include -DENABLE_OPENMC_COUPLING -O3 -DNDEBUG -fPIC -DH5Oget_info_by_idx_vers=1 -DH5O_info_t_vers=1 -DNDEBUG -pthread -fopenmp -std=c++17 -MD -MT CMakeFiles/libopenmc.dir/src/position.cpp.o -MF CMakeFiles/libopenmc.dir/src/position.cpp.o.d -o CMakeFiles/libopenmc.dir/src/position.cpp.o -c /home/fbsmith/cardinal/contrib/openmc/src/position.cpp
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Hello everyone,
I've installed MOOSE and I'm following the TLDR instructions on the Cardinal website (https://cardinal.cels.anl.gov/with_conda.html), but whenever I use the
make
command, I get the following fatal error:/home/fbsmith/cardinal/install/include/openmc/position.h:8:10: fatal error: fmt/format.h: No such file or directory 8 | #include "fmt/format.h" | ^~~~~~~~~~~~~~ compilation terminated. make: *** [/home/fbsmith/cardinal/contrib/moose/framework/build.mk:150: /home/fbsmith/cardinal/build/unity_src/auxkernels_Unity.x86_64-conda-linux-gnu.opt.lo] Error 1
I search for
fmt/format.h
in the Cardinal directory and find 2 results for files. My thoughts are that thegit clone https://github.com/neams-th-coe/cardinal.git
command doesn't get all the files it needs to compile so it doesn't have the correctformat.h
file that I need, the compiler is in the incorrect file path (which I think is unlikely because I don't do anything to the cardinal folder once I download it), or there's an issue on my linux system that I don't know about.Any help or suggestions? Thanks!
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