Problem compiling opm-grid on Arch Linux

[ducbueno]

Hello there everyone.

I've been trying to build OPM in a secondary machine I have which has Arch Linux installed, however I've been facing some issues. There problems start when the build reaches opm-grid and seem to be related to MPI. I get several of the following error messages from CMake:

CMake Error at /home/ducbueno/src/opm/opm-common/cmake/Modules/OpmCompile.cmake:41 (add_library):
  Target "opmgrid" links to target "MPI::MPI_C" but the target was not found.
  Perhaps a find_package() call is missing for an IMPORTED target, or an
  ALIAS target is missing?
Call Stack (most recent call first):
  /home/ducbueno/src/opm/opm-common/cmake/Modules/OpmLibMain.cmake:181 (opm_compile)
  CMakeLists.txt:119 (include)

The error happens whether I install openmpi or mpich. I haven't found any other MPI related packages for Arch Linux.

Does anyone have experience with this or knows how to fix this?

Thanks!

[ducbueno]

Here is the CMakeError.log:

Determining if the function sgemm_ exists failed with the following output:
Change Dir: /home/ducbueno/src/opm/opm-grid/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_50da3/fast && /usr/bin/make  -f CMakeFiles/cmTC_50da3.dir/build.make CMakeFiles/cmTC_50da3.dir/build
make[1]: Entering directory '/hdd/src/opm/opm-grid/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_50da3.dir/CheckFunctionExists.c.o
/usr/bin/cc   -std=c99 -DCHECK_FUNCTION_EXISTS=sgemm_ -o CMakeFiles/cmTC_50da3.dir/CheckFunctionExists.c.o -c /usr/share/cmake-3.22/Modules/CheckFunctionExists.c
Linking C executable cmTC_50da3
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_50da3.dir/link.txt --verbose=1
/usr/bin/cc -std=c99 -DCHECK_FUNCTION_EXISTS=sgemm_ CMakeFiles/cmTC_50da3.dir/CheckFunctionExists.c.o -o cmTC_50da3 
/usr/bin/ld: CMakeFiles/cmTC_50da3.dir/CheckFunctionExists.c.o: in function `main':
CheckFunctionExists.c:(.text+0x10): undefined reference to `sgemm_'
collect2: error: ld returned 1 exit status
make[1]: *** [CMakeFiles/cmTC_50da3.dir/build.make:99: cmTC_50da3] Error 1
make[1]: Leaving directory '/hdd/src/opm/opm-grid/build/CMakeFiles/CMakeTmp'
make: *** [Makefile:127: cmTC_50da3/fast] Error 2



Performing C SOURCE FILE Test CMAKE_HAVE_LIBC_PTHREAD failed with the following output:
Change Dir: /home/ducbueno/src/opm/opm-grid/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_ea0b3/fast && /usr/bin/make  -f CMakeFiles/cmTC_ea0b3.dir/build.make CMakeFiles/cmTC_ea0b3.dir/build
make[1]: Entering directory '/hdd/src/opm/opm-grid/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_ea0b3.dir/src.c.o
/usr/bin/cc -DCMAKE_HAVE_LIBC_PTHREAD  -std=c99  -o CMakeFiles/cmTC_ea0b3.dir/src.c.o -c /home/ducbueno/src/opm/opm-grid/build/CMakeFiles/CMakeTmp/src.c
Linking C executable cmTC_ea0b3
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_ea0b3.dir/link.txt --verbose=1
/usr/bin/cc -std=c99  CMakeFiles/cmTC_ea0b3.dir/src.c.o -o cmTC_ea0b3 
/usr/bin/ld: CMakeFiles/cmTC_ea0b3.dir/src.c.o: in function `main':
src.c:(.text+0x3e): undefined reference to `pthread_create'
/usr/bin/ld: src.c:(.text+0x4a): undefined reference to `pthread_detach'
/usr/bin/ld: src.c:(.text+0x56): undefined reference to `pthread_cancel'
/usr/bin/ld: src.c:(.text+0x67): undefined reference to `pthread_join'
collect2: error: ld returned 1 exit status
make[1]: *** [CMakeFiles/cmTC_ea0b3.dir/build.make:99: cmTC_ea0b3] Error 1
make[1]: Leaving directory '/hdd/src/opm/opm-grid/build/CMakeFiles/CMakeTmp'
make: *** [Makefile:127: cmTC_ea0b3/fast] Error 2


Source file was:
#include <pthread.h>

static void* test_func(void* data)
{
  return data;
}

int main(void)
{
  pthread_t thread;
  pthread_create(&thread, NULL, test_func, NULL);
  pthread_detach(thread);
  pthread_cancel(thread);
  pthread_join(thread, NULL);
  pthread_atfork(NULL, NULL, NULL);
  pthread_exit(NULL);

  return 0;
}

Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /home/ducbueno/src/opm/opm-grid/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_c5bc6/fast && /usr/bin/make  -f CMakeFiles/cmTC_c5bc6.dir/build.make CMakeFiles/cmTC_c5bc6.dir/build
make[1]: Entering directory '/hdd/src/opm/opm-grid/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_c5bc6.dir/CheckFunctionExists.c.o
/usr/bin/cc   -std=c99 -DCHECK_FUNCTION_EXISTS=pthread_create -o CMakeFiles/cmTC_c5bc6.dir/CheckFunctionExists.c.o -c /usr/share/cmake-3.22/Modules/CheckFunctionExists.c
Linking C executable cmTC_c5bc6
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_c5bc6.dir/link.txt --verbose=1
/usr/bin/cc -std=c99 -DCHECK_FUNCTION_EXISTS=pthread_create CMakeFiles/cmTC_c5bc6.dir/CheckFunctionExists.c.o -o cmTC_c5bc6  -lpthreads 
/usr/bin/ld: cannot find -lpthreads
collect2: error: ld returned 1 exit status
make[1]: *** [CMakeFiles/cmTC_c5bc6.dir/build.make:99: cmTC_c5bc6] Error 1
make[1]: Leaving directory '/hdd/src/opm/opm-grid/build/CMakeFiles/CMakeTmp'
make: *** [Makefile:127: cmTC_c5bc6/fast] Error 2



Determining if the function cheev_ exists failed with the following output:
Change Dir: /home/ducbueno/src/opm/opm-grid/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_012e2/fast && /usr/bin/make  -f CMakeFiles/cmTC_012e2.dir/build.make CMakeFiles/cmTC_012e2.dir/build
make[1]: Entering directory '/hdd/src/opm/opm-grid/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_012e2.dir/CheckFunctionExists.c.o
/usr/bin/cc   -std=c99 -DCHECK_FUNCTION_EXISTS=cheev_ -o CMakeFiles/cmTC_012e2.dir/CheckFunctionExists.c.o -c /usr/share/cmake-3.22/Modules/CheckFunctionExists.c
Linking C executable cmTC_012e2
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_012e2.dir/link.txt --verbose=1
/usr/bin/cc -std=c99 -DCHECK_FUNCTION_EXISTS=cheev_ CMakeFiles/cmTC_012e2.dir/CheckFunctionExists.c.o -o cmTC_012e2  /usr/lib/libblas.so -lpthread -lm -ldl 
/usr/bin/ld: CMakeFiles/cmTC_012e2.dir/CheckFunctionExists.c.o: in function `main':
CheckFunctionExists.c:(.text+0x10): undefined reference to `cheev_'
collect2: error: ld returned 1 exit status
make[1]: *** [CMakeFiles/cmTC_012e2.dir/build.make:100: cmTC_012e2] Error 1
make[1]: Leaving directory '/hdd/src/opm/opm-grid/build/CMakeFiles/CMakeTmp'
make: *** [Makefile:127: cmTC_012e2/fast] Error 2



Determining if the function cheev_ exists failed with the following output:
Change Dir: /home/ducbueno/src/opm/opm-grid/build/CMakeFiles/CMakeTmp

Run Build Command(s):/usr/bin/make -f Makefile cmTC_f0e4e/fast && /usr/bin/make  -f CMakeFiles/cmTC_f0e4e.dir/build.make CMakeFiles/cmTC_f0e4e.dir/build
make[1]: Entering directory '/hdd/src/opm/opm-grid/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_f0e4e.dir/CheckFunctionExists.c.o
/usr/bin/cc   -std=c99 -DCHECK_FUNCTION_EXISTS=cheev_ -o CMakeFiles/cmTC_f0e4e.dir/CheckFunctionExists.c.o -c /usr/share/cmake-3.22/Modules/CheckFunctionExists.c
Linking C executable cmTC_f0e4e
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_f0e4e.dir/link.txt --verbose=1
/usr/bin/cc -std=c99 -DCHECK_FUNCTION_EXISTS=cheev_ CMakeFiles/cmTC_f0e4e.dir/CheckFunctionExists.c.o -o cmTC_f0e4e  /usr/lib/liblapack.so /usr/lib/libblas.so -fortranlibs 
cc: error: unrecognized command-line option ‘-fortranlibs’
make[1]: *** [CMakeFiles/cmTC_f0e4e.dir/build.make:101: cmTC_f0e4e] Error 1
make[1]: Leaving directory '/hdd/src/opm/opm-grid/build/CMakeFiles/CMakeTmp'
make: *** [Makefile:127: cmTC_f0e4e/fast] Error 2

[ducbueno]

And here is what CMake prints before the errors:

-- The C compiler identification is GNU 11.1.0
-- The CXX compiler identification is GNU 11.1.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - 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: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Performing Test HAVE_C99
-- Performing Test HAVE_C99 - Success
-- Found C99: -std=c99  
-- Found Boost: /usr/lib64/cmake/Boost-1.76.0/BoostConfig.cmake (found suitable version "1.76.0", minimum required is "1.44.0") found components: system unit_test_framework 
-- Performing Test HAVE_CJSON
-- Performing Test HAVE_CJSON - Success
-- Found cjson: /usr/include/cjson  
CMake Deprecation Warning at /home/ducbueno/src/opm/opm-common/cmake/Modules/OpmInit.cmake:26 (cmake_policy):
  The OLD behavior for policy CMP0026 will be removed from a future version
  of CMake.

  The cmake-policies(7) manual explains that the OLD behaviors of all
  policies are deprecated and that a policy should be set to OLD only under
  specific short-term circumstances.  Projects should be ported to the NEW
  behavior and not rely on setting a policy to OLD.
Call Stack (most recent call first):
  CMakeLists.txt:65 (OpmSetPolicies)


-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE  
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/libblas.so  
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- Found LAPACK: /usr/lib/liblapack.so;/usr/lib/libblas.so  
-- Performing Test HAVE_CXA_DEMANGLE
-- Performing Test HAVE_CXA_DEMANGLE - Success
-- Found GMP: /usr/lib/libgmpxx.so  
-- Found dune-common: /usr/include  
-- Version 2.8.0 of dune-common from /usr/lib64/cmake/dune-common
-- Found dune-geometry: /usr/include  
-- Version 2.8.0 of dune-geometry from /usr/lib64/cmake/dune-geometry
-- Found dune-uggrid: /usr/include  
-- Version 2.8.0 of dune-uggrid from /usr/lib64/cmake/dune-uggrid
-- Found dune-grid: /usr/include  
-- Version 2.8.0 of dune-grid from /usr/lib64/cmake/dune-grid
CMake Warning at /home/ducbueno/src/opm/opm-common/cmake/Modules/FindParMETIS.cmake:116 (message):
  MPI not found ==> ParMETIS disabled! Plase make sure -DUSE_MPI=ON was set
  if you need ParMETIS.
Call Stack (most recent call first):
  /home/ducbueno/src/opm/opm-common/cmake/Modules/OpmFind.cmake:144 (find_package)
  /home/ducbueno/src/opm/opm-common/cmake/Modules/OpmPackage.cmake:189 (find_and_append_package_to)
  /home/ducbueno/src/opm/opm-common/cmake/Modules/OpmPackage.cmake:87 (find_package_deps)
  /home/ducbueno/src/opm/opm-common/cmake/Modules/Finddune-istl.cmake:14 (find_opm_package)
  /home/ducbueno/src/opm/opm-common/cmake/Modules/OpmFind.cmake:144 (find_package)
  /home/ducbueno/src/opm/opm-common/cmake/Modules/OpmPackage.cmake:189 (find_and_append_package_to)
  opm-grid-prereqs.cmake:34 (find_package_deps)
  CMakeLists.txt:74 (include)


-- Performing Test HAVE_UMFPACK_WITHOUT_CHOLMOD
-- Performing Test HAVE_UMFPACK_WITHOUT_CHOLMOD - Success
-- Creating target SuitSparse::umfpack
-- Found SuiteSparse: /usr/lib/libumfpack.so;/usr/lib/libamd.so  
-- Found dune-istl: /usr/include  
-- Version 2.8.0 of dune-istl from /usr/lib64/cmake/dune-istl
-- Found PTScotch: /usr/include/scotch  
-- Could NOT find ZOLTAN (missing: MPI_FOUND) 
-- Setting OPM_TESTS_ROOT: /hdd/src/opm/opm-grid/../opm-tests
-- Performing Test HAVE_ATTRIBUTE_ALWAYS_INLINE
-- Performing Test HAVE_ATTRIBUTE_ALWAYS_INLINE - Success
-- Performing Test HAS_ATTRIBUTE_UNUSED
-- Performing Test HAS_ATTRIBUTE_UNUSED - Success
-- Performing Test HAS_ATTRIBUTE_DEPRECATED
-- Performing Test HAS_ATTRIBUTE_DEPRECATED - Success
-- Performing Test HAS_ATTRIBUTE_DEPRECATED_MSG
-- Performing Test HAS_ATTRIBUTE_DEPRECATED_MSG - Success
-- CMake version: 3.22.1
-- Linux distribution: Arch Linux
-- Target architecture: x86_64
-- Found Git: /usr/bin/git (found version "2.34.1") 
-- Source code repository: git 4bee258d
-- GNU C++ compiler version: 11.1.0
-- Linker: ld 2.36.1
Processing opm_defaults opm-grid
-- Checking to see if CXX compiler accepts flag -Wl,--enable-new-dtags
-- Checking to see if CXX compiler accepts flag -Wl,--enable-new-dtags - yes
-- Precompiled headers: disabled
-- Build type: Release
-- Checking to see if CXX compiler accepts flag -mtune=native
-- Checking to see if CXX compiler accepts flag -mtune=native - yes
-- All warnings enabled: -Wall -Wextra -Wshadow
-- Found OpenMP_C: -fopenmp (found version "4.5") 
-- Found OpenMP_CXX: -fopenmp (found version "4.5") 
-- Found OpenMP: TRUE (found version "4.5")  
-- Checking to see if CXX compiler accepts flag -pthread
-- Checking to see if CXX compiler accepts flag -pthread - yes
-- Found CppCheck: /usr/bin/cppcheck  
-- Disabling clang-check as CMAKE_EXPORT_COMPILE_COMMANDS is not enabled
-- Generating debug symbols: -ggdb3
-- Looking for strip utility
-- Looking for strip utility - found
-- Performing Test HAVE_DYNAMIC_BOOST_TEST
-- Performing Test HAVE_DYNAMIC_BOOST_TEST - Success
-- Writing config file "/hdd/src/opm/opm-grid/build/config.h"...

[blattms]

This is a result of our current incompatible default settings with DUNE and using our own special way of building. It only happens for newer DUNE version that use imported targets. I have been bitten by this myself quite a few times.

The easiest work around is to set the defaults to DUNE's defaults e.g.

cmake -DUSE_MPI=ON -DUSE_SUPERLU=ON -DUSE_QUADMATH=ON

or in a options file passed to cmake cmake -C /path/to/opts.file with entries like

set(USE_MPI ON         CACHE STRING "Use mpi")
set(USE_SUPERLU ON CACHE String "Use superlu")
set(USE_QUADMATH ON CACHE String "Use quadmath")

[ducbueno]

That solved it! Thanks.