[petsc-users] CMake error in PETSc

[Yingjie Wu]

I'm so sorry that I've ignored your previous advices.

I added a global variable that seems works:


export
LD_LIBRARY_PATH=/home/lerui/petcs-3.12.2/arch-linux2-c-debug/lib:$LD_LIBRARY_PATH


How should I make petsc in a standard position?This eliminates the need to
set global variables.

It seems that some of the options before running fit become unavailable:


mpiexec -n 1 ./example01cmke -snes_view


Options-snes _ view are not used and how should I solve this problem?


Thank you for your response.

Yingjie




Yingjie Wu <yjwu16 at gmail.com> 于2019年12月5日周四 下午9:25写道：

> Hi,
>
> I installed the latest version of petsc, and compiled the example using
> cmke as described above. Compilation can be done, but there is a new
> problem while the program is running, as if the program could not find the
> shared library libpetsc.so.3.12. How can I solve this problem? The details
> are as follows:
>
> lerui at yu1994-ThinkPad-W520:~/tem$ cat CMakeLists.txt
> #This is a CMake makefile.
> cmake_minimum_required(VERSION 2.8.11)
>
> project(example01cmke)
>
> add_executable(example01cmke ex1.cpp)
>
> find_package(PkgConfig REQUIRED)
>
> set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
>
> pkg_search_module(PETSC REQUIRED PETSc)
>
> message("pkg include dirs: ${PETSC_INCLUDE_DIRS}")
>
> message("pkg include libs: ${PETSC_LIBRARIES}")
>
> message("pkg ldflags: ${PETSC_LDFLAGS}")
>
> include_directories(${PETSC_INCLUDE_DIRS})
>
> target_link_libraries(example01cmke ${PETSC_LDFLAGS})
>
> lerui at yu1994-ThinkPad-W520:~/tem$ mkdir build
> lerui at yu1994-ThinkPad-W520:~/tem$ cd build/
> lerui at yu1994-ThinkPad-W520:~/tem/build$
> PKG_CONFIG_PATH=$PETSC_DIR/$PETSC_ARCH/lib/pkgconfig cmake ..-- The C
> compiler identification is GNU 5.4.0
> -- The CXX compiler identification is GNU 5.4.0
> -- Check for working C compiler: /usr/bin/cc
> -- Check for working C compiler: /usr/bin/cc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
> -- Checking for one of the modules 'PETSc'
> pkg include dirs:
> /home/lerui/petsc-3.12.2/arch-linux2-c-debug/include;/home/lerui/petsc-3.12.2/include
> pkg include libs: petsc
> pkg ldflags: -L/home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib;-lpetsc
> -- Configuring done
> -- Generating done
> -- Build files have been written to: /home/lerui/tem/build
> lerui at yu1994-ThinkPad-W520:~/tem/build$ make
> Scanning dependencies of target example01cmke
> [ 50%] Building CXX object CMakeFiles/example01cmke.dir/ex1.cpp.o
> [100%] Linking CXX executable example01cmke
> [100%] Built target example01cmke
> lerui at yu1994-ThinkPad-W520:~/tem/build$ mpiexec -n 1 ./example01cmke
> -snes_monitor
> ./example01cmke: error while loading shared libraries: libpetsc.so.3.12:
> cannot open shared object file: No such file or directory
> -------------------------------------------------------
> Primary job  terminated normally, but 1 process returned
> a non-zero exit code.. Per user-direction, the job has been aborted.
> -------------------------------------------------------
> --------------------------------------------------------------------------
> mpiexec detected that one or more processes exited with non-zero status,
> thus causing
> the job to be terminated. The first process to do so was:
>
>   Process name: [[6716,1],0]
>   Exit code:    127
> --------------------------------------------------------------------------
>
> Thanks,
> Yingjie
>
> Jed Brown <jed at jedbrown.org> 于2019年12月5日周四 下午1:17写道：
>
>> Yingjie Wu <yjwu16 at gmail.com> writes:
>>
>> > Hi,
>> > I tried to use PKG to find the library file of PETSc, but there were
>> some
>> > errors. Because I am not very familiar with cmake, I refer to different
>> PKG
>> > tutorials. My CMakeList.txt is as follows. I don't know how to solve
>> this
>> > error message, please give me some suggestions.
>> >
>> > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake$ cat CMakeLists.txt
>> > #This is a CMake makefile.
>> > cmake_minimum_required(VERSION 2.8.11)
>> >
>> > project(example01cmke)
>> >
>> > add_executable(example01cmke ex1.cpp)
>> >
>> > find_package(PkgConfig REQUIRED)
>> >
>> > message("petsc directories: ${PETSC_DIR}")
>> >
>> > message("petsc arch: ${PETSC_ARCH}")
>> >
>> > set(ENV{PKG_CONFIG_PATH}
>> > /home/yjwu/petsc-3.10.1/arch-linux2-c-debug/lib/pkgconfig)
>> >
>> > pkg_search_module(PETSC REQUIRED PETSc)
>> >
>> > message("pkg include dirs: ${PETSC_INCLUDE_DIRS}")
>> >
>> > message("pkg include libs: ${PETSC_LIBRARIES}")
>> >
>> > message("pkg ldflags: ${PETSC_LDFLAGS}")
>> >
>> > include_directories(${PETSC_INCLUDE_DIRS})
>> >
>> > target_link_libraries(example01cmke ${PETSC_LDFLAGS})
>> >
>> > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake$ cd build/
>> > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake/build$ cmake ..
>> > -- The C compiler identification is GNU 5.4.0
>> > -- The CXX compiler identification is GNU 5.4.0
>> > -- Check for working C compiler: /usr/bin/cc
>> > -- Check for working C compiler: /usr/bin/cc -- works
>> > -- Detecting C compiler ABI info
>> > -- Detecting C compiler ABI info - done
>> > -- Detecting C compile features
>> > -- Detecting C compile features - done
>> > -- Check for working CXX compiler: /usr/bin/c++
>> > -- Check for working CXX compiler: /usr/bin/c++ -- works
>> > -- Detecting CXX compiler ABI info
>> > -- Detecting CXX compiler ABI info - done
>> > -- Detecting CXX compile features
>> > -- Detecting CXX compile features - done
>> > -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29.1")
>> > petsc directories:
>> > petsc arch:
>> > -- Checking for one of the modules 'PETSc'
>> > pkg include dirs:
>> >
>> /home/yjwu/petsc-3.10.1/include;/home/yjwu/petsc-3.10.1/arch-linux2-c-debug/include
>> > pkg include libs: petsc
>> > pkg ldflags: -L/home/yjwu/petsc-3.10.1/lib;-lpetsc
>> > -- Configuring done
>> > -- Generating done
>> > -- Build files have been written to:
>> /home/yjwu/PETSctest/Testcmake/build
>> > yjwu at yjwu-XPS-8910:~/PETSctest/Testcmake/build$ make
>> > Scanning dependencies of target example01cmke
>> > [ 50%] Building CXX object CMakeFiles/example01cmke.dir/ex1.cpp.o
>> > [100%] Linking CXX executable example01cmke
>> > /usr/bin/ld: cannot find -lpetsc
>> > collect2: error: ld returned 1 exit status
>>
>> Is your PETSc fully built/installed, or just configured?
>>
>> I just tested with this simplified file
>>
>> cmake_minimum_required(VERSION 2.8.11)
>> project(example01cmke)
>>
>> add_executable(example01cmke ex1.cpp)
>>
>> find_package(PkgConfig REQUIRED)
>> pkg_search_module(PETSC REQUIRED PETSc)
>> message("pkg include dirs: ${PETSC_INCLUDE_DIRS}")
>> message("pkg include libs: ${PETSC_LIBRARIES}")
>> message("pkg ldflags: ${PETSC_LDFLAGS}")
>>
>> include_directories(${PETSC_INCLUDE_DIRS})
>> target_link_libraries(example01cmke ${PETSC_LDFLAGS})
>>
>>
>> $ PKG_CONFIG_PATH=$PETSC_DIR/$PETSC_ARCH/lib/pkgconfig cmake ..
>> -- The C compiler identification is GNU 9.2.0
>> -- The CXX compiler identification is GNU 9.2.0
>> -- Check for working C compiler: /bin/cc
>> -- Check for working C compiler: /bin/cc -- works
>> -- Detecting C compiler ABI info
>> -- Detecting C compiler ABI info - done
>> -- Detecting C compile features
>> -- Detecting C compile features - done
>> -- Check for working CXX compiler: /bin/c++
>> -- Check for working CXX compiler: /bin/c++ -- works
>> -- Detecting CXX compiler ABI info
>> -- Detecting CXX compiler ABI info - done
>> -- Detecting CXX compile features
>> -- Detecting CXX compile features - done
>> -- Found PkgConfig: /bin/pkg-config (found version "1.6.3")
>> -- Checking for one of the modules 'PETSc'
>> pkg include dirs:
>> /home/jed/petsc/ompi-optg/include;/home/jed/petsc/include
>> pkg include libs: petsc
>> pkg ldflags: -L/home/jed/petsc/ompi-optg/lib;-lpetsc
>> -- Configuring done
>> -- Generating done
>> -- Build files have been written to: /tmp/jed/build
>> 22:12 jedjoule12  /tmp/jed/build$ make
>> Scanning dependencies of target example01cmke
>> [ 50%] Building CXX object CMakeFiles/example01cmke.dir/ex1.cpp.o
>> [100%] Linking CXX executable example01cmke
>> [100%] Built target example01cmke
>>
>>
>> Note that you may need to set RPATH (in CMake) or export a suitable
>> LD_LIBRARY_PATH if your PETSc is in a non-standard location.
>>
>
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