[petsc-users] CMake error in PETSc

Yingjie Wu yjwu16 at gmail.com
Mon Dec 9 08:37:02 CST 2019 

Thank you for your response, Barry
It works for me! I made some minor changes.

I found that there was no petsc.pc in my pkgconfig folder, but PETSc.pc.

So I rewrote it to:

execute_process ( COMMAND pkg-config PETSc .........

And the program can run and will not report an DSO error.


Thanks again for your help.

Yingjie
Smith, Barry F. <bsmith at mcs.anl.gov> 于2019年12月9日周一 下午9:56写道：

>
>    The problem is that your Cmake file knows nothing about the MPI
> compilers that are required and hence just selects some random compilers it
> found in the path which do not support MPI.
>
>    I have attached a new CMakeList.txt for you to try.
>
>    I uses the environmental variables PETSC_DIR and PETSC_ARCH to find the
> configuration file AND use the compilers from the configuration file. It
> works for me, please let me know if you have trouble.
>
>    Barry
>
>
>
> > On Dec 8, 2019, at 10:38 PM, Yingjie Wu <yjwu16 at gmail.com> wrote:
> >
> > Thank you very much for your help.
> > My programs are as follow
> > Smith, Barry F. <bsmith at mcs.anl.gov> 于2019年12月9日周一 下午12:29写道：
> >
> >    There is something missing in the cmake process that is causing
> needed libraries not to be linked.
> >
> >    Please email your program and your CMake stuff (files you use) so we
> can reproduce the problem and find a fix.
> >
> >    Barry
> >
> >
> > > On Dec 8, 2019, at 10:06 PM, Yingjie Wu <yjwu16 at gmail.com> wrote:
> > >
> > > Hi,
> > > Thank you for your response.
> > > This problem has not been solved. I've been reporting errors in the
> process of 'make'. The test example I used comes from: /snes /example
> /tutorials/ex3.c by modifying the suffix of ex3, there will be different
> error messages as following. I checked a lot of DSO problems on the
> Internet and installed a lot of libraries, but the error still haven't been
> solved. I was wondering if I was missing any prefix during the configure of
> PETSc(I use the simplest recommended installation), but there was no
> problem when the program was compiled with the 'makefile' which is
> recommended. Because I need some extra libraries, I have to use cmake.
> > > with ex3.c:
> > > yjwu at yjwu-XPS-8910:~/tem/build2$ make
> > > Scanning dependencies of target Test1
> > > [ 50%] Building C object CMakeFiles/Test1.dir/ex3.c.o
> > > [100%] Linking C executable Test1
> > > /usr/bin/ld: CMakeFiles/Test1.dir/ex3.c.o: undefined reference to
> symbol 'pow@@GLIBC_2.2.5'
> > > //lib/x86_64-linux-gnu/libm.so.6: error adding symbols: DSO missing
> from command line
> > > collect2: error: ld returned 1 exit status
> > > CMakeFiles/Test1.dir/build.make:94: recipe for target 'Test1' failed
> > > make[2]: *** [Test1] Error 1
> > > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/Test1.dir/all'
> failed
> > > make[1]: *** [CMakeFiles/Test1.dir/all] Error 2
> > > Makefile:83: recipe for target 'all' failed
> > > make: *** [all] Error 2
> > > with ex3.cpp:
> > > yjwu at yjwu-XPS-8910:~/tem/build2$ make
> > > Scanning dependencies of target Test1
> > > [ 50%] Building CXX object CMakeFiles/Test1.dir/ex3.cpp.o
> > > [100%] Linking CXX executable Test1
> > > /usr/bin/ld: CMakeFiles/Test1.dir/ex3.cpp.o: undefined reference to
> symbol 'MPI_Comm_rank'
> > > /home/yjwu/petsc-3.12.2/arch-linux2-c-debug/lib/libmpi.so.12: error
> adding symbols: DSO missing from command line
> > > collect2: error: ld returned 1 exit status
> > > CMakeFiles/Test1.dir/build.make:94: recipe for target 'Test1' failed
> > > make[2]: *** [Test1] Error 1
> > > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/Test1.dir/all'
> failed
> > > make[1]: *** [CMakeFiles/Test1.dir/all] Error 2
> > > Makefile:83: recipe for target 'all' failed
> > > make: *** [all] Error 2
> > > Thanks,
> > > Yingjie
> > >
> > > Matthew Knepley <knepley at gmail.com> 于2019年12月6日周五 下午11:46写道：
> > > It sounds like your C++ compiler is name mangling the symbol, but the
> library has no mangling.
> > > Why are you using C++.
> > >
> > >   Thanks,
> > >
> > >     Matt
> > >
> > > On Fri, Dec 6, 2019 at 10:44 AM Yingjie Wu <yjwu16 at gmail.com> wrote:
> > > Hi,
> > > Thank you for your email.
> > > The error in the previous program was indeed due to the missing
> "SNESSetFromOptions".
> > > I use the /snes/example/tutorial/ex1.cpp as test case. However, I
> found that some of the statements in the program were not compiled and
> deleted the statements containing "MPI_Comm_size", but I don't know how to
> solve this problem.
> > > lerui at yu1994-ThinkPad-W520:~/tem2/build2$ 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/tem2/build2
> > > lerui at yu1994-ThinkPad-W520:~/tem2/build2$ make
> > > Scanning dependencies of target main
> > > [ 50%] Building CXX object CMakeFiles/main.dir/ex1.cpp.o
> > > [100%] Linking CXX executable main
> > > /usr/bin/ld: CMakeFiles/main.dir/ex1.cpp.o: undefined reference to
> symbol 'MPI_Comm_size'
> > > /home/lerui/petsc-3.12.2/arch-linux2-c-debug/lib/libmpi.so.12: error
> adding symbols: DSO missing from command line
> > > collect2: error: ld returned 1 exit status
> > > CMakeFiles/main.dir/build.make:94: recipe for target 'main' failed
> > > make[2]: *** [main] Error 1
> > > CMakeFiles/Makefile2:67: recipe for target 'CMakeFiles/main.dir/all'
> failed
> > > make[1]: *** [CMakeFiles/main.dir/all] Error 2
> > > Makefile:83: recipe for target 'all' failed
> > > make: *** [all] Error 2
> > > Thanks,
> > > Yingjie
> > >
> > > Jed Brown <jed at jedbrown.org> 于2019年12月6日周五 上午10:54写道：
> > > Yingjie Wu <yjwu16 at gmail.com> writes:
> > >
> > > > 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.
> > >
> > > You can configure PETSc with --prefix=/your/standard/path, then make
> install.
> > >
> > > > 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?
> > >
> > > I don't have your ex1.cpp, but presumably you didn't
> SNESSetFromOptions?
> > >
> > >
> > > --
> > > What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> > > -- Norbert Wiener
> > >
> > > https://www.cse.buffalo.edu/~knepley/
> >
> > <CMakeLists.txt><ex3.cpp>
>
>
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