Hi ChrisI'm sorry, I think I made a mistake with the patch utility. The above output came because the root-level CMakeLists.txt was patched (running 'patch < pthread.patch'), not solvers/CMakeLists.txt. Running 'patch -p1 < pthread.patch', the correct file was patched. My fault.
The solvers are now compiled with no errors.
However, the compilation now fails similarly when linking utilities/NekMesh:https://pastebin.com/EfsqEQwR
Moreover, when compiling in parallel, the same error occurs when linking Tester (which I assume would be compiled after utilities/NekMesh, if not compiling in parallel):Cheers, MikkelOn Wed, Sep 12, 2018 at 10:48 AM Chris Cantwell <c.cantwell@imperial.ac.uk> wrote:Hi Mikkel,
That is strange, since it is the same CMake commands as used for the library executables! I am also using CMake 3.12.1, so should not be related to an API change.
Please can you confirm:
- you are still using an unmodified version of Nektar++ v4.4.1
- you have tried completely wiping the contents of your build directory and configuring from scratch
- you are using the default options for the NEKTAR_BUILD_* variables.
If you still encounter the error, please could you send me the file sys.txt produced by running
cmake --system-information sys.txt
and we can see if that sheds any light on the problem.
Cheers,
Chris
On Wed, 12 Sep 2018 10:04:25 +0100, Mikkel Bue Lykkegaard <mikkelbue@gmail.com> wrote:
> Hi Chris
>
> Thank you. After patching CMakeLists.txt, ccmake now throws the following
> errors:
>
> CMake Error at CMakeLists.txt:10 (GET_TARGET_PROPERTY):
> GET_TARGET_PROPERTY called with incorrect number of arguments
>
> CMake Error at CMakeLists.txt:11 (GET_TARGET_PROPERTY):
> GET_TARGET_PROPERTY called with incorrect number of arguments
>
> Best, Mikkel
>
> On Wed, Sep 12, 2018 at 9:49 AM Chris Cantwell <c.cantwell@imperial.ac.uk>
> wrote:
>
> > Hi Mikkel,
> >
> > Thanks for the output. The -pthread flag is missing from the solvers, but
> > not on the library demos, etc.
> >
> > The attached patch should fix the issue to make the solvers consistent
> > with the library executables. We will include this in the next patch
> > release.
> >
> > Please let me know if you still have problems.
> >
> > Cheers,
> > Chris
> >
> >
> > On Wed, 12 Sep 2018 09:17:59 +0100, Mikkel Bue Lykkegaard <
> > mikkelbue@gmail.com> wrote:
> > > Hi Chris
> > >
> > > Thanks for the reply. Sure, here is the output of 'make VERBOSE=1':
> > > https://pastebin.com/AtkuDCCi
> > >
> > > Also, here are the messages from ccmake (in case it has any relevance):
> > > https://pastebin.com/KpKYeDNM
> > >
> > > I am running Antergos (Arch) Linux with the following package versions:
> > > Linux 4.18.6
> > > gcc 8.2.1
> > > CMake 3.12.1
> > > binutils 2.31.1
> > > BLAS 3.8.0
> > > LAPACK 3.8.0
> > > boost 1.67.0
> > >
> > > Mikkel
> > >
> > > On Tue, Sep 11, 2018 at 10:37 PM Chris Cantwell <
> > c.cantwell@imperial.ac.uk>
> > > wrote:
> > >
> > > > Hi Mikkel,
> > > >
> > > > Which Linux distribution/version are you using?
> > > >
> > > > Could you send the output of running 'make VERBOSE=1'.
> > > >
> > > > Cheers,
> > > > Chris
> > > >
> > > >
> > > > On Tue, 11 Sep 2018 13:05:10 +0100, Mikkel Bue Lykkegaard <
> > > > mikkelbue@gmail.com> wrote:
> > > > > Hi all
> > > > >
> > > > > I am trying to install Nektar++ for the first time, on Linux 4.18.6
> > with
> > > > > CMake version 3.12.1.
> > > > >
> > > > > The compilation fails with:
> > > > >
> > > > > [ 66%] Linking CXX executable CardiacEPSolver
> > > > > /usr/bin/ld:
> > CMakeFiles/CardiacEPSolver.dir/CellModels/CellModel.cpp.o:
> > > > > undefined reference to symbol 'pthread_condattr_setclock@
> > @GLIBC_2.3.3'
> > > > > /usr/bin/ld: /usr/lib/libpthread.so.0: error adding symbols: DSO
> > missing
> > > > > from command line
> > > > > collect2: error: ld returned 1 exit status
> > > > > make[2]: ***
> > > > >
> > [solvers/CardiacEPSolver/CMakeFiles/CardiacEPSolver.dir/build.make:465:
> > > > > solvers/CardiacEPSolver/CardiacEPSolver] Error 1
> > > > > make[1]: *** [CMakeFiles/Makefile2:2907:
> > > > > solvers/CardiacEPSolver/CMakeFiles/CardiacEPSolver.dir/all] Error 2
> > > > > make: *** [Makefile:163: all] Error 2
> > > > >
> > > > > if I disable CardiacEPSolver in the configuration, I get a similar
> > error:
> > > > >
> > > > > [ 70%] Linking CXX executable CompressibleFlowSolver
> > > > > /usr/bin/ld:
> > > > >
> > > >
> > CMakeFiles/CompressibleFlowSolver.dir/ArtificialDiffusion/ArtificialDiffusion.cpp.o:
> >
> > > > > undefined reference to symbol 'pthread_condattr_setclock@
> > @GLIBC_2.3.3'
> > > > > /usr/bin/ld: /usr/lib/libpthread.so.0: error adding symbols: DSO
> > missing
> > > > > from command line
> > > > > collect2: error: ld returned 1 exit status
> > > > > make[2]: ***
> > > > >
> > > >
> > [solvers/CompressibleFlowSolver/CMakeFiles/CompressibleFlowSolver.dir/build.make:615:
> >
> > > > > solvers/CompressibleFlowSolver/CompressibleFlowSolver] Error 1
> > > > > make[1]: *** [CMakeFiles/Makefile2:2925:
> > > > >
> > solvers/CompressibleFlowSolver/CMakeFiles/CompressibleFlowSolver.dir/all]
> > > > > Error 2
> > > > > make: *** [Makefile:163: all] Error 2
> > > > >
> > > > > Can someone point me in the right direction?
> > > > >
> > > > > Thanks, Mikkel
> > > >
> > > >
> > > > --
> > > > Chris Cantwell
> > > > Imperial College London
> > > > South Kensington Campus
> > > > London SW7 2AZ
> > > > Email: c.cantwell@imperial.ac.uk
> > > > www.imperial.ac.uk/people/c.cantwell
> > > >
> >
> >
> > --
> > Chris Cantwell
> > Imperial College London
> > South Kensington Campus
> > London SW7 2AZ
> > Email: c.cantwell@imperial.ac.uk
> > www.imperial.ac.uk/people/c.cantwell
> >
--
Chris Cantwell
Imperial College London
South Kensington Campus
London SW7 2AZ
Email: c.cantwell@imperial.ac.uk
www.imperial.ac.uk/people/c.cantwell