Hi Chris I'm sorry, I thought I had linked to the error. Here it is: https://pastebin.com/zAn6cSer In the meantime, however, I found a fix :) ... NekMesh has its own CMakeList.txt (i.e. utilities/NekMesh/CMakeList.txt), which doesn't make use of the macro defined in the upper level /utilities/CMakeList.txt .. So I removed the changes from /utilities/CMakeList.txt and modified utilities/NekMesh/CMakeList.txt instead, and now it compiles without errors. Please find attached the modified utilities/NekMesh/CMakeList.txt, my changes are in lines 97-116. Thank you so much for your help. Best, Mikkel On Thu, Sep 13, 2018 at 10:05 AM Chris Cantwell <c.cantwell@imperial.ac.uk> wrote:
Hi Mikkel,
Sorry, as I cannot actually reproduce your problem, I cannot properly test the patches.
Please include the error message regarding Utilities.
Cheers, Chris
On Thu, 13 Sep 2018 09:07:33 +0100, Mikkel Bue Lykkegaard < mikkelbue@gmail.com> wrote:
Hi Chris
Thank you for this. Tester is now linked succesfully. However, the patch for utilities doesn't seem to work. Linking NekMesh still fails the same way as before: https://pastebin.com/zAn6cSer
Please find attached the patched utilities/CMakeLists.txt to confirm that it has been patched as intended.
Cheers, MIkkel
On Wed, Sep 12, 2018 at 10:56 PM Chris Cantwell < c.cantwell@imperial.ac.uk> wrote:
Hi Mikkel,
Please try the attached patch.
Cheers, Chris
On Wed, 12 Sep 2018 17:48:39 +0100, Chris Cantwell < c.cantwell@imperial.ac.uk> wrote:
Hi Mikkel,
A similar update to the corresponding CMakeLists.txt files in Utilities and tests should fix those errors. I will prepare a patch for you later tonight.
Tester is not dependent on other parts of Nektar++ so can be built straight away when running the build in parallel.
Cheers, Chris
On 12 September 2018 12:32:51 BST, Mikkel Bue Lykkegaard < mikkelbue@gmail.com> wrote:
Hi Chris
I'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): https://pastebin.com/qE8mfKcs
Cheers, Mikkel
On 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
-- 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