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