Hi Oliviu,

Thanks for providing the additional information and for reporting this issue.

I've been able to reproduce the problem on Ubuntu 18.04.3. It looks like this only affects builds of NekMesh that include the meshgen functionality so if you're building without this, the problem doesn't occur.

The issue seems to be caused by an incompatibility between the third party build version of zlib that Nektar++ uses (v1.2.7) and the libpng16.so.16 on Ubuntu 18.04. There's a little more info on the issue in this bug report: https://bugs.launchpad.net/ubuntu/+source/libpng1.6/+bug/1780233

I note that you have THIRDPARTY_BUILD_ZLIB set to ON in your configuration below. The solution is to set this to OFF and ensure that you have the zlib1g-dev Ubuntu package installed on your system. In order to resolve the problem, you'll probably need to completely clean your build directory and also clean the contents of the nektar/ThirdParty directory. Then you'll need to reconfigure with CMake and build again. When you reconfigure with CMake, you should see that the THIRDPARTY_BUILD_ZLIB option is set to OFF and if you are using the CMake GUI (via ccmake), you should be able to press "t" to see the advanced options and see that the ZLIB_LIBRARY_RELEASE option has been set to something like /usr/lib/x86_64-linux-gnu/libz.so (i.e. the system installed zlib).

Hope this helps and resolves the problem. Let me know if you're still having problems with the build. I'll file an issue for the zlib problem in the Nektar++ GitLab.

Regards,

Jeremy

On 15 Aug 2019, at 13:57, Oliviu Sugar <oliviu_sugar@yahoo.com> wrote:

Here is the code configuration in brief:

 CMAKE_BUILD_TYPE                 Release                                      
 CMAKE_INSTALL_PREFIX             /home/local/ISDADS/sgs475/Nektar/build/dist  
 CONVERT                          /usr/bin/convert                             
 HAS_PATCH                        /usr/bin/patch                               
 MAKE_EXECUTABLE                  /usr/bin/make                                
 NEKTAR_BUILD_DEMOS               ON                                           
 NEKTAR_BUILD_DOC                 OFF                                          
 NEKTAR_BUILD_LIBRARY             ON                                           
 NEKTAR_BUILD_PYTHON              ON                                           
 NEKTAR_BUILD_SOLVERS             ON                                           
 NEKTAR_BUILD_TESTS               ON                                           
 NEKTAR_BUILD_TIMINGS             ON                                           
 NEKTAR_BUILD_UNIT_TESTS          ON                                           
 NEKTAR_BUILD_UTILITIES           ON                                           
 NEKTAR_DISABLE_BACKUPS           OFF                                          
 NEKTAR_SOLVER_ACOUSTIC           ON                                           
 NEKTAR_SOLVER_ADR                ON                                           
 NEKTAR_SOLVER_CARDIAC_EP         ON                                           
 NEKTAR_SOLVER_COMPRESSIBLE_FLO   ON                                           
 NEKTAR_SOLVER_DIFFUSION          ON                                           
 NEKTAR_SOLVER_DUMMY              ON                                           
 NEKTAR_SOLVER_ELASTICITY         ON                                           
 NEKTAR_SOLVER_IMAGE_WARPING      ON                                           
 NEKTAR_SOLVER_INCNAVIERSTOKES    ON                                           
 NEKTAR_SOLVER_MMF                ON                                           
 NEKTAR_SOLVER_PULSEWAVE          ON                                           
 NEKTAR_SOLVER_SHALLOW_WATER      ON                                           
 NEKTAR_SOLVER_VORTEXWAVE         ON                                           
 NEKTAR_TEST_ALL                  ON                                           
 NEKTAR_TEST_FORCEMPIEXEC         OFF                                          
 NEKTAR_TEST_USE_HOSTFILE         OFF                                          
 NEKTAR_USE_ARPACK                ON                                           
 NEKTAR_USE_CCM                   OFF                                          
 NEKTAR_USE_CFI                   OFF                                          
 NEKTAR_USE_CWIPI                 OFF                                          
 NEKTAR_USE_FFTW                  ON                                           
 NEKTAR_USE_HDF5                  OFF                                          
 NEKTAR_USE_MESHGEN               ON                                           
 NEKTAR_USE_METIS                 OFF                                          
 NEKTAR_USE_MPI                   ON                                           
 NEKTAR_USE_PETSC                 ON             
 NEKTAR_USE_PYTHON3               OFF                                          
 NEKTAR_USE_SCOTCH                ON                                           
 NEKTAR_USE_SYSTEM_BLAS_LAPACK    ON                                           
 NEKTAR_USE_VTK                   ON                                           
 NEKTAR_UTILITY_FIELDCONVERT      ON                                           
 NEKTAR_UTILITY_NEKMESH           ON                                           
 OCE_DIR                          /usr/lib/x86_64-linux-gnu/oce-0.17           
 THIRDPARTY_BUILD_ARPACK          OFF                                          
 THIRDPARTY_BUILD_BLAS_LAPACK     OFF                                          
 THIRDPARTY_BUILD_BOOST           OFF                                          
 THIRDPARTY_BUILD_FFTW            OFF                                          
 THIRDPARTY_BUILD_GSMPI           ON                                           
 THIRDPARTY_BUILD_OCE             OFF                                          
 THIRDPARTY_BUILD_PETSC           OFF                                          
 THIRDPARTY_BUILD_SCOTCH          OFF                                          
 THIRDPARTY_BUILD_TETGEN          ON                                           
 THIRDPARTY_BUILD_TINYXML         ON                                           
 THIRDPARTY_BUILD_TRIANGLE        ON                                           
 THIRDPARTY_BUILD_ZLIB            ON                                           
 THIRDPARTY_USE_SSL               OFF                                          
 ZLIB_LIBRARIES                   /home/local/ISDADS/sgs475/Nektar/build/ThirdParty/zlib-1.2.7
 ZLIB_LIBRARIES_DEBUG             /home/local/ISDADS/sgs475/Nektar/build/ThirdParty/zlib-1.2.7

Best,

Oliviu

On Thursday, August 15, 2019, 1:48:37 PM GMT+1, Jeremy Cohen <jeremy.cohen@imperial.ac.uk> wrote:


Thanks Oliviu, can you also provide some information on your CMake configuration - what CMake options do you have switched on/off? In particular, it would be useful to know which of the THIRDPARY_BUILD_ options you have switched on and whether you're using boost and zlib from Ubuntu packages or whether they're being built as part of the Nektar build.

Regards,
Jeremy


On 15 Aug 2019, at 13:44, Oliviu Sugar <oliviu_sugar@yahoo.com> wrote:

Hello Jeremy,

Here is some additional information:
Linux distribution and version: Ubuntu 18.04.3
Nektar version: cloned latest Master branch from the repository
CMake: 3.10.2

Best regards,
Oliviu

On Thursday, August 15, 2019, 1:34:32 PM GMT+1, Jeremy Cohen <jeremy.cohen@imperial.ac.uk> wrote:


Hi Oliviu,

It looks like this is probably something to do with the version of libpng that you're using requiring zlib to be linked and this is not being picked up for some reason.

Can you give us some more information about the environment you're working on since that will assist in trying to identify the problem. e.g. can you please provide the Linux distribution and version that you're working on, the version of Nektar++ you're trying to build and whether you've cloned from GitHub or downloaded a source tarball from the website. Can you also tell us what CMake configuration you're using.

Thanks,
Jeremy

On 15 Aug 2019, at 13:25, Oliviu Sugar <oliviu_sugar@yahoo.com> wrote:

Dear all,

I get the following error when compiling:
//usr/lib/x86_64-linux-gnu/libpng16.so.16: undefined reference to `inflateValidate@ZLIB_1.2.9'
collect2: error: ld returned 1 exit status
utilities/NekMesh/CMakeFiles/NekMesh.dir/build.make:1083: recipe for target 'utilities/NekMesh/NekMesh' failed
make[2]: *** [utilities/NekMesh/NekMesh] Error 1
CMakeFiles/Makefile2:618: recipe for target 'utilities/NekMesh/CMakeFiles/NekMesh.dir/all' failed
make[1]: *** [utilities/NekMesh/CMakeFiles/NekMesh.dir/all] Error 2
Can anyone point me in the right direction about what could be causing this issue?

Many thanks,

Oliviu
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