ElmerGUI cmake compilation error, ubuntu 14.04

[stevemi]

Anil: OK, thanks for all the help. I only needed to stop the terminal window process in order to get the usual prompt, then proceeded with the install, which worked fine! The only "hitch" occurred right at the end, when I was advised I needed administrator privileges. Re-installing using sudo completed the install.
Stevemi

[annier]

Hi Stevemi,
-You need to type "sudo" (become root user) when you install Elmer in /usr/local/ directories.
By default, the install destination for Elmer will appear as following during the configuration process in the gui of cmake-gui:

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CMAKE_INSTALL_PREFIX                                  /usr/local
ELMER_SOLVER_HOME                                     /usr/local/share/elmersolver

-You can install Elmer in $HOME directory just at the side of elmerfem and build directories/folders by defining the install path during cmake build process in the cmake-gui. For this path setting, you can proceed without requiring to be the root user. The path for installation will be then given to Cmake interface as:

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CMAKE_INSTALL_PREFIX                 /home/username/elmer/install
ELMER_SOLVER_HOME                           /home/username/elmer/install/share/elmersolver

For details, please refer step 4(d) and figure at 4 (f) as described in this thread.



Yours
Anil Kunwar

[stevemi]

Hi Anil: Two remaining secondary issues, FYI. Non-critical, as I can go ahead without these:
1) PythonQT option: Cmake is looking for both the Python libs and associated include files. It found the libs, but no python include files exist as nearly as I can tell.
2) VTK option: Cmake can't find the VTK directory. The error message indicates it's looking for the directory containing VTKConfig.cmake, but the only thing on my system is VTKConfig-Python.cmake, located under /usr/lib/vtk-5.8.
stevemi

[annier]

Hi Stevemi,
In my context:

I) Prelogue:
Minimal configuration of Elmer:
This is the Cmake-gui configure log for Elmer configuration with
-WITH_MPI (only)

Code: Select all

The Fortran compiler identification is GNU
The C compiler identification is GNU 4.8.2
The CXX compiler identification is GNU 4.8.2
Check for working Fortran compiler: /usr/bin/f95
Check for working Fortran compiler: /usr/bin/f95  -- works
Detecting Fortran compiler ABI info
Detecting Fortran compiler ABI info - done
Checking whether /usr/bin/f95 supports Fortran 90
Checking whether /usr/bin/f95 supports Fortran 90 -- yes
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
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
Found MPI_C: /usr/lib/libmpi.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libhwloc.so  
Found MPI_CXX: /usr/lib/libmpi_cxx.so;/usr/lib/libmpi.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libhwloc.so  
Found MPI_Fortran: /usr/lib/libmpi_f90.so;/usr/lib/libmpi_f77.so;/usr/lib/libmpi.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libhwloc.so  
Looking for Fortran dgemm
Looking for Fortran dgemm - found
Looking for include file pthread.h
Looking for include file pthread.h - found
Looking for pthread_create
Looking for pthread_create - not found
Looking for pthread_create in pthreads
Looking for pthread_create in pthreads - not found
Looking for pthread_create in pthread
Looking for pthread_create in pthread - found
Found Threads: TRUE  
A library with BLAS API found.
A library with BLAS API found.
Looking for Fortran cheev
Looking for Fortran cheev - found
A library with LAPACK API found.
Checking whether /usr/bin/f95 supports CONTIGUOUS
Checking whether /usr/bin/f95 supports CONTIGUOUS -- yes
Checking whether /usr/bin/f95 supports EXECUTE_COMMAND_LINE
Checking whether /usr/bin/f95 supports EXECUTE_COMMAND_LINE -- yes
Looking for include file inttypes.h
Looking for include file inttypes.h - found
Looking for sys/types.h
Looking for sys/types.h - found
Looking for stdint.h
Looking for stdint.h - found
Looking for stddef.h
Looking for stddef.h - found
Check size of long
Check size of long - done
------------------------------------------------
  BLAS library:   /usr/lib/libf77blas.so.3gf;/usr/lib/libatlas.so.3gf
  LAPACK library: /usr/lib/liblapack.so;/usr/lib/libf77blas.so.3gf;/usr/lib/libatlas.so.3gf
------------------------------------------------
  Fortran compiler:        /usr/bin/f95
  Fortran flags:           
------------------------------------------------
  C compiler:              /usr/bin/cc
  C flags:                 
------------------------------------------------
  MPI Fortran:             TRUE
  MPI Fortran compiler:    /usr/bin/mpif90
  MPI Fortran flags:       
  MPI Fortran include dir: /usr/lib/openmpi/include;/usr/lib/openmpi/lib
  MPI Fortran libraries:   /usr/lib/libmpi_f90.so;/usr/lib/libmpi_f77.so;/usr/lib/libmpi.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libhwloc.so
  MPI Fortran link flags:  
------------------------------------------------
  MPI C:             TRUE
  MPI C compiler:    /usr/bin/mpicc
  MPI C flags:       
  MPI C include dir: /usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi
  MPI C libraries:   /usr/lib/libmpi.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libhwloc.so
  MPI C flags:       
------------------------------------------------
------------------------------------------------
  Package filename: elmerfem-7.0-8eaded3-20141231_Linux-x86_64 
  Patch version: 7.0-8eaded3 
Configuring done

1. PythonQtoption (i.e. Minimal + ElmerGUI<with PythonQT>):
This is the Cmake -gui configure log for Elmer configuration with following options:
-WITH_ELMERGUI ---->>>>WITH_PythonQT (only)
-WITH_MPI

Code: Select all

A library with BLAS API found.
A library with BLAS API found.
A library with LAPACK API found.
Checking whether /usr/bin/f95 supports CONTIGUOUS
Checking whether /usr/bin/f95 supports CONTIGUOUS -- yes
Checking whether /usr/bin/f95 supports EXECUTE_COMMAND_LINE
Checking whether /usr/bin/f95 supports EXECUTE_COMMAND_LINE -- yes
  Building ElmerGUI
------------------------------------------------
------------------------------------------------
CMake Warning (dev) at /usr/share/cmake-2.8/Modules/CheckCXXSymbolExists.cmake:38 (include):
  File /usr/share/cmake-2.8/Modules/CheckCXXSymbolExists.cmake includes
  /usr/share/cmake-2.8/Modules/CheckSymbolExists.cmake (found via
  CMAKE_MODULE_PATH) which shadows
  /usr/share/cmake-2.8/Modules/CheckSymbolExists.cmake.  This may cause
  errors later on .

  Policy CMP0017 is not set: Prefer files from the CMake module directory
  when including from there.  Run "cmake --help-policy CMP0017" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.
Call Stack (most recent call first):
  /usr/share/cmake-2.8/Modules/FindQt4.cmake:392 (include)
  ElmerGUI/CMakeLists.txt:16 (FIND_PACKAGE)
This warning is for project developers.  Use -Wno-dev to suppress it.

Found Qt4: /usr/bin/qmake (found version "4.8.6") 
  [ElmerGUI] Qt4:               TRUE
  [ElmerGUI] Qt4_LIBRARIES:     
------------------------------------------------
CMake Warning (dev) at /usr/share/cmake-2.8/Modules/CheckCXXSymbolExists.cmake:38 (include):
  File /usr/share/cmake-2.8/Modules/CheckCXXSymbolExists.cmake includes
  /usr/share/cmake-2.8/Modules/CheckSymbolExists.cmake (found via
  CMAKE_MODULE_PATH) which shadows
  /usr/share/cmake-2.8/Modules/CheckSymbolExists.cmake.  This may cause
  errors later on .

  Policy CMP0017 is not set: Prefer files from the CMake module directory
  when including from there.  Run "cmake --help-policy CMP0017" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.
Call Stack (most recent call first):
  /usr/share/cmake-2.8/Modules/FindQt4.cmake:392 (include)
  ElmerGUI/PythonQt/CMakeLists.txt:2 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

Found Qt4: /usr/bin/qmake (found version "4.8.6") 
PYTHON_LIBRARIES /usr/local/lib/libpython2.7.a
CMake Warning at ElmerGUI/Application/CMakeLists.txt:238 (MESSAGE):
  PythonQT is not tested.


------------------------------------------------
  BLAS library:   /usr/lib/libf77blas.so.3gf;/usr/lib/libatlas.so.3gf
  LAPACK library: /usr/lib/liblapack.so;/usr/lib/libf77blas.so.3gf;/usr/lib/libatlas.so.3gf
------------------------------------------------
  Fortran compiler:        /usr/bin/f95
  Fortran flags:           
------------------------------------------------
  C compiler:              /usr/bin/cc
  C flags:                 
------------------------------------------------
  MPI Fortran:             TRUE
  MPI Fortran compiler:    /usr/bin/mpif90
  MPI Fortran flags:       
  MPI Fortran include dir: /usr/lib/openmpi/include;/usr/lib/openmpi/lib
  MPI Fortran libraries:   /usr/lib/libmpi_f90.so;/usr/lib/libmpi_f77.so;/usr/lib/libmpi.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libhwloc.so
  MPI Fortran link flags:  
------------------------------------------------
  MPI C:             TRUE
  MPI C compiler:    /usr/bin/mpicc
  MPI C flags:       
  MPI C include dir: /usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi
  MPI C libraries:   /usr/lib/libmpi.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libhwloc.so
  MPI C flags:       
------------------------------------------------
------------------------------------------------
  Package filename: elmerfem-7.0-8eaded3-20141231_Linux-x86_64 
  Patch version: 7.0-8eaded3 
Configuring done

Although, this configuration issues some warning, the ElmerGUI configuration with PythonQT is successful.

2. WITH_VTK (i.e. minimal +ElmerGUI<with VTK>)
This is the Cmake -gui configure log for Elmer configuration with following options:
-WITH_ELMERGUI ---->>>>WITH_VTK (only)
-WITH_MPI

Code: Select all

A library with BLAS API found.
A library with BLAS API found.
A library with LAPACK API found.
Checking whether /usr/bin/f95 supports CONTIGUOUS
Checking whether /usr/bin/f95 supports CONTIGUOUS -- yes
Checking whether /usr/bin/f95 supports EXECUTE_COMMAND_LINE
Checking whether /usr/bin/f95 supports EXECUTE_COMMAND_LINE -- yes
  Building ElmerGUI
------------------------------------------------
------------------------------------------------
CMake Warning (dev) at /usr/share/cmake-2.8/Modules/CheckCXXSymbolExists.cmake:38 (include):
  File /usr/share/cmake-2.8/Modules/CheckCXXSymbolExists.cmake includes
  /usr/share/cmake-2.8/Modules/CheckSymbolExists.cmake (found via
  CMAKE_MODULE_PATH) which shadows
  /usr/share/cmake-2.8/Modules/CheckSymbolExists.cmake.  This may cause
  errors later on .

  Policy CMP0017 is not set: Prefer files from the CMake module directory
  when including from there.  Run "cmake --help-policy CMP0017" for policy
  details.  Use the cmake_policy command to set the policy and suppress this
  warning.
Call Stack (most recent call first):
  /usr/share/cmake-2.8/Modules/FindQt4.cmake:392 (include)
  ElmerGUI/CMakeLists.txt:16 (FIND_PACKAGE)
This warning is for project developers.  Use -Wno-dev to suppress it.

  [ElmerGUI] Qt4:               TRUE
  [ElmerGUI] Qt4_LIBRARIES:     
------------------------------------------------
CMake Error at /usr/share/cmake-2.8/Modules/FindVTK.cmake:135 (message):
  VTK not found.  Set the VTK_DIR cmake cache entry to the directory
  containing VTKConfig.cmake.  This is either the root of the build tree, or
  PREFIX/lib/vtk for an installation.  For VTK 4.0, this is the location of
  UseVTK.cmake.  This is either the root of the build tree or
  PREFIX/include/vtk for an installation.
Call Stack (most recent call first):
  ElmerGUI/CMakeLists.txt:58 (FIND_PACKAGE)


Configuring incomplete, errors occurred!
See also "/home/username/buildelmer/CMakeFiles/CMakeOutput.log".
See also "/home/username/buildelmer/CMakeFiles/CMakeError.log".

The configuration cannot proceed because of not finding the VTK libraries. The error message is:

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VTK_DIR                                    VTK_DIR-NOTFOUND

So, i have installed Elmer without using the VTK (please refer the pictures in page 2 of this thread.)


Yours
Anil Kunwar

[annier]

Hi Stevemi,
The solution for using ElmerGUI with VTK is as follows:

• 1, Download the version of VTK from http://www.vtk.org/VTK/resources/software.html.
  2. Extract the VTK-5.8.0.tar.gz file and keep it in the $HOME directory.
  So, its location will be /home/username/VTK.
  3. create a VTK_build directory(also in $HOME) and jump into the directory.

  Code: Select all

  $mkdir build_VTK
  $cd build_VTK

  4. Run cmake-gui

  Code: Select all

  $cmake-gui

  5. Configure and generate the VTK Makefile using cmake.
  a. Locate the source and build paths of VTK as shown in the figure.

  

  the source and build folders for VTK build using cmake-gui

  VTK_build_using_cmake-gui.png (56.08 KiB) Viewed 7307 times

  b. Click configure.
  c. Click generate (Makefile will be generated with other necessary files)
  6. Now start the Elmer configuration and generate process as described in the thread till the following error message appears.

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  VTK_DIR                                    VTK_DIR-NOTFOUND

  Then, browse the path exactly at the place where this VTK_DIR-NOTFOUND is written and define this path where the Makefiles and other files/folders of previously built VTK are located. So, the path for VTK_DIR will be written as:

  Code: Select all

  VTK_DIR                                    /home/username/build_VTK

  6. Click configure for update of "Elmer build configuration" and then click generate.
  7. The Makefile for Elmerbuild is generate along with WITH_VTK option for ELMER_GUI.

Yours
Anil Kunwar

[stevemi]

Anil: Thanks for the input, which I tried, with the following results:
1) Added VTK and tetgen options (after first installing tetgen). Configure/generate were successful.
2) Cmake exited with errors, reporting "compilation stopped".
3) 10 tests failed, but all the rest passed.
4) GUI runs OK, but I'm not sure of its capability at this point. It seems to suggest that it's OK for most applications, but I'm not sure.
5) Have uploaded elmer build log files with this message, plus 3 VTK build logs with the next message.
Stevemi

[stevemi]

Anil: Here are the VTK logs.
stevemi

[annier]

Hi Stevemi,
I could not point out the reasons behind the occurrence of such messages during the installation of VTK. I hope we will both learn about it on times to come or may be i can learn it from your experiences. If you find out the solution, please share it here so that we all can learn more about programming interfaces in computational science. Thank you.


Yours
Anil Kunwar

[stevemi]

Annier: Re-installation, taking great care re the required paths, worked OK. Please see my comments in the SOLVER forum as well. FYI, this time I got a message that some files were no longer required, and that I should remove them, which I did. No other differences from previous installations observed.
stevemi