Compiling the Latest Elmer on Linux Mint 17

Discussion about building and installing Elmer
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Z.Losonc
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Joined: 21 Dec 2017, 16:05
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Compiling the Latest Elmer on Linux Mint 17

Post by Z.Losonc »

This is the continuation of my previous two posts on this thread:
http://elmerfem.org/forum/viewtopic.php?f=2&t=4918
It is continued here because this subject is not directly related to Launchpad, but rather to the direct compilation of the source code.

The objective is to demystify the building/compilation method of the latest Elmer version on Linux 17.

The best result achieved so far is based on this method using Cmake:
http://www.elmerfem.org/elmerwiki/index ... sing_Cmake

It builds a package, but not perfect. Here is the log:

Code: Select all

zoltan@zoltan-Inspiron-1501 ~/elmerfem/builddir $ $CMAKE $ELMERSRC -DCMAKE_TOOLCHAIN_FILE=$TOOLCHAIN \
>     -DCMAKE_INSTALL_PREFIX=$IDIR \
>     -DCMAKE_C_COMPILER=/usr/bin/gcc \
>     -DCMAKE_Fortran_COMPILER=/usr/bin/gfortran \
>     -DWITH_MPI:BOOL=TRUE \
>     -DWITH_Mumps:BOOL=TRUE \
>     -DWITH_Hypre:BOOL=TRUE \
>     -DWITH_Trilinos:BOOL=FALSE \
>     -DWITH_ELMERGUI:BOOL=TRUE \
>     -DWITH_OCC:BOOL=TRUE \
>     -DWITH_PARAVIEW:BOOL=TRUE \
>     -DWITH_QWT:BOOL=TRUE \
>     -DWITH_VTK:BOOL=TRUE \
>     -DWITH_PYTHONQT:BOOL=FALSE \
>     -DWITH_MATC:BOOL=TRUE 
-- The Fortran compiler identification is GNU
-- The C compiler identification is GNU 4.8.4
-- The CXX compiler identification is GNU 4.8.4
-- Check for working Fortran compiler: /usr/bin/gfortran
-- Check for working Fortran compiler: /usr/bin/gfortran  -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/bin/gfortran supports Fortran 90
-- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
-- Check for working C compiler: /usr/bin/gcc
-- Check for working C compiler: /usr/bin/gcc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/g++
-- Check for working CXX compiler: /usr/bin/g++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Checking whether GFortran version >= 4.8 -- yes
-- 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 sgemm
-- Looking for Fortran sgemm - 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.
-- Finding Mumps
-- Finding SCALAPACK
-- Checking if BLACS library is needed by SCALAPACK
-- Looking for Fortran blacs_gridinit
-- Looking for Fortran blacs_gridinit - not found
-- Checking if BLACS library is needed by SCALAPACK -- yes
-- Finding BLACS
-- A library with BLACS API found.
-- BLACS libraries: /usr/lib/libblacs-openmpi.so
-- Checking if Metis library is needed by Mumps
-- Checking if Metis library is needed by Mumps -- yes
-- Finding Metis
-- Checking if ParMetis library is needed by Mumps
-- Checking if ParMetis library is needed by Mumps -- yes
-- Finding ParMetis
-- A library with Mumps API found.
-- Mumps include dir: /usr/include
-- Mumps libraries: /usr/lib/libdmumps.so;/usr/lib/libmumps_common.so;/usr/lib/libpord.so;/usr/lib/libscalapack-openmpi.so;/usr/lib/libblacs-openmpi.so;/usr/lib/libmetis.so;/usr/lib/libparmetis.so
-- Checking whether /usr/bin/gfortran supports PROCEDURE POINTER
-- Checking whether /usr/bin/gfortran supports PROCEDURE POINTER -- yes
-- Checking whether /usr/bin/gfortran supports CONTIGUOUS
-- Checking whether /usr/bin/gfortran supports CONTIGUOUS -- yes
-- Checking whether /usr/bin/gfortran supports EXECUTE_COMMAND_LINE
-- Checking whether /usr/bin/gfortran 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
You have called ADD_LIBRARY for library CMakeFiles without any source files. This typically indicates a problem with your CMakeLists.txt file
-- Found 108 modules from /home/zoltan/elmerfem/fem/src/modules
-- Skipping test WinkelPoissonMetisKwayNodal with 16 procs
-- Skipping test WinkelPoissonMetisKwayDual with 16 procs
-- Found 501 tests
CMake Warning at elmergrid/src/CMakeLists.txt:11 (MESSAGE):
  Crosscompiling ElmerGrid, no native build flags set


-- Looking for execinfo.h
-- Looking for execinfo.h - found
-- Looking for getline
-- Looking for getline - found
-- checking for thread-local storage - found
--   Building ElmerGUI
-- ------------------------------------------------
-- ------------------------------------------------
-- Looking for Q_WS_X11
-- Looking for Q_WS_X11 - found
-- Looking for Q_WS_WIN
-- Looking for Q_WS_WIN - not found
-- Looking for Q_WS_QWS
-- Looking for Q_WS_QWS - not found
-- Looking for Q_WS_MAC
-- Looking for Q_WS_MAC - not found
-- Found Qt4: /usr/bin/qmake (found version "4.8.6") 
--   [ElmerGUI] Qt4:               TRUE
--   [ElmerGUI] Qt4_LIBRARIES:     
-- ------------------------------------------------
-- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so
-- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for IceConnectionNumber in ICE
-- Looking for IceConnectionNumber in ICE - found
-- Found X11: /usr/lib/x86_64-linux-gnu/libX11.so
-- Found OpenGL: /usr/lib/x86_64-linux-gnu/libGL.so  
-- Found Qt4: /usr/bin/qmake (found version "4.8.6") 
--   [ElmerGUI] Qwt:             TRUE
--   [ElmerGUI] QWT_LIBRARY:     /usr/lib/libqwt.so
--   [ElmerGUI] QWT_INCLUDE_DIR: /usr/include/qwt
-- ------------------------------------------------
--   [ElmerGUI] OCE:               1
--   [ElmerGUI] OCE_VERSION:       0.15
--   [ElmerGUI] OCE_INCLUDE_DIRS:  /usr/lib/x86_64-linux-gnu/oce-0.15/../../../include/oce
--   [ElmerGUI] ELMER_OCC_LIBS:    TKernel;TKMath;TKG3d;TKG2d;TKBRep;TKSTEP;TKMesh;TKIGES;TKG2d;TKGeomBase;TKBool;TKBO;TKGeomAlgo;TKPrim;TKShHealing;TKSTEP209;TKSTEPAttr;TKSTEPBase;TKTopAlgo;TKXSBase
-- ------------------------------------------------
--   [ElmerGUI] VTK version:       6.0.0
--   [ElmerGUI] VTK_LIBS:          vtkInteractionImage;vtkImagingColor;vtkImagingCore;vtkCommonExecutionModel;vtkCommonDataModel;vtkCommonMath;vtkCommonCore;vtksys;vtkCommonMisc;vtkCommonSystem;vtkCommonTransforms;vtkInteractionStyle;vtkRenderingCore;vtkFiltersExtraction;vtkFiltersCore;vtkFiltersGeneral;vtkCommonComputationalGeometry;vtkFiltersStatistics;vtkImagingFourier;vtkalglib;vtkFiltersGeometry;vtkFiltersSources;vtkIOImage;vtkDICOMParser;vtkIOCore;/usr/lib/x86_64-linux-gnu/libz.so;vtkmetaio;/usr/lib/x86_64-linux-gnu/libjpeg.so;/usr/lib/x86_64-linux-gnu/libpng.so;/usr/lib/x86_64-linux-gnu/libtiff.so;vtkIOXMLParser;/usr/lib/x86_64-linux-gnu/libexpat.so;vtkInteractionWidgets;vtkFiltersHybrid;vtkImagingSources;vtkFiltersModeling;vtkImagingGeneral;vtkImagingHybrid;vtkRenderingAnnotation;vtkRenderingFreeType;/usr/lib/x86_64-linux-gnu/libfreetype.so;vtkftgl;vtkRenderingVolume;vtkViewsGeovis;vtkGeovisCore;vtkIOXML;vtkIOGeometry;vtkInfovisLayout;vtkInfovisCore;vtkRenderingOpenGL;vtkViewsCore;vtkproj4;vtkViewsInfovis;vtkFiltersImaging;vtkRenderingContext2D;vtkRenderingLabel;vtkFiltersVerdict;verdict;vtkFiltersParallelFlowPaths;vtkFiltersAMR;vtkParallelCore;vtkIOLegacy;vtkFiltersFlowPaths;vtkParallelMPI;vtkWrappingJava;vtkWrappingTools;vtkIOAMR;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/libhdf5_hl.so;vtkIOPLY;vtkGUISupportQtOpenGL;vtkGUISupportQt;vtkRenderingVolumeAMR;vtkRenderingParallel;vtkFiltersParallel;vtkTestingRendering;vtkIOFFMPEG;vtkIOMovie;/usr/lib/x86_64-linux-gnu/libogg.so;/usr/lib/x86_64-linux-gnu/libtheoraenc.so;/usr/lib/x86_64-linux-gnu/libtheoradec.so;vtkIOPostgreSQL;vtkIOSQL;vtksqlite;vtkRenderingQt;vtkFiltersTexture;vtkIOParallelLSDyna;vtkIOLSDyna;vtkRenderingGL2PS;/usr/lib/libgl2ps.so;vtkexoIIc;vtkNetCDF;vtkNetCDF_cxx;vtkImagingStatistics;vtkIOParallel;vtkIONetCDF;vtkRenderingImage;vtkGUISupportQtWebkit;vtkViewsQt;vtkIOGDAL;vtkImagingStencil;vtkIOParallelNetCDF;vtkRenderingFreeTypeOpenGL;vtkInfovisBoostGraphAlgorithms;vtkIOXdmf2;vtkxdmf2;/usr/lib/x86_64-linux-gnu/libxml2.so;vtkIOExodus;vtkIOEnSight;vtkIOMySQL;vtkImagingMorphological;vtkChartsCore;vtkCommonColor;vtkFiltersProgrammable;vtkFiltersGeneric;vtkIOVPIC;VPIC;vtkIOMPIImage;vtkRenderingLOD;vtkViewsContext2D;vtkRenderingVolumeOpenGL;vtkIOExport;vtkIOInfovis;vtkIOMPIParallel;vtkIOVideo;vtkIOMINC;vtkIOImport;vtkRenderingFreeTypeFontConfig;vtkFiltersSelection;/usr/lib/x86_64-linux-gnu/libpython2.7.so;vtkFiltersCosmo;Cosmo;vtkFiltersParallelStatistics;vtkWrappingPythonCore;vtkDomainsChemistry;vtkFiltersParallelMPI;vtkImagingMath;vtkTestingGenericBridge;vtkTestingIOSQL;vtkFiltersParallelImaging;vtkFiltersParallelGeometry;vtkLocalExample;vtkRenderingMatplotlib;vtkPythonInterpreter;vtkIOParallelExodus;vtkGUISupportQtSQL;vtkFiltersReebGraph;vtkIOODBC;vtkjsoncpp;vtkRenderingHybridOpenGL;vtkFiltersHyperTree
--   [ElmerGUI] VTK_INCLUDE_DIRS:  /usr/include/vtk-6.0;/usr/include;/usr/include/x86_64-linux-gnu;/usr/include/freetype2;/usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi;/usr/include/tcl8.6;/usr/include/libxml2;/usr/include/python2.7
-- ------------------------------------------------
--   [ElmerGUI] Compiling in matc
-- ------------------------------------------------
-- ------------------------------------------------
--   BLAS library:   /usr/lib/libblas.so
--   LAPACK library: /usr/lib/liblapack.so;/usr/lib/libblas.so
-- ------------------------------------------------
--   Fortran compiler:        /usr/bin/gfortran
--   Fortran flags:           -O3 -O2 -g -DNDEBUG
-- ------------------------------------------------
--   C compiler:              /usr/bin/gcc
--   C flags:                 -O3 -O2 -g -DNDEBUG
-- ------------------------------------------------
--   CXX compiler:            /usr/bin/g++
--   CXX flags:               -O3 -O2 -g -DNDEBUG
-- ------------------------------------------------
--   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:       
-- ------------------------------------------------
--   Mumps:             TRUE
--   Mumps include:     /usr/include
--   Mumps libraries:   /usr/lib/libdmumps.so;/usr/lib/libmumps_common.so;/usr/lib/libpord.so;/usr/lib/libscalapack-openmpi.so;/usr/lib/libblacs-openmpi.so;/usr/lib/libmetis.so;/usr/lib/libparmetis.so
-- ------------------------------------------------
--   Hypre:             TRUE
--   Hypre include:     /usr/include
--   Hypre libraries:   /usr/lib/libHYPRE.so;/usr/lib/libHYPRE_Euclid.so;/usr/lib/libHYPRE_parcsr_ls.so;/usr/lib/libHYPRE_ParaSails.so;/usr/lib/libHYPRE_IJ_mv.so
-- ------------------------------------------------
-- ------------------------------------------------
--   Package filename: elmerfem-8.3-0cc4224-20171228_Linux-x86_64 
--   Patch version: 8.3-0cc4224 
-- Configuring done
-- Generating done
-- Build files have been written to: /home/zoltan/elmerfem/builddir
after starting the installation with:

make -j4 && sudo make install

It has progressed to 81% and stopped with these error messages (snippets only):

Code: Select all

[ 74%] Building Fortran object fem/src/CMakeFiles/elmersolver.dir/BandMatrix.F90.o
/home/zoltan/elmerfem/ElmerGUI/netgen/libsrc/general/profiler.cpp: In static member function ‘static void netgen::NgProfiler::Print(FILE*)’:
/home/zoltan/elmerfem/ElmerGUI/netgen/libsrc/general/profiler.cpp:85:91: warning: format ‘%i’ expects argument of type ‘int’, but argument 3 has type ‘long int’ [-Wformat=]
    fprintf(prof,"calls %8i, time %6.2f sec",counts[i],double(tottimes[i]) / CLOCKS_PER_SEC);
                                                                                           ^
...

Scanning dependencies of target ElmerGUI
[ 76%] Building CXX object ElmerGUI/Application/CMakeFiles/ElmerGUI.dir/src/bodypropertyeditor.cpp.o
In file included from /home/zoltan/elmerfem/ElmerGUI/Application/src/mainwindow.h:78:0,
                 from /home/zoltan/elmerfem/ElmerGUI/Application/src/bodypropertyeditor.cpp:43:
/home/zoltan/elmerfem/ElmerGUI/Application/cad/cadview.h:53:28: fatal error: TopoDS_Shape.hxx: No such file or directory
 #include <TopoDS_Shape.hxx>
                            ^
compilation terminated.
[ 76%] Building Fortran object fem/src/CMakeFiles/elmersolver.dir/HashTable.F90.o
make[2]: *** [ElmerGUI/Application/CMakeFiles/ElmerGUI.dir/src/bodypropertyeditor.cpp.o] Error 1
make[1]: *** [ElmerGUI/Application/CMakeFiles/ElmerGUI.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
...

Linking Fortran shared library libelmersolver.so
[ 81%] Built target elmersolver
make: *** [all] Error 2
zoltan@zoltan-Inspiron-1501 ~/elmerfem/builddir $ 
Any suggestions what may be the problem, and how to make the compilation/installation work?
Based on the error messages it looks like there are bugs in the source code and/or CMakeLists.txt file, which can be fixed only by the developers. But of course, there is always the possibility that I have to install some more prerequisite software to get it right...

Thanks for help in advance.
Zoltan
mzenker
Posts: 1999
Joined: 07 Dec 2009, 11:49
Location: Germany

Re: Compiling the Latest Elmer on Linux Mint 17

Post by mzenker »

Hi Zoltan,

if I understand correctly, your compilation problems are in ElmerGUI. That would mean that you have successfully compiled ElmerSolver and ElmerGrid, i.e. the essential of the Elmer package.
If that is correct, I would suggest you use those in combination with ElmerGUI from the launchpad installation. You would just have to tell the GUI where to find the solver from your compilation. The GUI is not under intense development anyway, so the version from launchpad is the newest one and is not sensible to frequent change.

HTH,

Matthias
raback
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Re: Compiling the Latest Elmer on Linux Mint 17

Post by raback »

Hi Zoltan

Linux Mint 17 comes with VTK 6.0 but ElmerGUI is compatible with VTK 5.?. Hence we should make some modifications to the code to allow compilation with VTK 6.0. This is on the todo list, but not at the top of it.

In the meantime you should be able to compile everything else except the GUI. Perhaps even the GUI with VTK switched off.

-Peter
Z.Losonc
Posts: 40
Joined: 21 Dec 2017, 16:05
Antispam: Yes

Re: Compiling the Latest Elmer on Linux Mint 17

Post by Z.Losonc »

Hi,

Thanks Matthias and Peter for the tips, and for finally revealing the cause of the failure.

I prefer to wait until the developers fix the problem, and enable us to perform a smooth and error-free compilation of the complete package. While you are at it, please also show/explain how to include Pardiso and SuperLU into the binary (this is not only my request, see here: viewtopic.php?f=3&t=4968)

Since the developers are busy with other projects, keeping this subject and the acoustic modules on the unimportant to-do list, why not give them a break until their main project is finished? So, I will briefly touch on two more acoustics related subjects in new threads, and wait until problems get resolved; features get added.

Zoltan
raback
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Re: Compiling the Latest Elmer on Linux Mint 17

Post by raback »

Hi

If there are problems to compile there are two precompiled options in:

http://www.nic.funet.fi/pub/sci/physics/elmer/bin/

One for Windows, and a LinuxMint based virtual machine. Additionally there is the launchpad. If you have any precompiled version the compilation of a module should be easy,

>elmerf90 -o MySolver.so MySolver.f90

The elmerf90 script includes all the needed compilation flags. Then you can develop the modules freely. They are not part of the library. ElmerSolver library is mostly physics agnostic. So hacking the solvers can be done without recompiling the whole code. Just take the HelmholtzSolver.F90 and make a modified version of it.

I do agree that the PML is something that would be nice. Does the Sommerfeld condition not do it in your cases?

Now actually I realized that out virtual machine uses LinuxMint18 already. I think it is only LinuxMint19 that does not have the option for vtk5. So perhaps on your Mint17 you could revert to an older vtk library on your current installation. Unfortunately, my expertise is not in the compilation business.

-Peter
Z.Losonc
Posts: 40
Joined: 21 Dec 2017, 16:05
Antispam: Yes

Re: Compiling the Latest Elmer on Linux Mint 17

Post by Z.Losonc »

Hi Peter,

Thanks for the explanation. This opens the door to modifying the code, which is very useful, and I might use it in the future.

The original goal of compiling Elmer instead of installing a pre-compiled binary is twofold. First, there are many Linux distros out there, which are likely to be incompatible with the Launchpad versions. If someone is forced to use an incompatible distro for whatever reason, then there supposed be an established and well tested method to compile the source code on a new, arbitrary Linux installation that has been proven to work without errors. The method described on the page http://www.elmerfem.org/elmerwiki/index ... sing_Cmake has been proven not to work, and if you (or someone else) have not fixed the mistakes yet, then it is still misleading people and unnecessarily wasting their time.

The second reason why a detailed compilation method needs to be published is for empowering people to include the Pardiso and SuperLU solvers as well, for those who want to have them. So even though the hacking of the solvers seems to be possible now for this Linux Mint platform with the Elmer binary from Launchpad (didn't try it yet), users still need a comprehensive compilation procedure that works flawlessly on freshly installed OS that doesn't have any prerequisites installed yet.

If the compilation is not your strength, then please prod those developers who are compiling the source code routinely to remove the deceiving instructions from Elmer pages, and upload a working method. I will attempt such a full compilation again only when a new method explains in detail how to include Pardiso and SuperLU as well.

Regarding the PML issue, I will expand on it with more detail in a new thread in the ElmerSolver section.

Zoltan
vencels
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Re: Compiling the Latest Elmer on Linux Mint 17

Post by vencels »

For me compiling/installing Elmer on many different Linux distros was a piece of cake, comparing with other open-source software. Elmer has very few dependencies and for most users build-in iterative solvers are enough, they simply work out-of-the-box. For those who really need third-party solvers I would advise to take a look on CMakeLists.txt file - this is the best instruction for how to compile Elmer with anything.

If you have special needs or want to prioritize development of particular solver of prioritize fixing particular bug, then there is section on this forum called "Commercial services". Feel free to leave your special needs there.
Z.Losonc
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Re: Compiling the Latest Elmer on Linux Mint 17

Post by Z.Losonc »

Vencels, are you part of the Elmer development or management team?
Did you write the compilation instructions on this page?
http://www.elmerfem.org/elmerwiki/index ... sing_Cmake
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