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KratosMultiphysics / Kratos

Kratos Multiphysics (A.K.A Kratos) is a framework for building parallel multi-disciplinary simulation software. Modularity, extensibility and HPC are the main objectives. Kratos has BSD license and is written in C++ with extensive Python interface.
https://kratosmultiphysics.github.io/Kratos/
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Error in Kratos Pfem application while compling #2895

Closed BilalTsinghua closed 5 years ago

BilalTsinghua commented 6 years ago

@roigcarlo [ 49%] Built target KratosSolidMechanicsApplication make[2]: No rule to make target 'applications/PfemApplication/CMakeFiles/external_tetgen.dir/build'. Stop. CMakeFiles/Makefile2:815: recipe for target 'applications/PfemApplication/CMakeFiles/external_tetgen.dir/all' failed make[1]: [applications/PfemApplication/CMakeFiles/external_tetgen.dir/all] Error 2 Makefile:116: recipe for target 'all' failed make: *** [all] Error 2 When i am compling the kratos Pfem application in my computer, it shows the above mention error.

josep-m-carbonell commented 6 years ago

To compile the pfem application you must checkout the master branch or the pfem/develop branch. It seems like your kratos version is not up to date. Now the tetgen submodule is located in the DelaunayMeshingApplication. You can check it looking at its external_modules folder. In the compilation options (cmake configure file) you must set: -DDELAUNAY_MESHING_APPLICATION=ON -DPFEM_FLUID_DYNAMICS_APPLICATION=ON For pfem fluids only. If you want the general pfem for fluids and solids: -DDELAUNAY_MESHING_APPLICATION=ON -DCONSTITUTIVE_MODELS_APPLICATION=ON -DSOLID_MECHANICS_APPLICATION=ON -DCONTACT_MECHANICS_APPLICATION=ON -DPFEM_APPLICATION=ON

BilalTsinghua commented 6 years ago

Dear @josep-m-carbonell Thanks for your reply.I have updated the Kratos with 'git pull' And then I changed the configure.sh followed your suggestion.But there are more errors after I recompile the file.As followed: -- Found Git: /usr/bin/git (found version "2.7.4") additional default options were set for gcc CMAKE_CXX_FLAGS = -msse3 -std=c++11 -funroll-loops -Wall -std=c++11 -Wsuggest-override CMAKE_C_FLAGS = -msse3 -funroll-loops -Wall KRATOS_BUILD_TESTING not defined. Setting to ON -- Found PythonInterp: /usr/bin/python3 (found version "3.5.2") -- Found PythonLibs: /usr/lib/x86_64-linux-gnu/libpython3.5m.so -- Performing Test HAS_CPP14_FLAG -- Performing Test HAS_CPP14_FLAG - Success KRATOS_EXCLUDE_OPENMP OpenMP included -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp
-- Boost version: 1.68.0 Boost Include: /home/bilal/boost_1_68_0 Boost Linkdir: -- Looking for Fortran sgemm -- Looking for Fortran sgemm - found -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - found -- Found Threads: TRUE
-- A library with BLAS API found. linker flags with blas = BLA_VENDOR = All -- A library with BLAS API found. -- Looking for Fortran cheev -- Looking for Fortran cheev - found -- A library with LAPACK API found. LAPACK = /usr/lib/liblapack.so/usr/lib/libblas/libblas.so.3.6.0 LAPACK modified = /usr/lib/lapack/liblapack.so.3.6.0/usr/lib/libblas/libblas.so.3.6.0 -- Could NOT find ZLIB (missing: ZLIB_LIBRARY ZLIB_INCLUDE_DIR) -- Preparing local ZLIB compilation. -- 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 off64_t -- Check size of off64_t - done -- Looking for fseeko -- Looking for fseeko - found -- Looking for unistd.h -- Looking for unistd.h - found AMatrix not found. Please define the AMATRIX_DIR pointing to the AMatrix root directory.

CMAKE_BUILD_TYPE ........ Release

WARNING: YOUR GIDPOST IS BEING COMPILED WITHOUT DEBUG (ALL ASSERTS WILL BE AVOIDED) -- Performing Test HAS_FLTO -- Performing Test HAS_FLTO - Success -- LTO enabled

LIST OF KRATOS APPLICATIONS THAT ARE GOING TO BE COMPILED: 

            CONVECTION_DIFFUSION_APPLICATION - ON
            STRUCTURAL_MECHANICS_APPLICATION - ON
            SOLID_MECHANICS_APPLICATION - ON
            CONTACT_MECHANICS_APPLICATION - ON
            CONSTITUTIVE_MODELS_APPLICATION - ON
            FLUID_DYNAMICS_APPLICATION - ON
            FSI_APPLICATION - ON
            MIXED_ELEMENT_APPLICATION - ON
            PFEM_APPLICATION - ON
            PFEM_FLUID_DYNAMICS_APPLICATION - ON
            EXTERNAL_SOLVERS_APPLICATION - ON
            MESHING_APPLICATION - ON

** LIST OF KRATOS APPLICATIONS THAT ARE SET TO OFF: **

            STRUCTURAL_APPLICATION - OFF
            INCOMPRESSIBLE_FLUID_APPLICATION - OFF
            DEM_APPLICATION - OFF
            SWIMMING_DEM_APPLICATION - OFF
            OPENCL_APPLICATION - OFF
            TRILINOS_APPLICATION - OFF
            METIS_APPLICATION - OFF
            SHAPE_OPTIMIZATION_APPLICATION - OFF
            TOPOLOGY_OPTIMIZATION_APPLICATION - OFF
            MAPPING_APPLICATION - OFF
            HDF5_APPLICATION - OFF

configuring KratosExternalSolversApplication configuring KratosSolidMechanicsApplication configuring KratosPfemApplication configuring KratosPfemFluidDynamicsApplication configuring KratosContactMechanicsApplication configuring KratosConstitutiveModelsApplication configuring KratosConvectionDiffusionApplication configuring KratosMeshingApplication configuring KratosStructuralMechanicsApplication configuring KratosFluidDynamicsApplication configuring KratosFSIApplication configuring KratosMixedElementApplication CMake Warning (dev) at applications/MixedElementApplication/CMakeLists.txt:21 (target_link_libraries): Policy CMP0023 is not set: Plain and keyword target_link_libraries signatures cannot be mixed. Run "cmake --help-policy CMP0023" for policy details. Use the cmake_policy command to set the policy and suppress this warning.

The keyword signature for target_link_libraries has already been used with the target "KratosMixedElementApplication". All uses of target_link_libraries with a target should be either all-keyword or all-plain.

The uses of the keyword signature are here:

This warning is for project developers. Use -Wno-dev to suppress it.

*****-------------**** /home/bilal/Kratos/external_libraries/triangle python libraries to be installed are: /usr/lib/x86_64-linux-gnu/libpython3.5m.so.1.0 -------------------------------- standard install dir /home/bilal/Kratos installed blas = /usr/lib/libblas/libblas.so.3.6.0 installed lapack = /usr/lib/lapack/liblapack.so.3.6.0/usr/lib/libblas/libblas.so.3.6.0 -- Configuring done CMake Error at applications/PfemApplication/CMakeLists.txt:57 (add_library): Cannot find source file:

/home/bilal/Kratos/applications/PfemApplication/external_modules/tetgen/tetgen.cxx

Tried extensions .c .C .c++ .cc .cpp .cxx .m .M .mm .h .hh .h++ .hm .hpp .hxx .in .txx

CMake Error: Cannot determine link language for target "external_tetgen". CMake Error: CMake can not determine linker language for target: external_tetgen -- Generating done CMake Warning: Manually-specified variables were not used by the project:

ALE_APPLICATION
DELAUNAY_MESHING_APPLICATION
MKLSOLVER_INCLUDE_DIR
MKLSOLVER_LIB_DIR
MKL_SOLVERS_APPLICATION
PARMETIS_ROOT_DIR
TRILINOS_ROOT

-- Build files have been written to: /home/bilal/Kratos/cmake_build [ 4%] Built target zlib [ 5%] Built target zlibstatic make[2]: No rule to make target 'applications/PfemApplication/CMakeFiles/external_tetgen.dir/build'. Stop. CMakeFiles/Makefile2:812: recipe for target 'applications/PfemApplication/CMakeFiles/external_tetgen.dir/all' failed make[1]: [applications/PfemApplication/CMakeFiles/external_tetgen.dir/all] Error 2 make[1]: Waiting for unfinished jobs.... [ 13%] Built target superlu Makefile:116: recipe for target 'all' failed make: [all] Error 2 [ 2%] Built target zlib [ 2%] Built target minigzip [ 2%] Built target example [ 5%] Built target zlibstatic [ 6%] Built target example64 [ 6%] Built target minigzip64 [ 7%] Built target gidpost [ 27%] Built target KratosCore [ 32%] Built target Kratos [ 40%] Built target superlu [ 41%] Built target KratosExternalSolversApplication [ 53%] Built target KratosSolidMechanicsCore [ 55%] Built target KratosSolidMechanicsApplication make[2]: No rule to make target 'applications/PfemApplication/CMakeFiles/external_tetgen.dir/build'. Stop. CMakeFiles/Makefile2:812: recipe for target 'applications/PfemApplication/CMakeFiles/external_tetgen.dir/all' failed make[1]: [applications/PfemApplication/CMakeFiles/external_tetgen.dir/all] Error 2 Makefile:116: recipe for target 'all' failed make: *** [all] Error 2 I have attached my configure.sh file. congigure.txt

BilalTsinghua commented 6 years ago

The file attached is configure.sh,but I can't select it at there so I exchange it from .sh to .txt. The contents as followed:

!/bin/sh

this is an example file...please DO NOT MODIFY if you don't want to do it for everyone

to use it, copy it to another file and run it

additional compiler flags could be added customizing the corresponding var, for example

-DCMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS} -msse3 ". Note that the "defaults are already correctly coded"

so we should ass here only machine specific stuff

an effort is made to autodetect all of the libraries needed HOWEVER:

METIS_APPLICATION needs the var PARMETIS_ROOT_DIR to be specified by the user (not needed if the app is set to OFF)

TRILINOS_APPLICATION needs the var PARMETIS_ROOT_DIR to be specified by the user (not needed if the app is set to OFF)

MKL_SOLVERS_APPLICATION needs the var MKLSOLVER_INCLUDE_DIR and MKLSOLVER_LIB_DIR to be specified by the user (not needed if the app is set to OFF)

note that the MKLSOLVER_LIB_DIR should include /lib/em64t. This is needed as intel is changing location of mkl at every update of the compiler!!

the user should also note that the symbol "\" marks that the command continues on the next line. IT SHOULD ONLY BE FOLLOWED

BY the "ENTER" and NOT by any space!!

clear

you may want to decomment this the first time you compile

rm CMakeCache.txt rm *.cmake rm -rf CMakeFiles\

export BOOST_ROOT=/path/to/your/boost

cmake .. \ -DCMAKE_C_COMPILER=/usr/bin/gcc \ -DCMAKE_CXX_COMPILER=/usr/bin/g++ \ -DCMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS} -msse3 -std=c++11 " \ -DCMAKE_C_FLAGS="${CMAKE_C_FLAGS} -msse3 " \ -DBOOST_ROOT="/home/bilal/boost_1_68_0" \ -DPYTHON_EXECUTABLE="/usr/bin/python3" \ -DCMAKE_BUILD_TYPE=Release \ -DMESHING_APPLICATION=ON \ -DEXTERNAL_SOLVERS_APPLICATION=ON \ -DSOLID_MECHANICS_APPLICATION=ON \ -DFLUID_DYNAMICS_APPLICATION=ON \ -DCONVECTION_DIFFUSION_APPLICATION=ON \ -DDEM_APPLICATION=OFF \ -DSWIMMING_DEM_APPLICATION=OFF \ -DINCOMPRESSIBLE_FLUID_APPLICATION=OFF \ -DSTRUCTURAL_APPLICATION=OFF \ -DSTRUCTURAL_MECHANICS_APPLICATION=ON \ -DPFEM_APPLICATION=ON \ -DDELAUNAY_MESHING_APPLICATION=ON \ -DPFEM_FLUID_DYNAMICS_APPLICATION=ON \ -DCONSTITUTIVE_MODELS_APPLICATION=ON \ -DCONTACT_MECHANICS_APPLICATION=ON \ -DALE_APPLICATION=ON \ -DFSI_APPLICATION=ON \ -DMAPPING_APPLICATION=OFF \ -DOPENCL_APPLICATION=OFF \ -DMIXED_ELEMENT_APPLICATION=ON \ -DMKL_SOLVERS_APPLICATION=OFF \ -DMKLSOLVER_INCLUDE_DIR="/opt/intel/Compiler/11.1/072/mkl/include" \ -DMKLSOLVER_LIB_DIR="/opt/intel/Compiler/11.1/072/mkl/lib/em64t" \ -DMETIS_APPLICATION=OFF \ -DPARMETIS_ROOT_DIR="/home/fengzekang/compiled_libraries/ParMetis-3.1.1" \ -DTRILINOS_APPLICATION=OFF \ -DTRILINOS_ROOT="/home/fengzekang/compiled_libraries/trilinos-10.2.0" \ -DINSTALL_EMBEDDED_PYTHON=ON \ -DSHAPE_OPTIMIZATION_APPLICATION=OFF \ -DTOPOLOGY_OPTIMIZATION_APPLICATION=OFF \ -DHDF5_APPLICATION=OFF \

decomment this to have it verbose

make VERBOSE=1 -j4

make -j2 make install

josep-m-carbonell commented 6 years ago

Try to "make clean". It is still taking the CmakeFile of the old Pfem Apliccation. Also look into the configure.sh to detect some trailing white space. Delaunay Application is not detected as ON.

lluis-mv commented 6 years ago

Hey, I think this error is related to tetgen. (tetgen is not donwloaded automatically). In a terminal you may donwload these submodules by typing: "git submodule init git submodule update"

fengzekang commented 6 years ago

Hello, @josep-m-carbonell ,how to Delaunay Application in the configure.sh file. I add the -DDELAUNAY_MESHING_APPLICATION=ON But when I compile the file,there is no information showing that compiling Delaunay Application. And then I run the example Test_3D_Newtonian_Sloshing,some erorrs showed that Traceback (most recent call last): File "MainKratos.py", line 3, in import KratosMultiphysics.DelaunayMeshingApplication ImportError: No module named 'KratosMultiphysics.DelaunayMeshingApplication' KRATOS TERMINATED WITH ERROR So what should I do to add the DelaunayMeshingApplication? Best regards

josep-m-carbonell commented 6 years ago

cmake additions must be in the same line, so look at the configure.sh to have the corresponding \ before adding the Delaunay app and exist no extra space after the \ It must be compiled to be imported by python

fengzekang commented 6 years ago

Dear @josep-m-carbonell I think I have add the application in the configure.sh file,the configure.sh as followed: clear

you may want to decomment this the first time you compile

rm CMakeCache.txt rm *.cmake rm -rf CMakeFiles\

export BOOST_ROOT=/path/to/your/boost

cmake .. \ -DCMAKE_C_COMPILER=/usr/bin/gcc \ -DCMAKE_CXX_COMPILER=/usr/bin/g++ \ -DCMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS} -msse3 -std=c++11 " \ -DCMAKE_C_FLAGS="${CMAKE_C_FLAGS} -msse3 " \ -DBOOST_ROOT="/home/dongxueyang/Downloads/boost_1_61_0" \ -DPYTHON_EXECUTABLE="/usr/bin/python3" \ -DCMAKE_BUILD_TYPE=Release \ -DMESHING_APPLICATION=ON \ -DEXTERNAL_SOLVERS_APPLICATION=ON \ -DSOLID_MECHANICS_APPLICATION=ON \ -DFLUID_DYNAMICS_APPLICATION=ON \ -DCONVECTION_DIFFUSION_APPLICATION=ON \ -DDEM_APPLICATION=ON \ -DSWIMMING_DEM_APPLICATION=ON \ -DINCOMPRESSIBLE_FLUID_APPLICATION=OFF \ -DSTRUCTURAL_APPLICATION=OFF \ -DSTRUCTURAL_MECHANICS_APPLICATION=ON \ -DPFEM_APPLICATION=ON \ -DPFEM_FLUID_DYNAMICS_APPLICATION=ON \ -DDELAUNAY_MESHING_APPLICATION=ON \ -DCONSTITUTIVE_MODELS_APPLICATION=ON \ -DALE_APPLICATION=ON \ -DFSI_APPLICATION=ON \ -DMAPPING_APPLICATION=OFF \ -DOPENCL_APPLICATION=OFF \ -DMIXED_ELEMENT_APPLICATION=ON \ -DMKL_SOLVERS_APPLICATION=OFF \ -DMKLSOLVER_INCLUDE_DIR="/opt/intel/Compiler/11.1/072/mkl/include" \ -DMKLSOLVER_LIB_DIR="/opt/intel/Compiler/11.1/072/mkl/lib/em64t" \ -DMETIS_APPLICATION=OFF \ -DPARMETIS_ROOT_DIR="/home/fengzekang/compiled_libraries/ParMetis-3.1.1" \ -DTRILINOS_APPLICATION=OFF \ -DTRILINOS_ROOT="/home/fengzekang/compiled_libraries/trilinos-10.2.0" \ -DINSTALL_EMBEDDED_PYTHON=ON \ -DSHAPE_OPTIMIZATION_APPLICATION=OFF \ -DTOPOLOGY_OPTIMIZATION_APPLICATION=OFF \ -DHDF5_APPLICATION=ON \

decomment this to have it verbose

make VERBOSE=1 -j4

make -j4 make install

But there is not the Delaunay application in the compiling.Should I download any other software or package? Best regards

josep-m-carbonell commented 6 years ago

If you have alredy downloaded the submodule: git submodule init git submodule update

Pull (update) changes in master and try to add this two lines to the configure.sh

-DCONTAC_MECHANICS_APPLICATION=ON -DADD_DEPENDENT_APPLICATIONS=ON

If it doesn't work. Please, attach the text file with the compilation output to see if any error ocurrs during the compilation.

fengzekang commented 6 years ago

Dear @josep-m-carbonell After I add the commands -DCONTACT_MECHANICS_APPLICATION=ON -DADD_DEPENDENT_APPLICATIONS=ON ,contact_mechanics_application has been compiled,but cmake didn't find the ADD_DEPENDENT_APPLICATIONS In the terminal: CMake Warning: Manually-specified variables were not used by the project:

ADD_DEPENDENT_APPLICATIONS
ALE_APPLICATION
MKLSOLVER_INCLUDE_DIR
MKLSOLVER_LIB_DIR
MKL_SOLVERS_APPLICATION
PARMETIS_ROOT_DIR
TRILINOS_ROOT

It doesn't work.

josep-m-carbonell commented 6 years ago

cmake didn't find the ADD_DEPENDENT_APPLICATIONS, because you have not updated the Kratos branch via git, it is a new feature. You can delete ADD_DEPENDENT_APPLICATIONS if is not working now. Pfem application needs:

-DEXTERNAL_SOLVERS_APPLICATION=ON -DSOLID_MECHANICS_APPLICATION=ON -DCONSTITUTIVE_MODELS_APPLICATION=ON -DCONTACT_MECHANICS_APPLICATION=ON -DDELAUNAY_MESHING_APPLICATION=ON -DPFEM_APPLICATION=ON -DPFEM_FLUID_DYNAMICS_APPLICATION=ON

I think you have all of them in your configure.sh. If it compiles correctly, then, when you import KratosMultiphysics, or when you import KatosMultiphysics.DelaunayMeshingApplication from python, no error must appear. So please, attach the compilation text and the error you got to have a little bit more of information about what is happening.

fengzekang commented 6 years ago

Dear @josep-m-carbonell compile_configure.sh.txt I added all of them in the configure.sh,and the information as followed,we can see that there is also the cmake warnings: CMake Warning: Manually-specified variables were not used by the project:

ADD_DEPENDENT_APPLICATIONS
ALE_APPLICATION
DELAUNAY_MESHING_APPLICATION
MKLSOLVER_INCLUDE_DIR
MKLSOLVER_LIB_DIR
MKL_SOLVERS_APPLICATION
PARMETIS_ROOT_DIR
TRILINOS_ROOT

No errors occured.I can't find the reason. As what you said,I have updated the submodule in the Kratos use"git pull". Best regards.

josep-m-carbonell commented 6 years ago

You are right, it is very strange. Without delaunay application Pfem must not compile.

Take a look on Kratos/applications/CMakeLists.txt it must be like this one: CMakeLists.txt.zip

try to: make clean sh configure.sh

fengzekang commented 6 years ago

I tried to recompile with your suggestion,"make clean",and then "sh configure.sh",But cmake warning also includes:CMake Warning: Manually-specified variables were not used by the project:

ADD_DEPENDENT_APPLICATIONS
ALE_APPLICATION
DELAUNAY_MESHING_APPLICATION
MKLSOLVER_INCLUDE_DIR
MKLSOLVER_LIB_DIR
MKL_SOLVERS_APPLICATION
PARMETIS_ROOT_DIR
TRILINOS_ROOT

I think I can try it on another computer. Best regards

fengzekang commented 6 years ago

Dear @josep-m-carbonell Do you have time to deal with the problem with me?We can use the teamviewer.Do you have time help me check the problem? Best regards

josep-m-carbonell commented 6 years ago

Hi @fengzekang. Yes I have time. We can do it next week, on Monday. I'm in Barcelona, please send me an email and propose the hour. cpuigbo@cimne.upc.edu.

fengzekang commented 6 years ago

Dear @josep-m-carbonell
Ok,thanks for your help.I will send you my ID of teamviewer. Best regards

BilalTsinghua commented 6 years ago

Dear @josep-m-carbonell I think I have add the application in the configure.sh file,the configure.sh as followed: clear

you may want to decomment this the first time you compile

rm CMakeCache.txt rm *.cmake rm -rf CMakeFiles

export BOOST_ROOT=/path/to/your/boost

cmake ..
-DCMAKE_C_COMPILER=/usr/bin/gcc
-DCMAKE_CXX_COMPILER=/usr/bin/g++ -DCMAKE_CXX_FLAGS="${CMAKE_CXX_FLAGS} -msse3 -std=c++11 " -DCMAKE_C_FLAGS="${CMAKE_C_FLAGS} -msse3 " -DBOOST_ROOT="/home/dongxueyang/Downloads/boost_1_61_0" -DPYTHON_EXECUTABLE="/usr/bin/python3" -DCMAKE_BUILD_TYPE=Release -DMESHING_APPLICATION=ON -DEXTERNAL_SOLVERS_APPLICATION=ON -DSOLID_MECHANICS_APPLICATION=ON -DFLUID_DYNAMICS_APPLICATION=ON -DCONVECTION_DIFFUSION_APPLICATION=ON -DDEM_APPLICATION=ON
-DSWIMMING_DEM_APPLICATION=ON -DINCOMPRESSIBLE_FLUID_APPLICATION=OFF -DSTRUCTURAL_APPLICATION=OFF -DSTRUCTURAL_MECHANICS_APPLICATION=ON -DPFEM_APPLICATION=ON -DPFEM_FLUID_DYNAMICS_APPLICATION=ON -DDELAUNAY_MESHING_APPLICATION=ON -DCONSTITUTIVE_MODELS_APPLICATION=ON -DALE_APPLICATION=ON -DFSI_APPLICATION=ON -DMAPPING_APPLICATION=OFF -DOPENCL_APPLICATION=OFF
-DMIXED_ELEMENT_APPLICATION=ON
-DMKL_SOLVERS_APPLICATION=OFF -DMKLSOLVER_INCLUDE_DIR="/opt/intel/Compiler/11.1/072/mkl/include"
-DMKLSOLVER_LIB_DIR="/opt/intel/Compiler/11.1/072/mkl/lib/em64t"
-DMETIS_APPLICATION=OFF
-DPARMETIS_ROOT_DIR="/home/fengzekang/compiled_libraries/ParMetis-3.1.1" -DTRILINOS_APPLICATION=OFF
-DTRILINOS_ROOT="/home/fengzekang/compiled_libraries/trilinos-10.2.0" -DINSTALL_EMBEDDED_PYTHON=ON -DSHAPE_OPTIMIZATION_APPLICATION=OFF -DTOPOLOGY_OPTIMIZATION_APPLICATION=OFF -DHDF5_APPLICATION=ON

decomment this to have it verbose

make VERBOSE=1 -j4

make -j4 make install

But there is not the Delaunay application in the compiling.Should I download any other software or package? Best regards

josep-m-carbonell commented 6 years ago

Hello @BilalTsinghua, could you finally compile the Kratos with Pfem?

BilalTsinghua commented 6 years ago

@josep-m-carbonell yes i already complied it with Pfem Thanks for your help

josep-m-carbonell commented 6 years ago

You are welcome. I recommend you before running examples to update with last changes and compile again. In Kratos folder: git pull In cmake_build folder: sh configure.sh (with sudo if you have compiled the first time with sudo)

The compilation have to be fast this time.

BilalTsinghua commented 6 years ago

@josep-m-carbonell While compling configure.sh, i will face this error CMakeFiles/KratosPfemApplication.dir/custom_python/add_custom_bounding_to_python.cpp.o: file not recognized: File truncated collect2: error: ld returned 1 exit status applications/PfemApplication/CMakeFiles/KratosPfemApplication.dir/build.make:236: recipe for target 'applications/PfemApplication/CMakeFiles/CMakeRelink.dir/KratosPfemApplication.cpython-35m-x86_64-linux-gnu.so' failed make[2]: [applications/PfemApplication/CMakeFiles/CMakeRelink.dir/KratosPfemApplication.cpython-35m-x86_64-linux-gnu.so] Error 1 CMakeFiles/Makefile2:884: recipe for target 'applications/PfemApplication/CMakeFiles/KratosPfemApplication.dir/preinstall' failed make[1]: [applications/PfemApplication/CMakeFiles/KratosPfemApplication.dir/preinstall] Error 2 Makefile:133: recipe for target 'preinstall' failed make: *** [preinstall] Error 2

AND WHEN I RUN THE EXAMPLES I WILL THIS ERROR / | _` | _| \ | . \ | ( | | ( |_ \ |__| _,|__|_/ __/ Multi-Physics 6.0.0-4990161 Traceback (most recent call last): File "MainKratos.py", line 2, in import KratosMultiphysics.ExternalSolversApplication File "/home/bilal/Kratos/KratosMultiphysics/ExternalSolversApplication.py", line 2, in from KratosExternalSolversApplication import * ImportError: libf77blas.so.3: cannot open shared object file: No such file or directory KRATOS TERMINATED WITH ERROR

josep-m-carbonell commented 6 years ago

Something is wrong in your compilation. Try to clean the compilation and compike again: In cmake_build folder

make clean sh configure.sh

If it fails it means that your Kratos is not downloaded correctly in local directory. Look for information with git status.

BilalTsinghua commented 6 years ago

@josep-m-carbonell In cmake_build folder MAKE CLEAN means remove all the files in folder?

josep-m-carbonell commented 6 years ago

It removes compiled object files. If there is a broken file or an old version one you must remove it to force new compilation to generate it again.

BilalTsinghua commented 6 years ago

@josep-m-carbonell
I did it cmake_build folder make clean sh configure.sh

now i run the example with the command runkratos Mainkratos.py, it show the following error: | / |
' / | _` | _| \ | . \ | ( | | ( |_ \ |__| _,|__|_/ __/ Multi-Physics 6.0.0-4990161 Importing KratosExternalSolversApplication Initializing KratosExternalSolversApplication... Importing KratosPfemApplication 

 KRATOS| _ \/ _|___ _ __            
       |  _/  _/ -_) '  \            
       |_| |_| \___|_|_|_|APPLICATION

Initializing KratosPfemApplication ...
Importing KratosPfemFluidDynamicsApplication 

 KRATOS| _ \/ _|___ _ __ | __| |_  _(_)__| |         
       |  _/  _/ -_) '  \| _|| | || | / _` |         
       |_| |_| \___|_|_|_|_| |_|\_,_|_\__,_|DYNAMICS

Initializing KratosPfemFluidDynamicsApplication...
Importing KratosSolidMechanicsApplication 

 KRATOS/ __| ___| (_)__| |         
       \__ \/ _ \ | / _` |         
       |___/\___/_|_\__,_|MECHANICS

Initializing KratosSolidMechanicsApplication...
Wed Oct 17 15:59:21 2018 Traceback (most recent call last): File "MainKratos.py", line 9, in MainFluidPFEM.Solution().Run() File "/home/bilal/Kratos/applications/PfemFluidDynamicsApplication/python_scripts/MainFluidPFEM.py", line 37, in init parameter_file = open("ProjectParameters.json",'r') FileNotFoundError: [Errno 2] No such file or directory: 'ProjectParameters.json' KRATOS TERMINATED WITH ERROR

josep-m-carbonell commented 6 years ago

I attach you a case extracted from tests. Just go to the folder and:

python3 RunMainPfem.py

dam_break_2D.zip

loumalouomega commented 6 years ago

Did we solved this?

philbucher commented 5 years ago

Closing since inactive, pls reopen if otherwise