[OpenFOAM.org] OpenFOAM 2.3.0 on CentOS 6.5

Alhasan · October 7, 2015, 12:24

Dear Everyone,

I have followed the steps https://openfoamwiki.net/index.php/I...HEL#CentOS_6.5

step by step to install OpenFOAM 2.3 on Centos 6.7 and for some reason I am having problems in Allwmake (step 14), I have no clue why this is happening as none of the previous steps showed any errors,

When i run which gcc
/users/lm15898/OpenFOAM/ThirdParty-2.3.0/platforms/linux64/gcc-4.8.1/bin/gcc

when i run which g++
/users/lm15898/OpenFOAM/ThirdParty-2.3.0/platforms/linux64/gcc-4.8.1/bin/g++

First Error

Code:

make[2]: Entering directory `/space/lm15898/Softwares/OpenFOAM/ThirdParty-2.3.0/scotch_6.0.0/src/libscotchmetis'
gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -fPIC -I../../include -I../libscotch -c metis_graph_order.c -o metis_graph_order.o
gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -fPIC -I../../include -I../libscotch -c metis_graph_order_f.c -o metis_graph_order_f.o
gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -fPIC -I../../include -I../libscotch -c metis_graph_part.c -o metis_graph_part.o
gcc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -Drestrict=__restrict -shared -fPIC -I../../include -I../libscotch -c metis_graph_part_f.c -o metis_graph_part_f.o
gcc -shared -o libscotchmetis.so metis_graph_order.o metis_graph_order_f.o metis_graph_part.o metis_graph_part_f.o
echo libscotchmetis.so
libscotchmetis.so
make[2]: Leaving directory `/space/lm15898/Softwares/OpenFOAM/ThirdParty-2.3.0/scotch_6.0.0/src/libscotchmetis'
make[1]: Leaving directory `/space/lm15898/Softwares/OpenFOAM/ThirdParty-2.3.0/scotch_6.0.0/src/libscotchmetis'
make[1]: Entering directory `/space/lm15898/Softwares/OpenFOAM/ThirdParty-2.3.0/scotch_6.0.0/src/libscotchmetis'
make CC="gcc" SCOTCHLIB=ptscotch						\
					libscotchmetis.so
make[2]: Entering directory `/space/lm15898/Softwares/OpenFOAM/ThirdParty-2.3.0/scotch_6.0.0/src/libscotchmetis'
make[2]: `libscotchmetis.so' is up to date.
make[2]: Leaving directory `/space/lm15898/Softwares/OpenFOAM/ThirdParty-2.3.0/scotch_6.0.0/src/libscotchmetis'
cp metis.h ../../include
cp libscotchmetis.so ../../lib
make[1]: Leaving directory `/space/lm15898/Softwares/OpenFOAM/ThirdParty-2.3.0/scotch_6.0.0/src/libscotchmetis'
+ make prefix=/users/lm15898/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/scotch_6.0.0 libdir=/users/lm15898/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48DPOpt/lib install
mkdir /users/lm15898/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/scotch_6.0.0/bin
mkdir /users/lm15898/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/scotch_6.0.0/include
mkdir /users/lm15898/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/scotch_6.0.0/share
mkdir /users/lm15898/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/scotch_6.0.0/share/man
mkdir /users/lm15898/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/scotch_6.0.0/share/man/man1
cp -f ../bin/[agm]* /users/lm15898/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/scotch_6.0.0/bin
cp -f ../bin/d[agm]* /users/lm15898/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/scotch_6.0.0/bin
cp: cannot stat `../bin/d[agm]*': No such file or directory
make: [install] Error 1 (ignored)

Last Error

Code:

'/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/libphaseIncompressibleTurbulenceModels.so' is up to date.
+ wmake
SOURCE=twoPhaseEulerFoam.C ;  g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -O3  -DNoRepository -ftemplate-depth-100 -I/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/thermophysicalModels/basic/lnInclude -I/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/finiteVolume/lnInclude -I/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/transportModels/incompressible/lnInclude -I/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/TurbulenceModels/turbulenceModels/lnInclude -I/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/TurbulenceModels/incompressible/lnInclude -I/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/TurbulenceModels/phaseIncompressible/lnInclude -IphaseIncompressibleTurbulenceModels/lnInclude -IinterfacialModels/lnInclude -ItwoPhaseSystem/lnInclude -Iaveraging -IlnInclude -I. -I/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX/lnInclude   -fPIC -c $SOURCE -o Make/linux64Gcc48DPOpt/twoPhaseEulerFoam.o
In file included from twoPhaseEulerFoam.C:51:0:
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/finiteVolume/lnInclude/initContinuityErrs.H: In function ‘int main(int, char**)’:
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/finiteVolume/lnInclude/initContinuityErrs.H:37:8: warning: unused variable ‘cumulativeContErr’ [-Wunused-variable]
 scalar cumulativeContErr = 0;
        ^
In file included from twoPhaseEulerFoam.C:52:0:
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/finiteVolume/lnInclude/readTimeControls.H:38:8: warning: unused variable ‘maxDeltaT’ [-Wunused-variable]
 scalar maxDeltaT =
        ^
g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -O3  -DNoRepository -ftemplate-depth-100 -I/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/thermophysicalModels/basic/lnInclude -I/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/finiteVolume/lnInclude -I/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/transportModels/incompressible/lnInclude -I/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/TurbulenceModels/turbulenceModels/lnInclude -I/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/TurbulenceModels/incompressible/lnInclude -I/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/TurbulenceModels/phaseIncompressible/lnInclude -IphaseIncompressibleTurbulenceModels/lnInclude -IinterfacialModels/lnInclude -ItwoPhaseSystem/lnInclude -Iaveraging -IlnInclude -I. -I/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/OpenFOAM/lnInclude -I/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/src/OSspecific/POSIX/lnInclude   -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64Gcc48DPOpt/twoPhaseEulerFoam.o -L/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib \
	     -lfluidThermophysicalModels -lspecie -lturbulenceModels -lincompressibleTurbulenceModels -lphaseIncompressibleTurbulenceModels -lincompressibleTransportModels -lcompressibleTwoPhaseSystem -lcompressibleEulerianInterfacialModels -lfiniteVolume -lmeshTools -lOpenFOAM -ldl   -lm -o /users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/bin/twoPhaseEulerFoam
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Waitall'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_comm_null'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Abort'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_double'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Get_count'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Comm_create'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Group_incl'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Init'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_group_null'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Probe'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Comm_group'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Send'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Allreduce'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_op_min'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Buffer_detach'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Bsend'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_byte'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Irecv'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Recv'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Comm_free'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_comm_world'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Wait'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Test'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Isend'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Finalize'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `ompi_mpi_op_sum'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Buffer_attach'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Comm_size'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Group_free'
/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Comm_rank'
collect2: error: ld returned 1 exit status
make[2]: *** [/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/bin/twoPhaseEulerFoam] Error 1
make[1]: *** [twoPhaseEulerFoam] Error 2
make[1]: Target `application' not remade because of errors.
make: *** [multiphase] Error 2
make: Target `application' not remade because of errors.

someone please help me figure out why is installation is always aborted with errors, I have been on this for 2 weeks now so please help me.

If there is anything I should do to better explain my problem please do let me know.

Kind Regards,
Hasan K.J

wyldckat · October 8, 2015, 18:07

Quick answers:

Quote:

Originally Posted by Alhasan

Code:

cp: cannot stat `../bin/d[agm]*': No such file or directory
make: [install] Error 1 (ignored)

As the last line indicates: this error can be ignored.

Quote:

Originally Posted by Alhasan

Last Error

Code:

/users/lm15898/OpenFOAM/OpenFOAM-2.3.0/platforms/linux64Gcc48DPOpt/lib/openmpi-system/libPstream.so: undefined reference to `MPI_Waitall'

On the other hand, this cannot be ignored. This is related to the shell environment for Open-MPI not being activated. The instructions on the wiki assume the person following the instructions has "root access" to the system (for more details see here).

My guess is that in step #7, the following command is not working as intended:

Code:

module load openmpi-x86_64 || export PATH=$PATH:/usr/lib64/openmpi/bin

If you run these commands, what do they give you?

Code:

mpirun --version
which mpirun
mpicc --version
which mpicc

If most of these commands give you error messages or do not mention Open-MPI, then in step #7, you need to change this line:

Code:

source $HOME/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc WM_NCOMPPROCS=4 foamCompiler=ThirdParty WM_COMPILER=Gcc48 WM_MPLIB=SYSTEMOPENMPI

to this:

Code:

source $HOME/OpenFOAM/OpenFOAM-2.3.0/etc/bashrc WM_NCOMPPROCS=4  foamCompiler=ThirdParty WM_COMPILER=Gcc48 WM_MPLIB=OPENMPI

Alhasan · October 9, 2015, 10:10

Hi Bruno,

Thanks for your reply, ( I was playing with it suddenly it worked )

sorry for wasting your time, but I have been on this for 2 weeks just now suddenly worked but there are some errors in log will they bother me later on ?

for the commands you asked

Code:

bash-4.1$ mpirun --version
mpirun (Open MPI) 1.8.1

Code:

bash-4.1$ which mpirun
/usr/lib64/openmpi/bin/mpirun

Code:

bash-4.1$ mpicc --version
gcc (OpenFOAM) 4.8.1

Code:

bash-4.1$ which mpicc
/usr/lib64/openmpi/bin/mpicc

and I have this error with ParaView any suggestion as to what its saying and how to rectify it

Code:

[ 11%] Building CXX object VTK/Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGL.dir/vtkXRenderWindowInteractor.cxx.o
[ 11%] Building CXX object VTK/Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGL.dir/vtkXOpenGLRenderWindow.cxx.o
In file included from /usr/include/GL/glx.h:333:0,
                 from /users/lm15898/OpenFOAM/ThirdParty-2.3.0/ParaView-4.1.0/VTK/Rendering/OpenGL/vtkXOpenGLRenderWindow.cxx:31:
/usr/include/GL/glxext.h:480:143: error: ‘GLintptr’ has not been declared
 typedef void ( *PFNGLXCOPYBUFFERSUBDATANVPROC) (Display *dpy, GLXContext readCtx, GLXContext writeCtx, GLenum readTarget, GLenum writeTarget, GLintptr readOffset, GLintptr writeOffset, GLsizeiptr size);
                                                                                                                                               ^
/usr/include/GL/glxext.h:480:164: error: ‘GLintptr’ has not been declared
 typedef void ( *PFNGLXCOPYBUFFERSUBDATANVPROC) (Display *dpy, GLXContext readCtx, GLXContext writeCtx, GLenum readTarget, GLenum writeTarget, GLintptr readOffset, GLintptr writeOffset, GLsizeiptr size);
                                                                                                                                                                    ^
/usr/include/GL/glxext.h:480:186: error: ‘GLsizeiptr’ has not been declared
 typedef void ( *PFNGLXCOPYBUFFERSUBDATANVPROC) (Display *dpy, GLXContext readCtx, GLXContext writeCtx, GLenum readTarget, GLenum writeTarget, GLintptr readOffset, GLintptr writeOffset, GLsizeiptr size);
                                                                                                                                                                                          ^
/usr/include/GL/glxext.h:481:148: error: ‘GLintptr’ has not been declared
 typedef void ( *PFNGLXNAMEDCOPYBUFFERSUBDATANVPROC) (Display *dpy, GLXContext readCtx, GLXContext writeCtx, GLuint readBuffer, GLuint writeBuffer, GLintptr readOffset, GLintptr writeOffset, GLsizeiptr size);
                                                                                                                                                    ^
/usr/include/GL/glxext.h:481:169: error: ‘GLintptr’ has not been declared
 typedef void ( *PFNGLXNAMEDCOPYBUFFERSUBDATANVPROC) (Display *dpy, GLXContext readCtx, GLXContext writeCtx, GLuint readBuffer, GLuint writeBuffer, GLintptr readOffset, GLintptr writeOffset, GLsizeiptr size);
                                                                                                                                                                         ^
/usr/include/GL/glxext.h:481:191: error: ‘GLsizeiptr’ has not been declared
 typedef void ( *PFNGLXNAMEDCOPYBUFFERSUBDATANVPROC) (Display *dpy, GLXContext readCtx, GLXContext writeCtx, GLuint readBuffer, GLuint writeBuffer, GLintptr readOffset, GLintptr writeOffset, GLsizeiptr size);
                                                                                                                                                                                               ^
make[2]: *** [VTK/Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGL.dir/vtkXOpenGLRenderWindow.cxx.o] Error 1
make[1]: *** [VTK/Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGL.dir/all] Error 2
make: *** [all] Error 2
    ---
    Installation complete for paraview-4.1.0
    Set environment variables:

        export ParaView_DIR=/users/lm15898/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0
        export PATH=$ParaView_DIR/bin:$PATH
        export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-4.1
    ---

Done

Thanks again,
Hasan K.J

wyldckat · October 10, 2015, 05:22

Quick answer: That's a bit strange... but I know how to fix it. Run the following commands:

Code:

cd $WM_THIRD_PARTY_DIR
sed -i -e 's=//#define GLX_GLXEXT_LEGACY=#define GLX_GLXEXT_LEGACY=' ParaView-4.1.0/VTK/Rendering/OpenGL/vtkXOpenGLRenderWindow.cxx
./makeParaView4 -qmake $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/qt-4.8.4/bin/qmake -mpi -python > log.makePV 2>&1

If all goes well, it should build ParaView 4.1.0 without problems.

Alhasan · October 14, 2015, 13:10

Hi Bruno,

Thanks for your reply and sorry for the late response,

I tried what you suggested and It kind of worked and got me believing everything was going fine until this error that appeared after 98%

Code:

Linking CXX shared library ../../lib/libQuadView.so
[ 97%] Built target QuadView
[ 97%] Generating Documentation HTMLs from xmls
Processing wiki sources
Processing wiki filters
Processing wiki writers
Processing wiki readers
[ 97%] Compiling Qt help project UncertaintyRendering.qhp
Building up file structure...
Insert custom filters...
Insert help data for filter section (1 of 1)...
Insert files...
Warning: The file /users/lm15898/OpenFOAM/ThirdParty-2.3.0/build/linux64Gcc48/ParaView-4.1.0/Plugins/UncertaintyRendering/doc/*.html does not exist! Skipping it.
Warning: The file /users/lm15898/OpenFOAM/ThirdParty-2.3.0/build/linux64Gcc48/ParaView-4.1.0/Plugins/UncertaintyRendering/doc/*.css does not exist! Skipping it.
Warning: The file /users/lm15898/OpenFOAM/ThirdParty-2.3.0/build/linux64Gcc48/ParaView-4.1.0/Plugins/UncertaintyRendering/doc/*.png does not exist! Skipping it.
Warning: The file /users/lm15898/OpenFOAM/ThirdParty-2.3.0/build/linux64Gcc48/ParaView-4.1.0/Plugins/UncertaintyRendering/doc/*.jpg does not exist! Skipping it.
Insert contents...
Insert indices...
Documentation successfully generated.
[ 97%] Generating UncertaintyRendering_doc.h
-- Generate module: UncertaintyRendering
[ 97%] Generating vtkUncertaintySurfacePainter_vs.cxx
[ 97%] Generating vtkUncertaintySurfacePainter_fs.cxx
[ 97%] CS Wrapping - generating vtkUncertaintySurfacePainterClientServer.cxx
[ 97%] CS Wrapping - generating vtkUncertaintySurfaceDefaultPainterClientServer.cxx
[ 97%] CS Wrapping - generating vtkUncertaintySurfaceRepresentationClientServer.cxx
[ 97%] CS Wrapping - generating vtkSMUncertaintySurfaceRepresentationProxyClientServer.cxx
[ 97%] Generating vtkSMXML_UncertaintyRendering.h
-- Generate module: vtkUncertaintyRendering
-- Generate module: vtkUncertaintyRenderingExtension
Scanning dependencies of target UncertaintyRendering
[ 97%] Building CXX object Plugins/UncertaintyRendering/CMakeFiles/UncertaintyRendering.dir/vtkUncertaintySurfacePainter.cxx.o
[ 97%] Building CXX object Plugins/UncertaintyRendering/CMakeFiles/UncertaintyRendering.dir/vtkUncertaintySurfaceDefaultPainter.cxx.o
[ 97%] Building CXX object Plugins/UncertaintyRendering/CMakeFiles/UncertaintyRendering.dir/vtkUncertaintySurfaceRepresentation.cxx.o
[ 97%] Building CXX object Plugins/UncertaintyRendering/CMakeFiles/UncertaintyRendering.dir/vtkSMUncertaintySurfaceRepresentationProxy.cxx.o
[ 97%] Building CXX object Plugins/UncertaintyRendering/CMakeFiles/UncertaintyRendering.dir/vtkUncertaintySurfacePainter_vs.cxx.o
[ 98%] Building CXX object Plugins/UncertaintyRendering/CMakeFiles/UncertaintyRendering.dir/vtkUncertaintySurfacePainter_fs.cxx.o
[ 98%] Building CXX object Plugins/UncertaintyRendering/CMakeFiles/UncertaintyRendering.dir/vtkUncertaintySurfacePainterClientServer.cxx.o
[ 98%] Building CXX object Plugins/UncertaintyRendering/CMakeFiles/UncertaintyRendering.dir/vtkUncertaintySurfaceDefaultPainterClientServer.cxx.o
[ 98%] Building CXX object Plugins/UncertaintyRendering/CMakeFiles/UncertaintyRendering.dir/vtkUncertaintySurfaceRepresentationClientServer.cxx.o
[ 98%] Building CXX object Plugins/UncertaintyRendering/CMakeFiles/UncertaintyRendering.dir/vtkSMUncertaintySurfaceRepresentationProxyClientServer.cxx.o
[ 98%] Building CXX object Plugins/UncertaintyRendering/CMakeFiles/UncertaintyRendering.dir/UncertaintyRenderingInit.cxx.o
[ 98%] Building CXX object Plugins/UncertaintyRendering/CMakeFiles/UncertaintyRendering.dir/UncertaintyRendering_Plugin.cxx.o
Linking CXX shared library ../../lib/libUncertaintyRendering.so
[ 98%] Built target UncertaintyRendering
[ 98%] Generating Documentation HTMLs from xmls
Processing wiki sources
Processing wiki filters
Processing wiki writers
Processing wiki readers
[ 98%] Generating qrc_ArrowGlyph.cxx
[ 98%] Compiling Qt help project ArrowGlyph.qhp
Building up file structure...
Insert custom filters...
Insert help data for filter section (1 of 1)...
Insert files...
Warning: The file /users/lm15898/OpenFOAM/ThirdParty-2.3.0/build/linux64Gcc48/ParaView-4.1.0/Plugins/ArrowGlyph/doc/*.css does not exist! Skipping it.
Warning: The file /users/lm15898/OpenFOAM/ThirdParty-2.3.0/build/linux64Gcc48/ParaView-4.1.0/Plugins/ArrowGlyph/doc/*.png does not exist! Skipping it.
Warning: The file /users/lm15898/OpenFOAM/ThirdParty-2.3.0/build/linux64Gcc48/ParaView-4.1.0/Plugins/ArrowGlyph/doc/*.jpg does not exist! Skipping it.
Insert contents...
Insert indices...
Documentation successfully generated.
[ 98%] Generating ArrowGlyph_doc.h
-- Generate module: ArrowGlyph
[ 98%] CS Wrapping - generating vtkArrowGlyphFilterClientServer.cxx
[ 98%] Generating vtkSMXML_ArrowGlyph.h
-- Generate module: vtkArrowGlyphFilter
[ 98%] Generating moc_ArrowGlyph_Plugin.cxx
Scanning dependencies of target ArrowGlyph
[ 98%] Building CXX object Plugins/ArrowGlyph/CMakeFiles/ArrowGlyph.dir/qrc_ArrowGlyph.cxx.o
[ 98%] Building CXX object Plugins/ArrowGlyph/CMakeFiles/ArrowGlyph.dir/vtkArrowGlyphFilter.cxx.o
[ 98%] Building CXX object Plugins/ArrowGlyph/CMakeFiles/ArrowGlyph.dir/vtkArrowGlyphFilterClientServer.cxx.o
[ 98%] Building CXX object Plugins/ArrowGlyph/CMakeFiles/ArrowGlyph.dir/ArrowGlyphInit.cxx.o
[ 98%] Building CXX object Plugins/ArrowGlyph/CMakeFiles/ArrowGlyph.dir/ArrowGlyph_Plugin.cxx.o
[ 98%] Building CXX object Plugins/ArrowGlyph/CMakeFiles/ArrowGlyph.dir/moc_ArrowGlyph_Plugin.cxx.o
Linking CXX shared library ../../lib/libArrowGlyph.so
[ 98%] Built target ArrowGlyph
[ 98%] Building NVCC (Device) object Plugins/SciberQuestToolKit/SciberQuest/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_CUDAConvolutionDriver.cu.o
/space/lm15898/Softwares/OpenFOAM/ThirdParty-2.3.0/platforms/linux64/gcc-4.8.1/include/c++/4.8.1/cstdlib(178): error: identifier "__int128" is undefined

/space/lm15898/Softwares/OpenFOAM/ThirdParty-2.3.0/platforms/linux64/gcc-4.8.1/include/c++/4.8.1/cstdlib(179): error: identifier "__int128" is undefined

/space/lm15898/Softwares/OpenFOAM/ThirdParty-2.3.0/platforms/linux64/gcc-4.8.1/include/c++/4.8.1/ext/atomicity.h(47): error: identifier "__atomic_fetch_add" is undefined

/space/lm15898/Softwares/OpenFOAM/ThirdParty-2.3.0/platforms/linux64/gcc-4.8.1/include/c++/4.8.1/ext/atomicity.h(51): error: identifier "__atomic_fetch_add" is undefined

/space/lm15898/Softwares/OpenFOAM/ThirdParty-2.3.0/platforms/linux64/gcc-4.8.1/include/c++/4.8.1/iomanip(64): error: expected an expression

/space/lm15898/Softwares/OpenFOAM/ThirdParty-2.3.0/platforms/linux64/gcc-4.8.1/include/c++/4.8.1/iomanip(94): error: expected an expression

/space/lm15898/Softwares/OpenFOAM/ThirdParty-2.3.0/platforms/linux64/gcc-4.8.1/include/c++/4.8.1/iomanip(125): error: expected an expression

/space/lm15898/Softwares/OpenFOAM/ThirdParty-2.3.0/platforms/linux64/gcc-4.8.1/include/c++/4.8.1/iomanip(193): error: expected an expression

/space/lm15898/Softwares/OpenFOAM/ThirdParty-2.3.0/platforms/linux64/gcc-4.8.1/include/c++/4.8.1/iomanip(223): error: expected an expression

/users/lm15898/OpenFOAM/ThirdParty-2.3.0/ParaView-4.1.0/VTK/Common/Core/vtkObject.h(53): warning: extra ";" ignored

/users/lm15898/OpenFOAM/ThirdParty-2.3.0/ParaView-4.1.0/VTK/Common/Core/vtkAbstractArray.h(62): warning: extra ";" ignored

/users/lm15898/OpenFOAM/ThirdParty-2.3.0/ParaView-4.1.0/VTK/Common/Core/vtkDataArray.h(48): warning: extra ";" ignored

9 errors detected in the compilation of "/tmp/tmpxft_00001918_00000000-4_CUDAConvolutionDriver.cpp1.ii".
CMake Error at cuda_compile_generated_CUDAConvolutionDriver.cu.o.cmake:264 (message):
  Error generating file
  /users/lm15898/OpenFOAM/ThirdParty-2.3.0/build/linux64Gcc48/ParaView-4.1.0/Plugins/SciberQuestToolKit/SciberQuest/CMakeFiles/cuda_compile.dir//./cuda_compile_generated_CUDAConvolutionDriver.cu.o


make[2]: *** [Plugins/SciberQuestToolKit/SciberQuest/CMakeFiles/cuda_compile.dir/./cuda_compile_generated_CUDAConvolutionDriver.cu.o] Error 1
make[1]: *** [Plugins/SciberQuestToolKit/SciberQuest/CMakeFiles/vtkSciberQuest.dir/all] Error 2
make: *** [all] Error 2
    ---
    Installation complete for paraview-4.1.0
    Set environment variables:

        export ParaView_DIR=/users/lm15898/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0
        export PATH=$ParaView_DIR/bin:$PATH
        export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-4.1
    ---

Done

can you please suggest me something to workaround this issue.

Kind Regards,
Hasan K.J

wyldckat · October 17, 2015, 08:03

Hi Hasan,

Fortunately I'm already familiar with this issue... CUDA can be a pain sometimes... let me search my notes... oops, I didn't have this on my notes (Related issues to ParaView with OpenFOAM - Fixes and solutions), so I had to Google for it. I've updated my notes as well now.

I'll quote the solution:

Quote:

Originally Posted by wyldckat

Assuming you don't need CUDA, please follow these steps:

Code:

cd $WM_THIRD_PARTY_DIR

sed -i -e 's=CUDA_FOUND=OFF=g' ParaView-4.1.0/Plugins/SciberQuestToolKit/SciberQuest/CMakeLists.txt

Then run:

Code:

./makeParaView4 -qmake $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/qt-4.8.4/bin/qmake -mpi -python > log.makePV 2>&1

Best regards,
Bruno

Hrushi · February 24, 2016, 14:02

Hi Bruno,

I am trying to build OpenFOAM-2.3.1 on CentOS-6.6. I have followed the steps given in https://openfoamwiki.net/index.php/I...HEL#CentOS_6.5
At step 7, for the command

Code:

module load openmpi-i386 || export PATH=$PATH:/usr/lib/openmpi/bin

I got error as

Code:

-bash: module: command not found

I went ahead and followed next steps. I got an error while building OpenFOAM. But icoFoam -help worked correctly. I have attached log file.

Then I found this post http://www.cfd-online.com/Forums/ope...tml#post567222 As post suggest, the following command is not working as intended

Code:

module load openmpi-x86_64 || export PATH=$PATH:/usr/lib64/openmpi/bin

So I went ahead with changes proposed in that post.

Code:

source $HOME/OpenFOAM/OpenFOAM-2.3.1/etc/bashrc WM_NCOMPPROCS=4 foamCompiler=ThirdParty WM_COMPILER=Gcc48 WM_MPLIB=OPENMPI

Now there are no errors at least in log file. I tested the installation for icoFoam as well as interFoam tutorial (damBreak parallel processing) case with foamJob command. Everything is working perfectly.

For building ParaView, I got the error at Step 16, i.e., while building qt-4.8.6. Please see the log file for the same. How can we get around this?

Bashar · February 26, 2016, 16:50

Hi

I am following the instruction for the installation on Centos 6.5. I got an error message for the step 17 :

ERROR: ParaView not found in /home/bashar/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0

I hope someone have any suggestions for me.

Edit: I start with a new setup but this time on Centos6.7, and I followed the instructions for installing OpenFoam2.4 on Centos 6.6 .Unfortunately I got exactly the same error message regarding the para-view!

[bashar@basharhpc PV4Readers]$ ./Allwmake
ERROR: ParaView not found in /home/bashar/OpenFOAM/ThirdParty-2.4.0/platforms/linux64Gcc48/ParaView-4.1.

wyldckat · March 13, 2016, 18:50

Quick answers:

@Hrushi:

Quote:

Originally Posted by Hrushi

For building ParaView, I got the error at Step 16, i.e., while building qt-4.8.6. Please see the log file for the same. How can we get around this?

I suspect that you do not have administrative powers to properly install the necessary packages in the machine you are using, because the error messages that you described indicate that:

Either you did not properly follow the installation instructions, because the system Open-MPI should have worked as intended, if you had done steps #1 to #4; or you don't have administrative powers.
The error message that Qt gave when building usually occur when either the graphics card drivers are not properly installed or if the machine is being used remotely via SSH.

@Bashar1978:

Quote:

Originally Posted by Bashar1978

[bashar@basharhpc PV4Readers]$ ./Allwmake
ERROR: ParaView not found in /home/bashar/OpenFOAM/ThirdParty-2.4.0/platforms/linux64Gcc48/ParaView-4.1.

Please run these commands:

Code:

cd $WM_THIRD_PARTY_DIR
gzip < mkqt.log > mkqt.log.gz
gzip < log.makePV > log.makePV.gz

pwd

And then attach the files "mkqt.log.gz" and "log.makePV.gz" to your next post. The last command will tell you where the files are located.

H3000 · December 2, 2016, 06:52

Dear All,

when installing OpenFOAM2.3.0 on CentOS 6.7, following the instructions (https://openfoamwiki.net/index.php/I...HEL#CentOS_6.5), I faced the same Error at step #17 as described here:

Quote:

Originally Posted by Alhasan

Hi Bruno,

Thanks for your reply, ( I was playing with it suddenly it worked )

sorry for wasting your time, but I have been on this for 2 weeks just now suddenly worked but there are some errors in log will they bother me later on ?

for the commands you asked

Code:

bash-4.1$ mpirun --version
mpirun (Open MPI) 1.8.1

Code:

bash-4.1$ which mpirun
/usr/lib64/openmpi/bin/mpirun

Code:

bash-4.1$ mpicc --version
gcc (OpenFOAM) 4.8.1

Code:

bash-4.1$ which mpicc
/usr/lib64/openmpi/bin/mpicc

and I have this error with ParaView any suggestion as to what its saying and how to rectify it

Code:

[ 11%] Building CXX object VTK/Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGL.dir/vtkXRenderWindowInteractor.cxx.o
[ 11%] Building CXX object VTK/Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGL.dir/vtkXOpenGLRenderWindow.cxx.o
In file included from /usr/include/GL/glx.h:333:0,
                 from /users/lm15898/OpenFOAM/ThirdParty-2.3.0/ParaView-4.1.0/VTK/Rendering/OpenGL/vtkXOpenGLRenderWindow.cxx:31:
/usr/include/GL/glxext.h:480:143: error: ‘GLintptr’ has not been declared
 typedef void ( *PFNGLXCOPYBUFFERSUBDATANVPROC) (Display *dpy, GLXContext readCtx, GLXContext writeCtx, GLenum readTarget, GLenum writeTarget, GLintptr readOffset, GLintptr writeOffset, GLsizeiptr size);
                                                                                                                                               ^
/usr/include/GL/glxext.h:480:164: error: ‘GLintptr’ has not been declared
 typedef void ( *PFNGLXCOPYBUFFERSUBDATANVPROC) (Display *dpy, GLXContext readCtx, GLXContext writeCtx, GLenum readTarget, GLenum writeTarget, GLintptr readOffset, GLintptr writeOffset, GLsizeiptr size);
                                                                                                                                                                    ^
/usr/include/GL/glxext.h:480:186: error: ‘GLsizeiptr’ has not been declared
 typedef void ( *PFNGLXCOPYBUFFERSUBDATANVPROC) (Display *dpy, GLXContext readCtx, GLXContext writeCtx, GLenum readTarget, GLenum writeTarget, GLintptr readOffset, GLintptr writeOffset, GLsizeiptr size);
                                                                                                                                                                                          ^
/usr/include/GL/glxext.h:481:148: error: ‘GLintptr’ has not been declared
 typedef void ( *PFNGLXNAMEDCOPYBUFFERSUBDATANVPROC) (Display *dpy, GLXContext readCtx, GLXContext writeCtx, GLuint readBuffer, GLuint writeBuffer, GLintptr readOffset, GLintptr writeOffset, GLsizeiptr size);
                                                                                                                                                    ^
/usr/include/GL/glxext.h:481:169: error: ‘GLintptr’ has not been declared
 typedef void ( *PFNGLXNAMEDCOPYBUFFERSUBDATANVPROC) (Display *dpy, GLXContext readCtx, GLXContext writeCtx, GLuint readBuffer, GLuint writeBuffer, GLintptr readOffset, GLintptr writeOffset, GLsizeiptr size);
                                                                                                                                                                         ^
/usr/include/GL/glxext.h:481:191: error: ‘GLsizeiptr’ has not been declared
 typedef void ( *PFNGLXNAMEDCOPYBUFFERSUBDATANVPROC) (Display *dpy, GLXContext readCtx, GLXContext writeCtx, GLuint readBuffer, GLuint writeBuffer, GLintptr readOffset, GLintptr writeOffset, GLsizeiptr size);
                                                                                                                                                                                               ^
make[2]: *** [VTK/Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGL.dir/vtkXOpenGLRenderWindow.cxx.o] Error 1
make[1]: *** [VTK/Rendering/OpenGL/CMakeFiles/vtkRenderingOpenGL.dir/all] Error 2
make: *** [all] Error 2
    ---
    Installation complete for paraview-4.1.0
    Set environment variables:

        export ParaView_DIR=/users/lm15898/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0
        export PATH=$ParaView_DIR/bin:$PATH
        export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-4.1
    ---

Done

Thanks again,
Hasan K.J

Applying the provided solution to this problem, the building of paraview progressed, but I still get this error message:

Code:

[ 21%] Building CXX object VTK/IO/Geometry/CMakeFiles/vtkIOGeometry.dir/vtkSTLReader.cxx.o
/home/RN8000/OpenFOAM/ThirdParty-2.3.0/ParaView-4.1.0/VTK/IO/Geometry/vtkSTLReader.cxx:241:6: error: prototype for ‘bool vtkSTLReader::ReadBinarySTL(FILE*, vtkPoints*, vtkCellArray*)’ does not match any in class ‘vtkSTLReader’
 bool vtkSTLReader::ReadBinarySTL(FILE *fp, vtkPoints *newPts,
      ^
In file included from /home/RN8000/OpenFOAM/ThirdParty-2.3.0/ParaView-4.1.0/VTK/IO/Geometry/vtkSTLReader.cxx:15:0:
/home/RN8000/OpenFOAM/ThirdParty-2.3.0/ParaView-4.1.0/VTK/IO/Geometry/vtkSTLReader.h:95:7: error: candidate is: int vtkSTLReader::ReadBinarySTL(FILE*, vtkPoints*, vtkCellArray*)
   int ReadBinarySTL(FILE *fp, vtkPoints*, vtkCellArray*);
       ^
/home/RN8000/OpenFOAM/ThirdParty-2.3.0/ParaView-4.1.0/VTK/IO/Geometry/vtkSTLReader.cxx:336:6: error: prototype for ‘bool vtkSTLReader::ReadASCIISTL(FILE*, vtkPoints*, vtkCellArray*, vtkFloatArray*)’ does not match any in class ‘vtkSTLReader’
 bool vtkSTLReader::ReadASCIISTL(FILE *fp, vtkPoints *newPts,
      ^
In file included from /home/RN8000/OpenFOAM/ThirdParty-2.3.0/ParaView-4.1.0/VTK/IO/Geometry/vtkSTLReader.cxx:15:0:
/home/RN8000/OpenFOAM/ThirdParty-2.3.0/ParaView-4.1.0/VTK/IO/Geometry/vtkSTLReader.h:96:7: error: candidate is: int vtkSTLReader::ReadASCIISTL(FILE*, vtkPoints*, vtkCellArray*, vtkFloatArray*)
   int ReadASCIISTL(FILE *fp, vtkPoints*, vtkCellArray*,
       ^
make[2]: *** [VTK/IO/Geometry/CMakeFiles/vtkIOGeometry.dir/vtkSTLReader.cxx.o] Error 1
make[1]: *** [VTK/IO/Geometry/CMakeFiles/vtkIOGeometry.dir/all] Error 2
make: *** [all] Error 2
    ---
    Installation complete for paraview-4.1.0
    Set environment variables:

        export ParaView_DIR=/home/RN8000/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0
        export PATH=$ParaView_DIR/bin:$PATH
        export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-4.1
    ---

Done

I also attached the complete log file to his post.
Would be great to get some help on that.

Cheers,
Christian

wyldckat · December 3, 2016, 16:00

Greetings Christian,

The error actually happens earlier than that, it's this one:

Code:

Linking C shared module ../../../lib/site-packages/mpi4py/MPI.so
CMakeFiles/mpi4py.MPI.dir/src/MPI.c.o: In function `OPENMPI_dlopen_libmpi':
MPI.c:(.text+0x6eb1): undefined reference to `dlopen'
MPI.c:(.text+0x6ecd): undefined reference to `dlopen'
MPI.c:(.text+0x6ee3): undefined reference to `dlopen'
MPI.c:(.text+0x6ef9): undefined reference to `dlopen'
CMakeFiles/mpi4py.MPI.dir/src/MPI.c.o: In function `__pyx_pf_6mpi4py_3MPI_16Init':
MPI.c:(.text+0x1342b): undefined reference to `dlopen'
CMakeFiles/mpi4py.MPI.dir/src/MPI.c.o:MPI.c:(.text+0x1354d): more undefined references to `dlopen' follow
collect2: error: ld returned 1 exit status
make[2]: *** [lib/site-packages/mpi4py/MPI.so] Error 1
make[1]: *** [ThirdParty/mpi4py/vtkmpi4py/CMakeFiles/mpi4py.MPI.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....

This error is fixed as instructed in step #17:

Quote:

17. Now, in order to build ParaView 4.1.0 that comes with OpenFOAM, we need to first apply a fix and then we can build with both MPI and Python support:

Code:

cd $WM_THIRD_PARTY_DIR/ParaView-4.1.0
wget http://www.paraview.org/pipermail/paraview/attachments/20140210/464496cc/attachment.bin -O Fix.patch
patch -p1 < Fix.patch
cd ..

Which means that the file "Fix.patch" that should be located at "$WM_THIRD_PARTY_DIR/ParaView-4.1.0" is possibly broken or the patch command did not work as intended.
Please check the contents of that folder "ParaView-4.1.0" and see if the file "Fix.patch" exists and has the following content:

Code:

diff --git a/ThirdParty/mpi4py/vtkmpi4py/CMakeLists.txt b/ThirdParty/mpi4py/vtkmpi4py/CMakeLists.txt
index 2e6dc66..7d5380c 100644
--- a/ThirdParty/mpi4py/vtkmpi4py/CMakeLists.txt
+++ b/ThirdParty/mpi4py/vtkmpi4py/CMakeLists.txt
@@ -165,8 +165,9 @@ SET_TARGET_PROPERTIES(
   RUNTIME_OUTPUT_DIRECTORY "${mpi4py_BINARY_DIR}"
   LINKER_LANGUAGE C
   )
-TARGET_LINK_LIBRARIES(mpi4py.MPI ${PYTHON_LIBRARY})
-TARGET_LINK_LIBRARIES(mpi4py.MPI ${MPI_C_LIBRARIES})
+TARGET_LINK_LIBRARIES(mpi4py.MPI ${PYTHON_LIBRARY}
+                                 ${MPI_C_LIBRARIES}
+                                 ${CMAKE_DL_LIBS})
 
 
 # --- mpi4py.MPE ---

If it doesn't have this, then it's because the wget command failed.
Either manually copy-paste these contents to that file or download the file that is indicated in the link that is to the right of the wget command.
Then run the patch command, as instructed in the wiki and shown above.

Once the patch is applied, you can run makeParaView4 once again.

Best regards,
Bruno

H3000 · December 5, 2016, 04:58

Hi Bruno,

thanks for your reply and your help.
I checked the content of the ParaView-4.1.0 folder, and apparently the Fix.patch file does exist with the exact content you described in your post. Do you think there could be an other source of the error you mentioned?

Cheers,
Christian

wyldckat · December 27, 2016, 12:34

Quick answer: Sorry for the late reply.
I don't know if you've managed to solve the problem, but if you haven't, then I need to know what error message you get when you run the following commands:

Code:

cd $WM_THIRD_PARTY_DIR/ParaView-4.1.0
patch -p1 < Fix.patch

If the last command gives you a message something like "do you want to reverse this patch", then type 'N' for no. On the other hand, if it doesn't give any error message and simply states that the patch has been applied, then you should be able to proceed with the installation instructions.

H3000 · January 4, 2017, 05:01

Hi Bruno,

thanks for your help. I executed the commands you mentioned in your post and got the following

Code:

[RN8000@localhost ParaView-4.1.0]$ patch -p1 < Fix.patch
patching file ThirdParty/mpi4py/vtkmpi4py/CMakeLists.txt
Reversed (or previously applied) patch detected!  Assume -R? [n] n
Apply anyway? [n] y
Hunk #1 FAILED at 165.
1 out of 1 hunk FAILED -- saving rejects to file ThirdParty/mpi4py/vtkmpi4py/CMakeLists.txt.rej

The CMakeLists.txt.rej contains the following:

Code:

--- ThirdParty/mpi4py/vtkmpi4py/CMakeLists.txt
+++ ThirdParty/mpi4py/vtkmpi4py/CMakeLists.txt
@@ -165,8 +165,9 @@
   RUNTIME_OUTPUT_DIRECTORY "${mpi4py_BINARY_DIR}"
   LINKER_LANGUAGE C
   )
-TARGET_LINK_LIBRARIES(mpi4py.MPI ${PYTHON_LIBRARY})
-TARGET_LINK_LIBRARIES(mpi4py.MPI ${MPI_C_LIBRARIES})
+TARGET_LINK_LIBRARIES(mpi4py.MPI ${PYTHON_LIBRARY}
+                                 ${MPI_C_LIBRARIES}
+                                 ${CMAKE_DL_LIBS})


 # --- mpi4py.MPE ---
CMakeLists.txt.rej (END)

February 26, 2016, 16:50		#28
Bashar Member Bashar Join Date: Jul 2015 Posts: 74 Rep Power: 10	Hi I am following the instruction for the installation on Centos 6.5. I got an error message for the step 17 : ERROR: ParaView not found in /home/bashar/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc48/ParaView-4.1.0 I hope someone have any suggestions for me. Edit: I start with a new setup but this time on Centos6.7, and I followed the instructions for installing OpenFoam2.4 on Centos 6.6 .Unfortunately I got exactly the same error message regarding the para-view! [bashar@basharhpc PV4Readers]$ ./Allwmake ERROR: ParaView not found in /home/bashar/OpenFOAM/ThirdParty-2.4.0/platforms/linux64Gcc48/ParaView-4.1. Last edited by Bashar; February 29, 2016 at 20:48.

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October 10, 2015, 05:22		#24
wyldckat Retired Super Moderator Bruno Santos Join Date: Mar 2009 Location: Lisbon, Portugal Posts: 10,975 Blog Entries: 45 Rep Power: 128	Quick answer: That's a bit strange... but I know how to fix it. Run the following commands: Code: cd $WM_THIRD_PARTY_DIR sed -i -e 's=//#define GLX_GLXEXT_LEGACY=#define GLX_GLXEXT_LEGACY=' ParaView-4.1.0/VTK/Rendering/OpenGL/vtkXOpenGLRenderWindow.cxx ./makeParaView4 -qmake $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/qt-4.8.4/bin/qmake -mpi -python > log.makePV 2>&1 If all goes well, it should build ParaView 4.1.0 without problems.

December 5, 2016, 04:58		#32
H3000 New Member ChristianWindt Join Date: Dec 2016 Posts: 8 Rep Power: 9	Hi Bruno, thanks for your reply and your help. I checked the content of the ParaView-4.1.0 folder, and apparently the Fix.patch file does exist with the exact content you described in your post. Do you think there could be an other source of the error you mentioned? Cheers, Christian

December 27, 2016, 12:34		#33
wyldckat Retired Super Moderator Bruno Santos Join Date: Mar 2009 Location: Lisbon, Portugal Posts: 10,975 Blog Entries: 45 Rep Power: 128	Quick answer: Sorry for the late reply. I don't know if you've managed to solve the problem, but if you haven't, then I need to know what error message you get when you run the following commands: Code: cd $WM_THIRD_PARTY_DIR/ParaView-4.1.0 patch -p1 < Fix.patch If the last command gives you a message something like "do you want to reverse this patch", then type 'N' for no. On the other hand, if it doesn't give any error message and simply states that the patch has been applied, then you should be able to proceed with the installation instructions.