Dear Chuck, Finally, I got this done. I could get paraview to configure without giving any errors. I removed the build directory and started afresh. However, it fails at the same place during the compilation. Could you advise as to what might be the problem.
Linking C executable ../../../../bin/vtkmkg3states-pv4.3 /usr/lib/../lib64/libpthread.a(lowlevellock.o): In function `__lll_lock_wait_private': /usr/src/packages/BUILD/glibc-2.11.3/nptl/../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:81: multiple definition of `__lll_lock _wait_private' /usr/lib/../lib64/libc.a(libc-lowlevellock.o):/usr/src/packages/BUILD/glibc-2.11.3/nptl/../nptl/sysdeps/unix/sysv/linux/x86_64/lowleve llock.S:81: first defined here /usr/lib/../lib64/libpthread.a(lowlevellock.o): In function `__lll_unlock_wake_private': /usr/src/packages/BUILD/glibc-2.11.3/nptl/../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:323: multiple definition of `__lll_unl ock_wake_private' /usr/lib/../lib64/libc.a(libc-lowlevellock.o):/usr/src/packages/BUILD/glibc-2.11.3/nptl/../nptl/sysdeps/unix/sysv/linux/x86_64/lowleve llock.S:323: first defined here /usr/bin/ld: link errors found, deleting executable `../../../../bin/vtkmkg3states-pv4.3' collect2: error: ld returned 1 exit status make[2]: *** [bin/vtkmkg3states-pv4.3] Error 1 make[1]: *** [VTK/ThirdParty/tiff/vtktiff/CMakeFiles/vtkmkg3states.dir/all] Error 2 make: *** [all] Error 2 ganesh On Thu, Jul 16, 2015 at 2:19 PM Chuck Atkins <[email protected]> wrote: > If it's a problem with HDF5 library, I'm not sure where I need to point to >>>> the system installation. >>>> >>> If you load the cray-hdf5 module, that will set the HDF5_DIR environment >>> variable to the correct location. Unfortunately, CMake uses the HDF5_ROOT >>> variable instead to look for it so you'll neet to set it accordingly. >>> >> I don't have much experience with cmake, but can I set additional >> variables in the ccmake window? Should this variable show up there asking >> to be set if you turn on the advanced mode toggle? >> > > Different find modules work differently. The FindHDF5 module uses the > HDF5_ROOT environment variable (not CMake variable, which is why it won't > show up in the ccmake UI) as a hint for where to search, hence exporting it > as an env var prior to running CMake. You'll also want to be sure to > specify to use an external HDF5 rather than ParaView building it's own: > > -DVTK_USE_SYSTEM_HDF5:BOOL=ON > > > CMAKE_CXX_FLAGS -L/lustre/medusa/gantech/ >> software/mesa-10.6.0/lib >> > ... > >> CMAKE_C_FLAGS -L/lustre/medusa/gantech/ >> software/mesa-10.6.0/lib >> > ... > >> CMAKE_EXE_LINKER_FLAGS -L/lustre/medusa/gantech/ >> software/mesa-10.6.0/lib >> > > Instead of setting these in the compiler flags, it's better to tell > ParaView where to explicitly find the libraries and to configure > accordingly for OSMesa. You can pass these as command line arguments to > cmake or ccmake with -D, or set them in the ccmake UI: > > -DOPENGL_INCLUDE_DIR:PATH= > -DOPENGL_xmesa_INCLUDE_DIR:PATH= > -DOPENGL_gl_LIBRARY:FILEPATH= > -DOPENGL_glu_LIBRARY:FILEPATH= > -DOSMESA_INCLUDE_DIR:PATH=/lustre/medusa/gantech/ > software/mesa-10.6.0/include > -DOSMESA_LIBRARY:FILEPATH=/lustre/medusa/gantech/ > software/mesa-10.6.0/lib/libOSMesa.a > -DVTK_OPENGL_HAS_OSMESA:BOOL=ON > -DVTK_USE_X:BOOL=OFF > > > >> CMAKE_Fortran_COMPILER /opt/gcc/4.9.2/bin/gfortran >> > > Not that it will really matter since we're not compiling Fortran code, but > this should be /opt/cray/craype/2.2.1/bin/ftn > > > MPI_CXX_LIBRARIES /opt/cray/mpt/7.1.3/gni/ >> mpich2-gnu/49/lib/ >> > ... > >> MPI_C_LIBRARIES /opt/cray/mpt/7.1.3/gni/ >> mpich2-gnu/49/lib/ >> > ... > >> MPI_LIBRARY /opt/cray/mpt/7.1.3/gni/ >> mpich2-gnu/49/lib >> > > It does look like the wrappers are correctly getting used for mpicc and > mpiCC and you can see the include dirs getting set accordingly, but these > do not look right. Which version of CMake are you using? Here's what I > get using CMake 3.2.3 (current cmake) on a Cray XC30 when not setting any > MPI variables, just letting CMake auto-detect them by enabling > ParaView_USE_MPI=ON: > > MPI_CXX_COMPILER > /opt/cray/craype/2.1.0/bin/CC > MPI_CXX_COMPILE_FLAGS > > MPI_CXX_INCLUDE_PATH > > MPI_CXX_LIBRARIES > > MPI_CXX_LINK_FLAGS > > MPI_CXX_NO_INTERROGATE > /opt/cray/craype/2.1.0/bin/CC > MPI_C_COMPILER > /opt/cray/craype/2.1.0/bin/cc > MPI_C_COMPILE_FLAGS > > MPI_C_INCLUDE_PATH > > MPI_C_LIBRARIES > > MPI_C_LINK_FLAGS > > MPI_C_NO_INTERROGATE > /opt/cray/craype/2.1.0/bin/cc > MPI_EXTRA_LIBRARY > MPI_EXTRA_LIBRARY-NOTFOUND > MPI_Fortran_COMPILER > /opt/cray/craype/2.1.0/bin/ftn > MPI_Fortran_COMPILE_FLAGS > > MPI_Fortran_INCLUDE_PATH > > MPI_Fortran_LIBRARIES > > MPI_Fortran_LINK_FLAGS > > MPI_Fortran_NO_INTERROGATE > /opt/cray/craype/2.1.0/bin/ftn > MPI_LIBRARY MPI_LIBRARY-NOTFOUND > > Because the Cray wrappers automatically add the mpi libs and headers > (behaving like mpiCC), then the MPI code should compile without any > additional flags. >
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