<div dir="ltr"><div>Hello,<br> <br></div> Ooops.. I was trying to see if I did anything wrong and saw that I addressed my reply to only Chuck. I'm sorry (reply vs. reply all). <br><br>I've uploaded the CMakeCache.txt here <a href="https://psu.box.com/s/xsrbpsu73exqmz6v1rsy8jy2mtyzabhk" target="_blank">https://psu.box.com/s/xsrbpsu73exqmz6v1rsy8jy2mtyzabhk</a>. <br><br>This is the error message when using the verbose option. <br><br>[ 4%] Built target vtkWrappingTools<br>make -f VTK/Wrapping/Tools/CMakeFiles/vtkWrapHierarchy.dir/build.make VTK/Wrapping/Tools/CMakeFiles/vtkWrapHierarchy.dir/depend<br>make[2]: Entering directory `/lustre/medusa/gantech/software/Paraview-v4.3.1'<br>cd /lustre/medusa/gantech/software/Paraview-v4.3.1 && /nics/e/sw/xc30_cle5.2_pe2014-09/cmake/<a href="http://2.8.12.2/sles11.3_gnu4.3.4/bin/cmake" target="_blank">2.8.12.2/sles11.3_gnu4.3.4/bin/cmake</a> -E cmake_depends "Unix Makefiles" /nics/d/home/gantech/softw<br>are/ParaView-v4.3.1-source /nics/d/home/gantech/software/ParaView-v4.3.1-source/VTK/Wrapping/Tools /lustre/medusa/gantech/software/Paraview-v4.3.1 /lustre/medusa/gantech/software/Paraview-v4<br>.3.1/VTK/Wrapping/Tools /lustre/medusa/gantech/software/Paraview-v4.3.1/VTK/Wrapping/Tools/CMakeFiles/vtkWrapHierarchy.dir/DependInfo.cmake --color=<br>make[2]: Leaving directory `/lustre/medusa/gantech/software/Paraview-v4.3.1'<br>make -f VTK/Wrapping/Tools/CMakeFiles/vtkWrapHierarchy.dir/build.make VTK/Wrapping/Tools/CMakeFiles/vtkWrapHierarchy.dir/build<br>make[2]: Entering directory `/lustre/medusa/gantech/software/Paraview-v4.3.1'<br>Linking C executable ../../../bin/vtkWrapHierarchy-pv4.3<br>cd /lustre/medusa/gantech/software/Paraview-v4.3.1/VTK/Wrapping/Tools && /nics/e/sw/xc30_cle5.2_pe2014-09/cmake/<a href="http://2.8.12.2/sles11.3_gnu4.3.4/bin/cmake" target="_blank">2.8.12.2/sles11.3_gnu4.3.4/bin/cmake</a> -E cmake_link_script CMakeFiles/vtkWrapHi<br>erarchy.dir/link.txt --verbose=1<br>/opt/cray/craype/2.2.1/bin/cc
-O3 -DNDEBUG -Wl,--fatal-warnings -Wl,--no-undefined -lc
-Wl,--fatal-warnings -Wl,--no-undefined -lc
CMakeFiles/vtkWrapHierarchy.dir/vtkWrapHierarchy.c.o<br> -o ../../../bin/vtkWrapHierarchy-pv4.3 -rdynamic ../../../lib/libvtkWrappingTools-pv4.3.a<span class="im"><br>/usr/lib/../lib64/libpthread.a(lowlevellock.o): In function `__lll_lock_wait_private':<br>/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'<br></span>/usr/lib/../lib64/libc.a(libc-lowlevellock.o):/usr/src/packages/BUILD/glibc-2.11.3/nptl/../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:81: first defined here<span class="im"><br>/usr/lib/../lib64/libpthread.a(lowlevellock.o): In function `__lll_unlock_wake_private':<br>/usr/src/packages/BUILD/glibc-2.11.3/nptl/../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:323: multiple definition of `__lll_unlock_wake_private'<br></span>/usr/lib/../lib64/libc.a(libc-lowlevellock.o):/usr/src/packages/BUILD/glibc-2.11.3/nptl/../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:323: first defined here<br>/usr/bin/ld: link errors found, deleting executable `../../../bin/vtkWrapHierarchy-pv4.3'<span class="im"><br>collect2: error: ld returned 1 exit status<br></span>make[2]: *** [bin/vtkWrapHierarchy-pv4.3] Error 1<br>make[2]: Leaving directory `/lustre/medusa/gantech/software/Paraview-v4.3.1'<br>make[1]: *** [VTK/Wrapping/Tools/CMakeFiles/vtkWrapHierarchy.dir/all] Error 2<br>make[1]: Leaving directory `/lustre/medusa/gantech/software/Paraview-v4.3.1'<span class="im"><br>make: *** [all] Error 2<br><br></span><br></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Jul 23, 2015 at 8:11 AM, Chuck Atkins <span dir="ltr"><<a href="mailto:chuck.atkins@kitware.com" target="_blank">chuck.atkins@kitware.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Hi Ganesh,<br><br></div>Can you post your CMakeCache.txt? Also, if you build with "make VERBOSE=1" that will give the full command that gets executed for the failing link step. Posting both of those will be helpful.<span class="HOEnZb"><font color="#888888"><br></font></span></div></div><div class="gmail_extra"><span class="HOEnZb"><font color="#888888"><br clear="all"><div><div><div dir="ltr">- Chuck<br></div></div></div></font></span><div><div class="h5">
<br><div class="gmail_quote">On Wed, Jul 22, 2015 at 10:37 PM, Ganesh Vijayakumar <span dir="ltr"><<a href="mailto:ganesh.iitm@gmail.com" target="_blank">ganesh.iitm@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>Dear Chuck,<br><br></div> 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.<br><br>Linking C executable ../../../../bin/vtkmkg3states-pv4.3<br>/usr/lib/../lib64/libpthread.a(lowlevellock.o): In function `__lll_lock_wait_private':<br>/usr/src/packages/BUILD/glibc-2.11.3/nptl/../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:81: multiple definition of `__lll_lock<br>_wait_private'<br>/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<br>llock.S:81: first defined here<br>/usr/lib/../lib64/libpthread.a(lowlevellock.o): In function `__lll_unlock_wake_private':<br>/usr/src/packages/BUILD/glibc-2.11.3/nptl/../nptl/sysdeps/unix/sysv/linux/x86_64/lowlevellock.S:323: multiple definition of `__lll_unl<br>ock_wake_private'<br>/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<br>llock.S:323: first defined here<br>/usr/bin/ld: link errors found, deleting executable `../../../../bin/vtkmkg3states-pv4.3'<br>collect2: error: ld returned 1 exit status<br>make[2]: *** [bin/vtkmkg3states-pv4.3] Error 1<br>make[1]: *** [VTK/ThirdParty/tiff/vtktiff/CMakeFiles/vtkmkg3states.dir/all] Error 2<br>make: *** [all] Error 2<span><font color="#888888"><br><br><br></font></span></div><span><font color="#888888">ganesh<br></font></span></div><div><div><br><div class="gmail_quote"><div dir="ltr">On Thu, Jul 16, 2015 at 2:19 PM Chuck Atkins <<a href="mailto:chuck.atkins@kitware.com" target="_blank">chuck.atkins@kitware.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div class="gmail_quote"><div></div><span><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div><div class="gmail_quote"><div dir="ltr"><div>If it's a problem with HDF5 library, I'm not sure where I need to point to the system installation.<br></div></div></div></div></div></div></blockquote></div></div></div><div dir="ltr"><div class="gmail_extra"></div><div class="gmail_extra">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.<br></div></div></blockquote><div></div></span><div>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?<br></div></div></div></div></blockquote><div><br></div></div></div></div><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><div>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:<br><br><span style="font-family:monospace,monospace"> -DVTK_USE_SYSTEM_HDF5:BOOL=ON</span><br></div></div><br><span style="font-family:monospace,monospace"><br></span><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div class="gmail_quote"><div><span style="font-family:monospace,monospace"> CMAKE_CXX_FLAGS </span><span style="font-family:monospace,monospace"> -L/lustre/medusa/gantech/</span><span style="font-family:monospace,monospace">software/mesa-10.6.0/lib<br></span></div></div></div></div></blockquote><div><span style="font-family:monospace,monospace">... <br></span></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div class="gmail_quote"><div><span style="font-family:monospace,monospace"> CMAKE_C_FLAGS </span><span style="font-family:monospace,monospace"> -L/lustre/medusa/gantech/</span><span style="font-family:monospace,monospace">software/mesa-10.6.0/lib<br></span></div></div></div></div></blockquote><div><span style="font-family:monospace,monospace">... <br></span></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div class="gmail_quote"><div><span style="font-family:monospace,monospace"> CMAKE_EXE_LINKER_FLAGS </span><span style="font-family:monospace,monospace"> -L/lustre/medusa/gantech/</span><span style="font-family:monospace,monospace">software/mesa-10.6.0/lib</span><br></div></div></div></div></blockquote><div><br></div><div>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:<br><br><span style="font-family:monospace,monospace"> -DOPENGL_INCLUDE_DIR:PATH=<br> -DOPENGL_xmesa_INCLUDE_DIR:PATH=<br> -DOPENGL_gl_LIBRARY:FILEPATH=<br> -DOPENGL_glu_LIBRARY:FILEPATH=<br> -DOSMESA_INCLUDE_DIR:PATH=/lustre/medusa/gantech/</span><span style="font-family:monospace,monospace">software/mesa-10.6.0/include<br> -DOSMESA_LIBRARY:FILEPATH=/lustre/medusa/gantech/</span><span style="font-family:monospace,monospace">software/mesa-10.6.0/lib/libOSMesa.a<br></span></div><div><span style="font-family:monospace,monospace"> -DVTK_OPENGL_HAS_OSMESA:BOOL=ON<br> -DVTK_USE_X:BOOL=OFF</span><br></div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div class="gmail_quote"><div> CMAKE_Fortran_COMPILER /opt/gcc/4.9.2/bin/gfortran<br></div></div></div></div></blockquote><div> </div>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<br><br><br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div class="gmail_quote"><div><span style="font-family:monospace,monospace"> MPI_CXX_LIBRARIES </span><span style="font-family:monospace,monospace"> /opt/cray/mpt/7.1.3/gni/</span><span style="font-family:monospace,monospace">mpich2-gnu/49/lib/<br></span></div></div></div></div></blockquote><div><span style="font-family:monospace,monospace">... <br></span></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div class="gmail_quote"><div><span style="font-family:monospace,monospace"> MPI_C_LIBRARIES </span><span style="font-family:monospace,monospace"> /opt/cray/mpt/7.1.3/gni/</span><span style="font-family:monospace,monospace">mpich2-gnu/49/lib/<br></span></div></div></div></div></blockquote><div><span style="font-family:monospace,monospace">... <br></span></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div class="gmail_quote"><div><span style="font-family:monospace,monospace"> MPI_LIBRARY </span><span style="font-family:monospace,monospace"> /opt/cray/mpt/7.1.3/gni/</span><span style="font-family:monospace,monospace">mpich2-gnu/49/lib</span><br></div></div></div></div></blockquote><div> <br></div><div>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:<br><br><span style="font-family:monospace,monospace"> MPI_CXX_COMPILER /opt/cray/craype/2.1.0/bin/CC <br> MPI_CXX_COMPILE_FLAGS <br> MPI_CXX_INCLUDE_PATH <br> MPI_CXX_LIBRARIES <br> MPI_CXX_LINK_FLAGS <br> MPI_CXX_NO_INTERROGATE /opt/cray/craype/2.1.0/bin/CC <br> MPI_C_COMPILER /opt/cray/craype/2.1.0/bin/cc <br> MPI_C_COMPILE_FLAGS <br> MPI_C_INCLUDE_PATH <br> MPI_C_LIBRARIES <br> MPI_C_LINK_FLAGS <br> MPI_C_NO_INTERROGATE /opt/cray/craype/2.1.0/bin/cc <br> MPI_EXTRA_LIBRARY MPI_EXTRA_LIBRARY-NOTFOUND <br> MPI_Fortran_COMPILER /opt/cray/craype/2.1.0/bin/ftn <br> MPI_Fortran_COMPILE_FLAGS <br> MPI_Fortran_INCLUDE_PATH <br> MPI_Fortran_LIBRARIES <br> MPI_Fortran_LINK_FLAGS <br> MPI_Fortran_NO_INTERROGATE /opt/cray/craype/2.1.0/bin/ftn <br> MPI_LIBRARY MPI_LIBRARY-NOTFOUND </span><br></div><br></div><div class="gmail_extra">Because the Cray wrappers automatically add the mpi libs and headers (behaving like mpiCC), then the MPI code should compile without any additional flags.<br></div></div>
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</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature">ganesh<br></div>
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