Actually, never mind, it was an upstream issue after all and they have a patch ready (if anyone is interested, the merge req is here: https://gitlab.kitware.com/vtk/vtk/-/merge_requests/6862). Thanks. On Wed, 2020-05-06 at 20:21 +0200, Atri Bhattacharya wrote:
Hi, I am trying to get VTK updated to version 9.0 released a couple of days ago, and I mostly have it [1]. However, I have not been able to get the MPI-supported flavours to build due to a linking error that looks like this:
``` [ 1199s] [ 93%] Linking CXX shared library ../../lib64/java/vtk- Linux-x86_64/libvtkFiltersParallelGeometryJava.so [ 1199s] cd /home/abuild/rpmbuild/BUILD/VTK-9.0.0/build/Wrapping/Java && /usr/bin/cmake -E cmake_link_script CMakeFiles/vtkFiltersParallelGeometryJava.dir/link.txt --verbose =1 [ 1199s] /usr/lib64/mpi/gcc/openmpi2/bin/mpicxx -fPIC -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-prote ction -Werror=return-type -flto=auto -ffat-lto-objects -DNDEBUG -O2 -g -DNDEBUG -Wl,-lc -flto=auto -ffat-lto-objects -Wl,--as-needed -Wl,--no-undefined -Wl,-z,now -shared -Wl,-soname,libvtkFiltersParallelGeometryJava.so -o ../../lib64/java/vtk-Linux- x86_64/libvtkFiltersParallelGeometryJava.so CMakeFiles/vtkFiltersParallelGeometryJava.dir/CMa keFiles/vtkFiltersParallelGeometryJava/vtkPConnectivityFilterJava.cxx .o CMakeFiles/vtkFiltersParallelGeometryJava.dir/CMakeFiles/vtkFiltersPa rallelGeometryJava/vtkPDataSetGh ostGeneratorJava.cxx.o CMakeFiles/vtkFiltersParallelGeometryJava.dir/CMakeFiles/vtkFiltersPa rallelGeometryJava/vtkPDistributedDataFilterJava.cxx.o CMakeFiles/vtkFiltersParal lelGeometryJava.dir/CMakeFiles/vtkFiltersParallelGeometryJava/vtkPStr ucturedGridConnectivityJava.cxx.o CMakeFiles/vtkFiltersParallelGeometryJava.dir/CMakeFiles/vtkFiltersPa r allelGeometryJava/vtkPStructuredGridGhostDataGeneratorJava.cxx.o CMakeFiles/vtkFiltersParallelGeometryJava.dir/CMakeFiles/vtkFiltersPa rallelGeometryJava/vtkPUniformGridGhost DataGeneratorJava.cxx.o CMakeFiles/vtkFiltersParallelGeometryJava.dir/CMakeFiles/vtkFiltersPa rallelGeometryJava/vtkPUnstructuredGridGhostCellsGeneratorJava.cxx.o CMakeFiles/ vtkFiltersParallelGeometryJava.dir/CMakeFiles/vtkFiltersParallelGeome tryJava/vtkFiltersParallelGeometryModuleJava.cxx.o -Wl,- rpath,"\$ORIGIN/../../:\$ORIGIN:/usr/lib64/jvm/ java/lib:/usr/lib64/jvm/java/lib/server" ../../lib64/libvtkFiltersParallelGeometry.so.9.0.0 ../../lib64/java/vtk-Linux-x86_64/libvtkCommonSystemJava.so ../../lib64/java/vtk- Linux-x86_64/libvtkFiltersParallelJava.so ../../lib64/java/vtk-Linux- x86_64/libvtkParallelMPIJava.so ../../lib64/libvtkFiltersParallel.so.9.0.0 ../../lib64/libvtkFiltersExtr action.so.9.0.0 ../../lib64/java/vtk-Linux- x86_64/libvtkFiltersGeometryJava.so ../../lib64/libvtkFiltersHybrid.so.9.0.0 ../../lib64/libvtkFiltersGeometry.so.9.0.0 ../../lib6 4/libvtkFiltersModeling.so.9.0.0 ../../lib64/libvtkFiltersSources.so.9.0.0 ../../lib64/java/vtk-Linux- x86_64/libvtkCommonExecutionModelJava.so ../../lib64/libvtkFiltersTextu re.so.9.0.0 ../../lib64/libvtkFiltersGeneral.so.9.0.0 ../../lib64/libvtkFiltersCore.so.9.0.0 ../../lib64/libvtkParallelMPI.so.9.0.0 ../../lib64/java/vtk-Linux- x86_64/libvtkC ommonCoreJava.so ../../lib64/libvtkJava.so.9.0.0 /usr/lib64/jvm/java/lib/libjawt.so /usr/lib64/jvm/java/lib/server/libjvm.so ../../lib64/libvtkParallelCore.so.9.0.0 ../../li b64/libvtkCommonExecutionModel.so.9.0.0 ../../lib64/libvtkCommonDataModel.so.9.0.0 ../../lib64/libvtkCommonSystem.so.9.0.0 ../../lib64/libvtkCommonTransforms.so.9.0.0 ../../ lib64/libvtkCommonMisc.so.9.0.0 ../../lib64/libvtkCommonMath.so.9.0.0 ../../lib64/libvtkCommonCore.so.9.0.0 ../../lib64/libvtksys.so.9.0.0 -ldl -Wl,-rpath-link,/home/abuild/ rpmbuild/BUILD/VTK-9.0.0/build/lib64/java/vtk-Linux- x86_64:/home/abuild/rpmbuild/BUILD/VTK-9.0.0/build/lib64 [ 1199s] /usr/lib64/gcc/x86_64-suse-linux/9/../../../../x86_64-suse- linux/bin/ld: /tmp/libvtkFiltersParallelGeometryJava.so.ou8EgG.ltrans0.ltrans.o: in function `vtkPConnect ivityFilter_Typecast': [ 1199s] /home/abuild/rpmbuild/BUILD/VTK- 9.0.0/build/Wrapping/Java/CMakeFiles/vtkFiltersParallelGeometryJava/v tkPConnectivityFilterJava.cxx:18: undefined reference to `vtkCo nnectivityFilter_Typecast' [ 1199s] collect2: error: ld returned 1 exit status [ 1199s] make[2]: *** [Wrapping/Java/CMakeFiles/vtkFiltersParallelGeometryJava.dir/build.ma ke:297: lib64/java/vtk-Linux- x86_64/libvtkFiltersParallelGeometryJava.so] Error 1 [ 1199s] make[2]: Leaving directory '/home/abuild/rpmbuild/BUILD/VTK- 9.0.0/build' [ 1199s] make[1]: *** [CMakeFiles/Makefile2:21809: Wrapping/Java/CMakeFiles/vtkFiltersParallelGeometryJava.dir/all] Error 2 [ 1199s] make[1]: *** Waiting for unfinished jobs.... ```
The serial flavour -- without mpi support -- builds just fine, which leads me to believe the issue may be some env variable or path that is not exported when the MPI prefixes and paths are redefined. But, I don't know for sure.
Any pointers to help sort this out will be highly appreciated.
I have also tried to elicit a comment or suggestion from upstream [2].
Thanks in advance for any help.
[1] < https://build.opensuse.org/package/show/home:badshah400:branches:science/vtk
[2] < https://discourse.vtk.org/t/building-vtk-9-0-fails-when-using-mpi-support/32...
-- Atri Bhattacharya Wed 6 May 20:09:12 CEST 2020
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