Mailinglist Archive: opensuse-packaging (66 mails)

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[opensuse-packaging] Re: Build failures when building VTK 9.0 with mpi support
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/3227

--
Atri Bhattacharya
Wed 6 May 20:09:12 CEST 2020

Sent from openSUSE Tumbleweed on my laptop.


--
Atri Bhattacharya

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