[Paraview] Linker error involving ParaView's vtk and mvapich

Leonard Kern kern at math.hu-berlin.de
Wed Nov 10 12:31:38 EST 2010


Dear ParaView community!

I'm having a problem building ParaView on a linux x86-64 cluster. I intend to use pvserver (parallelized via mvapich2) to visualize results  from finite element compuations. There is no graphics hardware available on the machine, so I'm using osmesa.
Configuration works as described in the wiki but running make gives this:

# make
[  0%] Built target vtksys
... output truncated ... (nothing interesting here)
[ 35%] Built target ParallelCxxTests
Linking CXX executable ../../../../bin/ParallelIsoTest
../../../../bin/libvtkHybrid.a(vtkVRMLImporter.cxx.o):(.bss+0x40): multiple definition of `yyin'
/opt/software/mvapich2-1.4.1/lib/libmpich.a(parser.o):/install/software/src/mpich2/mvapich2-1.4.1/src/mpid/ch3/channels/mrail/src/plpa/parser.c:1164: first defined here
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: Warning: alignment 8 of symbol `yylval' in ../../../../bin/libvtkHybrid.a(vtkVRMLImporter.cxx.o) is smaller than 32 in /opt/software/mvapich2-1.4.1/lib/libmpich.a(tokens.o)
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: Warning: size of symbol `yylval' changed from 128 in /opt/software/mvapich2-1.4.1/lib/libmpich.a(tokens.o) to 8 in ../../../../bin/libvtkHybrid.a(vtkVRMLImporter.cxx.o)
../../../../bin/libvtkHybrid.a(vtkVRMLImporter.cxx.o):(.bss+0x48): multiple definition of `yyout'
/opt/software/mvapich2-1.4.1/lib/libmpich.a(parser.o):/install/software/src/mpich2/mvapich2-1.4.1/src/mpid/ch3/channels/mrail/src/plpa/parser.c:1164: first defined here
collect2: ld returned 1 exit status
make[2]: *** [bin/ParallelIsoTest] Error 1
make[1]: *** [VTK/Parallel/Testing/Cxx/CMakeFiles/ParallelIsoTest.dir/all] Error 2
make: *** [all] Error 2

To me, this looks like mvapich2 and vtk both use parsers generated by flex+bison where at least one of them should rename their yyin etc. Unfortunately, Google was unable to offer any useful help, so I'm turning to you.

Any ideas on how I could fix this (or work around it)?

Cheers,
Leonard Kern.

P.S. My CMakeCache.txt is appended.

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