[Paraview] Cannot compile 4.1 on Ubuntu 12.04 x64 with OpenMPI 1.8.1
Burlen Loring
bloring at lbl.gov
Thu Jun 19 12:36:56 EDT 2014
Hey Victor,
Editing the make file is a bad idea. CCFLAG is the wrong flag. I think
this is much simpler than it appears.
just set the compiler flags on your configure line. as in:
./configure *CFLAGS="-O2 -g -fPIC" CXXFLAGS="-O2 -g -fPIC"* --with-sge
--with-mx=/opt/open-mx --with-pic --with-mx-libdir=/opt/open-mx/lib
--prefix=/opt/openmpi-1.8.1
before you do anything rm it all including build and install just to be
sure you don't have any stale objects libs etc.
Burlen
On 06/17/2014 09:47 PM, Victor wrote:
> I still cannot compile Paraview. I attempted to recompile
> openmpi-1.8.1 with fPIC but something is causing either the fPIC to be
> set incorrectly or I am doing something wrong. In any case I am
> completely stuck so I would really appreciate some help in traversing
> this error:
>
> Linking CXX shared library ../../../lib/libvtkParallelMPI-pv4.1.so
> <http://libvtkParallelMPI-pv4.1.so>
> /usr/bin/ld: /opt/openmpi-1.8.1/lib/libmpi.a(comm_init.o): relocation
> R_X86_64_32 against `ompi_comm_f_to_c_table' can not be used when
> making a shared object; recompile with -fPIC
> /opt/openmpi-1.8.1/lib/libmpi.a: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make[2]: *** [lib/libvtkParallelMPI-pv4.1.so.1] Error 1
> make[1]: *** [VTK/Parallel/MPI/CMakeFiles/vtkParallelMPI.dir/all] Error 2
> make: *** [all] Error 2
>
>
> The latest openmpi configure command was: ./configure --with-sge
> --with-mx=/opt/open-mx --with-pic --with-mx-libdir=/opt/open-mx/lib
> --prefix=/opt/openmpi-1.8.1
>
> I also attempted to manually set -fPIC flag by editing the Makefile
> and by setting a global CCFLAG. Nothing worked.
>
>
>
> On 31 May 2014 07:35, Victor <victor.major at gmail.com
> <mailto:victor.major at gmail.com>> wrote:
>
> Here it is, I hope. I never attempted to attach anything to a
> mailing list post so I apologize if it doesn't actually attach.
>
>
> On 30 May 2014 20:07, Utkarsh Ayachit <utkarsh.ayachit at kitware.com
> <mailto:utkarsh.ayachit at kitware.com>> wrote:
>
> Can you post your CMakeCache.txt file?
>
> On Fri, May 30, 2014 at 2:40 AM, Victor
> <victor.major at gmail.com <mailto:victor.major at gmail.com>> wrote:
> > Thank you for the fast reply!
> >
> > I compiled an alternative openmpi-1.8.1 with -fPIC flag (I
> verified that it
> > was placed into the Makefile), removed the original Paraview
> build
> > directory, modified the Paraview build configuration by
> rerunning ccmake to
> > point to the alternative openmpi path, but the error remained.
> >
> > During Paraview compilation the alternative path for
> openmpi-1.8.1 is used
> > until it comes to the linking step where it attempts to link
> to the system
> > wide openmpi-1.8.1 location and of course fails.
> >
> > Linking CXX shared library
> ../../../lib/libvtkParallelMPI-pv4.1.so
> <http://libvtkParallelMPI-pv4.1.so>
> > /usr/bin/ld:
> /opt/openmpi-1.8.1/lib/libmpi_cxx.a(intercepts.o): relocation
> > R_X86_64_32S against `ompi_mpi_cxx_comm_throw_excptn_fctn'
> can not be used
> > when making a shared object; recompile with -fPIC
> > /opt/openmpi-1.8.1/lib/libmpi_cxx.a: could not read symbols:
> Bad value
> > collect2: ld returned 1 exit status
> > make[2]: *** [lib/libvtkParallelMPI-pv4.1.so.1] Error 1
> > make[1]: ***
> [VTK/Parallel/MPI/CMakeFiles/vtkParallelMPI.dir/all] Error 2
> > make: *** [all] Error 2
> >
> >
> > I cannot (will not) overwrite the system wide openmpi as I
> have a parallel
> > job running at the moment (CFD simulation) and this node is
> acting as a head
> > node serving openmpi from an NFS shared directory. I am
> confident that the
> > application will not need to call on openmpi now that it is
> already running,
> > but I'd rather not find out that I am wrong.
> >
> > Thus is there a way to force the Paraview installer to link
> against an
> > alternative build that was compiled with -fPIC?
> >
> > Thanks,
> >
> > Victor
> >
> >
> > On 29 May 2014 18:37, Utkarsh Ayachit
> <utkarsh.ayachit at kitware.com
> <mailto:utkarsh.ayachit at kitware.com>> wrote:
> >>
> >> You'll have to recompile openmpi with -fPIC or link against
> a shared
> >> build of the same.
> >>
> >> On Thu, May 29, 2014 at 5:06 AM, Victor
> <victor.major at gmail.com <mailto:victor.major at gmail.com>> wrote:
> >> > I am trying to compile Paraview 4.1 with MPI support but
> make exits at
> >> > this
> >> > point:
> >> >
> >> > /usr/bin/ld:
> /opt/openmpi-1.8.1/lib/libmpi.a(comm_init.o): relocation
> >> > R_X86_64_32 against `ompi_comm_f_to_c_table' can not be
> used when making
> >> > a
> >> > shared object; recompile with -fPIC
> >> > /opt/openmpi-1.8.1/lib/libmpi.a: could not read symbols:
> Bad value
> >> > collect2: ld returned 1 exit status
> >> > make[2]: *** [lib/libvtkParallelMPI-pv4.1.so.1] Error 1
> >> > make[1]: ***
> [VTK/Parallel/MPI/CMakeFiles/vtkParallelMPI.dir/all] Error
> >> > 2
> >> > make: *** [all] Error 2
> >> >
> >> > How can I fix this error?
> >> >
> >> > Thanks,
> >> >
> >> > Victor
> >> >
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>
>
>
>
>
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