[Trilinos-Users] problem with make

Tudor Buican tudor at timb.com
Thu May 29 14:01:31 MDT 2008


Hi, all.

Purely by coincidence, I was trying this morning to build Trilinos with
pytrilinos enabled and seemed to run into the same problem. Is there a
solution yet?

Just in case, here is my configure command (from a script):

....................................
../configure \
  --cache-file=config.cache \
  --prefix=/home/tudor/trilinos-install/LINUX_MPI \
  --with-gnumake \
  --with-cflags="-ansi -Wall -fPIC -O3 -m64" \
  --with-cxxflags="-ansi -Wall -fPIC -ftrapv -Wconversion -m64" \
  --enable-mpi --with-mpi-compilers \
  --with-mpi-libs=-lmpi \
  --with-flibs="-lg2c" \
  --with-libs=-L/home/tudor/libraries/trilinos_3pl/LINUX_MPI/lib \
  --enable-examples \
  --enable-tests \
  --enable-pytrilinos \
  --enable-teuchos \
  --enable-epetra \
  --enable-triutils \
  --enable-aztecoo \
  --enable-ifpack \
  --disable-ifpack-metis \
  --enable-ifpack-sparskit \
  --enable-epetraext \
  --enable-amesos \
  --enable-amesos-lapack \
  --enable-amesos-klu \
  --disable-amesos-umfpack \
  --disable-amesos-dscpack \
  --enable-didasko \
  --enable-ml \
  --enable-anasazi \
  --enable-nox \
  --enable-nox-epetra  | tee configure_LINUX_MPI.log
.......................................

and this is where "make everything" stumbles:

.......................................
Converting epetra to a shared library
changing directory to ../../epetra/src
mpicxx -shared -Wl,-soname,libepetra.so -o libepetra.so *.o -
L/home/tudor/trilinos-8.0.4/LINUX_MPI-ompi11-
pytrilinos/packages/PyTrilinos/shared -L/home/tudor/trilinos-
install/LINUX_M PI-ompi11-pytrilinos/packages/epetra/src -
L/home/tudor/trilinos-install/LINUX_MPI-ompi11-py
trilinos/packages/teuchos/src -lteuchos -
L/home/tudor/libraries/trilinos_3pl/LINUX_MPI/lib -L/usr/lib64/openmpi -
L/usr/lib/gcc/x86_64-redhat-linux/4.1.1 -L/usr/lib64 -L/lib64 -llapac k
-lblas -lmpi -lorte -lopal -ldl -lnsl -lutil -lgfortranbegin -lgfortran
-lm -lpthread
/usr/bin/ld: Epetra_dcrsmm.o: relocation R_X86_64_32 against `a local
symbol' can not be us ed when making a shared object; recompile with -
fPIC
Epetra_dcrsmm.o: could not read symbols: Bad value
collect2: ld returned 1 exit status
Traceback (most recent call last):
  File "../../../../packages/PyTrilinos/shared/setup.py", line 172, in ?
    main()
  File "../../../../packages/PyTrilinos/shared/setup.py", line 148, in
main
    builder.buildShared()
  File "../util/SharedUtils.py", line 312, in buildShared
  File "../util/SharedUtils.py", line 97, in runCommand
RuntimeError: Exit status = 256
make[4]: *** [package] Error 1
........................................
 
I did include -fPIC among the flags in the configure command. 

Thanks in advance.
-Tudor
-- 
Tudor N. Buican, PhD
Managing Member
SEA LLC
phone: 505-271-9925, 505-818-7303
fax: 505-271-9925
email: tudor at timb.com
On Thu, 2008-05-29 at 12:50 -0400, Joshua Bronson wrote:
> Oh right, as you said. Sorry I missed that.
> 
> 
> That error looks familiar to me, but I'm not sure if I ever got to the
> bottom of it or just disabled aztecoo... I will check when I get a
> chance and get back to you (unless someone else beats me to it).
> 
> On Thu, May 29, 2008 at 12:45 PM, Daniele Bettella <sunriis at gmail.com>
> wrote:
>         Yes, I've seen that issue; problem is I've disabled default
>         packages and am not enabling ML; I also tried to enable-
>         amesos, but the problem is still there...
>         
>         
>         On Thu, May 29, 2008 at 6:29 PM, Joshua Bronson
>         <jabronson at gmail.com> wrote:
>                 I believe you are hitting the issue referenced
>                 at http://trilinos.sandia.gov/packages/pytrilinos/faq.html:
>                 
>                 
>                         If ML is enabled, as is the default, then you
>                         currently need to --enable-amesos as well in
>                         order to get PyTrilinos to compile correctly.
>                         You could also --disable-ml if you so choose.
>                 
>                 
>                 Does it work if you --disable-ml or --enable-amesos?
>                 
>                 
>                 Josh
>                 
>                 
>                 On Thu, May 29, 2008 at 9:53 AM, Daniele Bettella
>                 <sunriis at gmail.com> wrote:
>                 
>                         Hi, I'm having a new error when making
>                         Trilinos version 8.0.7 (but the same happened
>                         with 8.0.4).
>                         The problem is this:
>                         
>                         Compiling the PyTrilinos source files
>                         mpicxx -I/home/bettella/trilfem 
>                         /Python/include/python2.5 -fPIC -m64 -
>                         DNUMPY_NOPREFIX -c ../src/AztecOO_wrap.cpp -
>                         o ../src/AztecOO_wrap.o
>                         ../src/AztecOO_wrap.cpp:3130:21: error:
>                         AztecOO.h: No such file or directory
>                         ../src/AztecOO_wrap.cpp:3131:29: error:
>                         AztecOO_Version.h: No such file or directory
>                         ../src/AztecOO_wrap.cpp:3144:31: error:
>                         numpy/arrayobject.h: No such file or directory
>                         
>                         the configure command was this
>                         ./configure --prefix=${TRILINOSDIR} --enable-
>                         mpi --with-mpi-compilers \
>                                 --disable-default-packages --enable-
>                         epetra \
>                                     --enable-teuchos --enable-triutils
>                         --enable-aztecoo \
>                                 --enable-aztecoo-teuchos  --enable-
>                         pytrilinos \
>                                     --with-python=
>                         ${PYTHONDIR}/bin/python \
>                                     --with-swig=${SWIGDIR}/bin/swig \
>                                     FFLAGS="-fPIC -O3 -m64" \
>                                     CFLAGS="-fPIC -m64" \
>                                     CXXFLAGS="-fPIC -m64"
>                         
>                         (I'm compiling from a sh script)
>                         
>                         I event tried with different configurations of
>                         "enables" and "disables", but everytime, when
>                         it says "compiling the PyTrilinos source
>                         files", it looks like it looses some -I
>                         options...
>                         
>                         Hope you can help!
>                         
>                         
>                         _______________________________________________
>                         Trilinos-Users mailing list
>                         Trilinos-Users at software.sandia.gov
>                         http://software.sandia.gov/mailman/listinfo/trilinos-users
>                         
>                 
>                 
>         
>         
> 
> 
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