[aspect-devel] [deal.II] Re: deal.ii problem during aspect compile, static libs
Thorsten Becker
twb at usc.edu
Tue Jul 1 14:28:11 PDT 2014
Thanks much, Jonathan!
Trying to compile shared objects using your approach (or my earlier
attempts, I think it was using the right compilers?), brings me back to
errors like the one below with trilinos. It does appears that there's
something funny with the local mpich2 install and how it calls the linker,
but we haven't experienced these problems with other software, I think.
Linking CXX shared library libteuchoscore.so
/usr/bin/ld: /usr/usc/mpich2/1.5/lib/libmpich.a(allreduce.o): relocation
R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared
obj
ect; recompile with -fPIC
/usr/usc/mpich2/1.5/lib/libmpich.a: could not read symbols: Bad value
collect2: error: ld returned 1 exit status
make[2]: *** [packages/teuchos/core/src/libteuchoscore.so.11.4.3] Error 1
make[1]: *** [packages/teuchos/core/src/CMakeFiles/teuchoscore.dir/all]
Error 2
make: *** [all] Error 2
Thorsten W Becker - USC
http://geodynamics.usc.edu/~becker
On Tue, Jul 1, 2014 at 9:03 PM, Jonathan Perry-Houts <jperryh2 at uoregon.edu>
wrote:
> -----BEGIN PGP SIGNED MESSAGE-----
> Hash: SHA1
>
> Hey Thorsten,
>
> I don't know if it's the same issue, but when I first installed
> deal.II I was having trouble with different build processes using
> different default compilers. For some reason cmake was choosing the
> wrong one when compiling Trilinos but not deal.II, or something. I
> found that specifying the compilers directly in the cmake calls helps.
> I ended up saving the following to a script that I can use when I want
> to update or reinstall these things. This works for me:
>
> Cheers,
> Jonathan
>
> # Build Trilinos
> echo "Building Trilinos"
> tar -C /tmp -xzf $HOME/Downloads/trilinos-11.8.1-Source.tar.gz
> cd /tmp/trilinos-11.8.1-Source
> mkdir build ; cd build
> cmake -D Trilinos_ENABLE_Sacado=ON \
> -D Trilinos_ENABLE_Stratimikos=ON \
> -D CMAKE_BUILD_TYPE=RELEASE \
> -D CMAKE_CXX_FLAGS="-g -O3" \
> -D CMAKE_C_FLAGS="-g -O3" \
> -D CMAKE_FORTRAN_FLAGS="-g -O5" \
> -D Trilinos_EXTRA_LINK_FLAGS="-lgfortran" \
> -D CMAKE_VERBOSE_MAKEFILE=FALSE \
> -D Trilinos_VERBOSE_CONFIGURE=FALSE \
> -D TPL_ENABLE_MPI=ON \
> -D BUILD_SHARED_LIBS=ON \
> -D CMAKE_INSTALL_PREFIX=$TRILINOS_DIR \
> -D CMAKE_C_COMPILER=`which mpicc` \
> -D CMAKE_CXX_COMPILER=`which mpicxx` \
> -D CMAKE_Fortran_COMPILER=`which mpif90` \
> -D MPI_EXEC=`which mpiexec` \
> -D MPI_Fortran_COMPILER=`which mpif90` \
> ..
> make install -j7
> cd ../../ ; rm -rf trilinos-11.8.1-Source*
>
> # Build p4est
> echo "Building p4est"
> mkdir /tmp/p4est-build ; cd /tmp/p4est-build
> wget http://www.p4est.org/tarball/p4est-0.3.4.2.tar.gz
> wget http://www.dealii.org/developer/external-libs/p4est-setup.sh
> chmod +x p4est-setup.sh
> ./p4est-setup.sh p4est-0.3.4.2.tar.gz $P4EST_DIR
> cd ..; rm -rf p4est-build
>
> # Build deal.II development version
> echo "Updating deal.II"
> if [ ! -d $HOME/packages/build ]; then
> mkdir -p $HOME/packages/build
> cd $HOME/packages/build
> svn checkout https://svn.dealii.org/trunk/deal.II
> fi
> cd $HOME/packages/build/deal.II
> svn update
> mkdir /tmp/deal.II-build ; cd /tmp/deal.II-build
> cmake -DDEAL_II_WITH_MPI=ON \
> -DCMAKE_INSTALL_PREFIX=$DEAL_II_DIR \
> -DTRILINOS_DIR=$TRILINOS_DIR \
> -DP4EST_DIR=$P4EST_DIR \
> $HOME/packages/build/deal.II
> make install -j7
> cd .. ; rm -rf /tmp/deal.II-build
>
> On 07/01/2014 11:53 AM, Thorsten Becker wrote:
> > Thanks much, Wolfgang and Timo, for your quick reply and comments!
> >
> >
> > This all makes sense, but I am not sure if any of it applies for
> > me. I spent a day+ trying to compile shared libraries, that's how
> > I ended up with my static attempts. (I should have kept track of
> > the shared compilation problems, and might go back and document
> > those.) During the whole process, I tried to make sure to have
> > "clean" compiles on the same head node, with the same compilers
> > and libraries.
> >
> > In the end, adding a -DCMAKE_EXE_LINKER_FLAGS="-static" to the deal
> > compiled "worked", though now both the test problems and Aspect are
> > stuck on something like
> >
> > Linking CXX executable aspect
> > /usr/lib/../lib64/libpthread.a(libpthread.o): In function
> > `sem_open': (.text+0x774d): warning: the use of `mktemp' is
> > dangerous, better use `mkstemp'
> > /usr/usc/mpich2/1.5/lib/libmpich.a(simple_pmi.o): In function
> > `PMI_Init': simple_pmi.c:(.text+0xc89): warning: Using
> > 'gethostbyname' in statically linked applications requires at
> > runtime the shared libraries from the glibc v ersion used for
> > linking /usr/bin/ld: dynamic STT_GNU_IFUNC symbol `strcmp' with
> > pointer equality in `/usr/lib/../lib64/libc.a(strcmp.o)' can not
> > be used when making an execut able; recompile with -fPIE and
> > relink with -pie collect2: error: ld returned 1 exit status
> > make[2]: *** [aspect] Error 1 make[1]: ***
> > [CMakeFiles/aspect.dir/all] Error 2 make: *** [all] Error 2
> >
> > This makes me think that there's still something wrong with the
> > compiler versions, or that the link line doesn't take into account
> > -static. I wonder (and Rene's been giving me good suggestions all
> > along) if I should really heed the -pie advice, or rather try
> > something else?
> >
> > Thanks!
> >
> > T
> >
> >
> >
> >
> > Thorsten W Becker - USC http://geodynamics.usc.edu/~becker
> >
> >
> > On Tue, Jul 1, 2014 at 7:59 PM, Timo Heister <heister at clemson.edu
> > <mailto:heister at clemson.edu>> wrote:
> >
> > Thorsten,
> >
> > two quick comments:
> >
> >>> to post. After numerous attempts to compile shared libraries,
> >>> I
> > am now
> >>> trying static.
> >
> > My personal experience is that shared compilation is a lot easier
> > to do.
> >
> >> 2/ It finds neither of these libraries because you are on a
> > cluster where
> >> the frontend node (where we are trying to execute
> > 'expand_instantiations')
> >> has a different operating system than the compute nodes
> >
> > If this is the case you can often configure/compile on a compute
> > node using an interactive session.
> >
> > -- Timo Heister http://www.math.clemson.edu/~heister/
> >
> >
> >
> >
> > _______________________________________________ Aspect-devel
> > mailing list Aspect-devel at geodynamics.org
> > http://lists.geodynamics.org/cgi-bin/mailman/listinfo/aspect-devel
> >
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