installation process on Ubuntu

[Juan Carlos Araujo Cabarcas]

Dear all,

After some very recent additions and fixes in the library, I am trying to install from:
    git clone https://github.com/dealii/dealii.git

with:

petsc_ver='3.6.0';
trilinos_ver=11.12.1;

cmake \
-DTRILINOS_DIR=${install_dir}/trilinos-${trilinos_ver} \
-DP4EST_DIR=${install_dir}/FAST \
-DDEAL_II_WITH_METIS=ON \
-DMETIS_DIR=$METIS_DIR \
-DDEAL_II_WITH_MPI=ON \
-DDEAL_II_WITH_THREADS=OFF \
-DDEAL_II_WITH_UMFPACK=ON \
-DDEAL_II_WITH_LAPACK=ON \
-DDEAL_II_WITH_PETSC=ON \
-DPETSC_ARCH=$PETSC_ARCH \
-DPETSC_DIR=$PETSC_DIR \
-DDEAL_II_WITH_SLEPC=ON \
-DSLEPC_DIR=$SLEPC_DIR \
-DDEAL_II_WITH_P4EST=ON \
-DDEAL_II_WITH_ARPACK=ON \
-DDEAL_II_WITH_TRILINOS=ON \
-DCMAKE_INSTALL_PREFIX=${install_dir}/dealii ${install_dir}/dealii;

make -j${virtual_proc} install;

and installed in my system:

$ gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.8/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.4-2ubuntu1~14.04.3' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --disable-libmudflap --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu
Thread model: posix
gcc version 4.8.4 (Ubuntu 4.8.4-2ubuntu1~14.04.3)


and I am getting some errors with Sacado of the type (see more below and in the attached file):

[ 64%] Building CXX object source/differentiation/ad/CMakeFiles/obj_differentiation_ad_debug.dir/sacado_number_types.cc.o

In file included from /soft/dealii/source/differentiation/ad/sacado_number_types.cc:21:0:
/soft/dealii/include/deal.II/differentiation/ad/sacado_number_types.h:541:75: error: ‘scalar_type’ in ‘struct dealii::Differentiation::AD::ADNumberTraits<Sacado::Rad::ADvar<float> >’ does not name a type
       : NumberTraits<typename ADNumberTraits<Sacado::Rad::ADvar<float> >::scalar_type,NumberTypes::sacado_rad>
                                                                           ^
/soft/dealii/include/deal.II/differentiation/ad/sacado_number_types.h:541:110: error: template argument 1 is invalid
       : NumberTraits<typename ADNumberTraits<Sacado::Rad::ADvar<float> >::scalar_type,NumberTypes::sacado_rad>
                                                                                                              ^
/soft/dealii/include/deal.II/differentiation/ad/sacado_number_types.h:542:5: error: expected ‘::’ before ‘{’ token
     {};
     ^
/soft/dealii/include/deal.II/differentiation/ad/sacado_number_types.h:542:5: error: expected class-name before ‘{’ token
/soft/dealii/include/deal.II/differentiation/ad/sacado_number_types.h:551:76: error: ‘scalar_type’ in ‘struct dealii::Differentiation::AD::ADNumberTraits<Sacado::Rad::ADvar<double> >’ does not name a type
       : NumberTraits<typename ADNumberTraits<Sacado::Rad::ADvar<double> >::scalar_type,NumberTypes::sacado_rad>

Any ideas on how to proceed?
Thanks in advance.

[Jean-Paul Pelteret]

Dear Juan Carlos,

Can you please tell me what the commit hash of the deal.II respository that you're working from is? I did briefly introduce a bug that showed similar symptoms but I thought that I fixed it. It might also have to do with your version of Trilinos, which appears to be older than the versions that we've most recently tested the developer version against. I'll look into that as well.

Kind regards,

Jean-Paul

[Juan Carlos Araujo Cabarcas]

Thanks for the quick reply ... I reported a missing instantiation in the forum:
  https://groups.google.com/forum/#!topic/dealii/ijJFbOTZxkk

from where Wolfgang sent the fix:
  https://github.com/dealii/dealii/pull/5448

As mentioned above I just install from:
  git clone https://github.com/dealii/dealii.git

but I don't know if should checkout a different version/branch. Please let me know if this is the case.
I guess I could also try with a newer Trilinos version, what version should work?

[Jean-Paul Pelteret]

Hi Juan Carlos,

Reading the error more closely it could be a compiler issue. But you’ve caught me literally at the end of my work day, so I can’t investigate this issue right now. I would say that commit

babb6ae7b2ef589a0998383214087fd60466beb6 is probably the last one that you could checkout before the issue likely arises. Thankfully that’s after the fix in fd01d88 was merged into the master branch.

I think that if you simply execute

git checkout fd01d88

after you’ve cloned the repo, then that should put it in a state that you can use.

May I please ask you to open an issue on github so that we can track this problem? I’ll try to reproduce and fix it as soon as I can. If you’re feeling adventurous, I’m currently using Trilinos 12.10.1, but as I inferred I’m no longer particularly confident that this is the root of the issue (this Trilinos number type does exist in the header thats included in our own header file).

Best,

Jean-Paul

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