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Jonathan O'Connell
Dec 1, 2015, 9:53:42 AM12/1/15
to deal.II User Group
Hi,
I'm trying to build deal.ii on my university cluster (http://www.cardiff.ac.uk/arcca/services/equipment/ravenintroduction.html), and the configure step work fine, but it's crashing out on the build step:
Configure:
cmake -DCMAKE_BUILD_TYPE=Release
-DCMAKE_INSTALL_PREFIX=/home/***/local
-DCMAKE_FIND_FRAMEWORK=LAST
-Wno-dev
-DDEAL_II_COMPONENT_COMPAT_FILES=OFF
-DDEAL_II_COMPONENT_EXAMPLES=ON
-DDEAL_II_COMPONENT_MESH_CONVERTER=ON
-DCMAKE_C_COMPILER=mpicc
-DCMAKE_CXX_COMPILER=mpicc
-DCMAKE_Fortran_COMPILER=mpif90
-DMUPARSER_DIR=/software/libraries/muparser/2.2.2
-DARPACK_DIR=/home/***/local
-DHDF5_DIR=/software/libraries/hdf5/1.8.12/intel-13.0/intel.4.1.0
-DZLIB_DIR=/software/libraries/zlib/1.2.7
-DPETSC_DIR=/software/libraries/petsc/3.4.2/intel-13.0
-DBOOST_DIR=/software/libraries/boost/boost_1_51_0
-DMETIS_DIR=/software/libraries/metis/5.1.0/intel-13.0
Build:
[91%] Building CXX object source/fe/CMakeFiles/obj_fe.release.dir/mapping_fe_field.cc.o
cd /home/***/build/dealii-8.3.0/build/source/fe && /software/compilers/intel/13.0/impi/4.1.0.024/bin64/mpicc -I/home/***/build/dealii-8.3.0/build/source/fe -I/home/***/build/dealii-8.3.0/build/include -I/home/***/build/dealii-8.3.0/include -I/home/***/build/dealii-8.3.0/bundled/tbb41_20130401oss/include -I/home/***/build/dealii-8.3.0/bundled/umfpack/UMFPACK/Include -I/home/***/build/dealii-8.3.0/bundled/umfpack/AMD/Include -I/software/compilers/intel/13.0/impi/4.1.0.024/intel64/include -I/software/libraries/zlib/1.2.7/include -I/software/libraries/metis/5.1.0/intel-13.0/include -I/software/libraries/petsc/3.4.2/intel-13.0/include -I/opt/mpi/bullxmpi/1.1.17.1/include -I/software/libraries/boost/boost_1_51_0/include -I/software/libraries/hdf5/1.8.12/intel-13.0/intel.4.1.0/include -I/software/libraries/muparser/2.2.2/include -fpic -ansi -w2 -wd68 -wd135 -wd175 -wd177 -wd191 -wd193 -wd279 -wd327 -wd383 -wd981 -wd1418 -wd1478 -wd1572 -wd2259 -wd21 -wd2536 -wd15531 -wd111 -wd128 -wd185 -wd280 -Wno-return-type -Wno-parentheses -O2 -no-ansi-alias -ip -funroll-loops -no-vec -o CMakeFiles/obj_fe.release.dir/mapping_fe_field.cc.o -c /home/***/build/dealii-8.3.0/source/fe/mapping_fe_field.cc
/home/***/build/dealii-8.3.0/source/fe/mapping_fe_field.cc(1224): error: class "dealii::Vector<double>" has no member "cell_iterator"
typename DH::cell_iterator dof_cell(*cell, euler_dof_handler);
detected during:
instantiation of "void dealii::MappingFEField<dim, spacedim, VECTOR, DH>::update_internal_dofs(const dealii::Triangulation<dim, spacedim>::cell_iterator &, dealii::MappingFEField<dim, spacedim, dealii::Vector<double>, dealii::DoFHandler<dim, spacedim>>::InternalData &) const [with dim=1, spacedim=1, VECTOR=dealii::DoFHandler<1, 1>, DH=dealii::Vector<double>]" at line 782
I wondered if anyone had any insight as to what could be failing, or what 3rd party component is responsible for that file which I should investigate?
Cheers! :)
Wolfgang Bangerth
Dec 1, 2015, 9:58:30 AM12/1/15
to dea...@googlegroups.com
On 12/01/2015 08:53 AM, Jonathan O'Connell wrote:
>
> /home/***/build/dealii-8.3.0/source/fe/mapping_fe_field.cc(1224): error:
> class "dealii::Vector<double>" has no member "cell_iterator"
> typename DH::cell_iterator dof_cell(*cell, euler_dof_handler);
>
> detected during:
> instantiation of "void dealii::MappingFEField<dim, spacedim,
> VECTOR, DH>::update_internal_dofs(const dealii::Triangulation<dim,
> spacedim>::cell_iterator &, dealii::MappingFEField<dim, spacedim,
> dealii::Vector<double>, dealii::DoFHandler<dim, spacedim>>::InternalData
> &) const [with dim=1, spacedim=1, VECTOR=dealii::DoFHandler<1, 1>,
> DH=dealii::Vector<double>]" at line 782
This is the problem:
>
> /home/***/build/dealii-8.3.0/source/fe/mapping_fe_field.cc(1224): error:
> class "dealii::Vector<double>" has no member "cell_iterator"
> typename DH::cell_iterator dof_cell(*cell, euler_dof_handler);
>
> detected during:
> instantiation of "void dealii::MappingFEField<dim, spacedim,
> VECTOR, DH>::update_internal_dofs(const dealii::Triangulation<dim,
> spacedim>::cell_iterator &, dealii::MappingFEField<dim, spacedim,
> dealii::Vector<double>, dealii::DoFHandler<dim, spacedim>>::InternalData
> &) const [with dim=1, spacedim=1, VECTOR=dealii::DoFHandler<1, 1>,
> DH=dealii::Vector<double>]" at line 782
VECTOR=dealii::DoFHandler<1, 1>,
DH=dealii::Vector<double>
This clearly makes no sense. I suspect that the error message you posted
DH=dealii::Vector<double>
is truncated. Is this line 782 of mapping_fe_field.cc?
Best
W.
--
------------------------------------------------------------------------
Wolfgang Bangerth email: bang...@math.tamu.edu
www: http://www.math.tamu.edu/~bangerth/
Jonathan O'Connell
Dec 1, 2015, 10:26:49 AM12/1/15
to deal.II User Group
It was truncated indeed, the full error message is in fact 499 lines long!
You can find the full output here: https://dl.dropboxusercontent.com/u/4763914/deal_error.txt
Thanks for any insight you can give! :)
Thanks for any insight you can give! :)
Bruno Turcksin
Dec 1, 2015, 10:36:03 AM12/1/15
to deal.II User Group
Hi,
are you using the Intel 13.0 compiler? If so, can you use a newer compiler?
Best,
Bruno
are you using the Intel 13.0 compiler? If so, can you use a newer compiler?
Best,
Bruno
Jonathan O'Connell
Dec 1, 2015, 10:42:54 AM12/1/15
to deal.II User Group
Hi,
I can use a newer compiler, but all the modules I load (petsc, hdf5 etc..) must be built against the same compiler, and as intel-13 is the default on the cluster, most modules are built against that. Also they're both providing the same version of GCC compatibility, 4.4.7.
I do however see GCC 4.9 sitting in the 'untested' branch of the available modules. I'll try with Intel 15, then GCC 4.9 to see if it is a compiler bug, and if that fixes it I guess I'll be building essential 3rd party libs in my home directory.
Cheers,
Jonathan
Bruno Turcksin
Dec 1, 2015, 10:51:33 AM12/1/15
to dea...@googlegroups.com
Jonathan,
Intel 15 should work. If you need to install third party libraries, you can use candi (https://github.com/koecher/candi). Look in candi.cfg to turn on/off the libraries that you want, then run:
./candi.sh -j8 --prefix=/path/to/home --platform=deal.II/platforms/supported/linux_cluster.platform
Best,
Bruno
Intel 15 should work. If you need to install third party libraries, you can use candi (https://github.com/koecher/candi). Look in candi.cfg to turn on/off the libraries that you want, then run:
./candi.sh -j8 --prefix=/path/to/home --platform=deal.II/platforms/supported/linux_cluster.platform
Best,
Bruno
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Wolfgang Bangerth
Dec 1, 2015, 11:28:38 AM12/1/15
to dea...@googlegroups.com
On 12/01/2015 09:26 AM, Jonathan O'Connell wrote:
> It was truncated indeed, the full error message is in fact 499 lines long!
>
> You can find the full output
> here: https://dl.dropboxusercontent.com/u/4763914/deal_error.txt
>
> Thanks for any insight you can give! :)
It's a real bug that was already fixed by Daniel Arndt in October.
> It was truncated indeed, the full error message is in fact 499 lines long!
>
> You can find the full output
> here: https://dl.dropboxusercontent.com/u/4763914/deal_error.txt
>
> Thanks for any insight you can give! :)
Please apply this patch
https://github.com/dealii/dealii/commit/aa0c479c0f6e39aee94b48b307d8c714f7c0c45c
by hand to your copy of deal.II and the compilation should be able to
continue.
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