p.s. given recent updates to petsc/slepc 3.9 you would need to install a current development version of deal.II, i.e. spack install dealii@develop The soon-to-be-release 9.0 will support new petsc/slepc.
On Wednesday, April 25, 2018 at 12:04:06 AM UTC+2, Denis Davydov wrote: > > @Jane > > If you need to get it going soon, try following > https://github.com/dealii/dealii/wiki/deal.II-in-Spack > Roughly it's only 3 steps (assuming that you have XCode and command-line > tools): > 1. install gcc with spack > 2. configure gfortran to be used with clang > http://spack.readthedocs.io/en/latest/getting_started.html#mixed-toolchains > > 3. install dealii > > Let me know if you have issues, I am running this setup on the latest > XCode/ Apple's clang without issues. > > @Daniel > > It's used from the pre-build app by Luca > > Denis. > > On Tuesday, April 24, 2018 at 5:36:21 PM UTC+2, Daniel Arndt wrote: >> >> Jane, >> >> this looks like you are using a compiler (clang on macOS?) that doesn't >> define std::auto_ptr anymore and the used boost library doesn't detect this. >> A recent developer version (there will soon be a release) should >> circumvent the problem. >> How did you install deal.II? Are you using spack directly or a >> pre-compiled package? >> If you are using spack directly you should just rerun it to get a recent >> developer version. >> >> Best, >> Daniel >> >> >> Am Dienstag, 24. April 2018 16:14:51 UTC+2 schrieb Jane Lee: >>> >>> Hi all, >>> I'm unfortunately not very good with computers and the nitty gritty >>> details of the things that go on behind the program. >>> I'm running dealii-9.0 instead of 8.5.1 because i did a system update >>> and 8.5.1 wasn't working. >>> I stupidly did a minor update forgetting that i had issues after updates >>> previously, and the same code which i was running fine just before the >>> update and restart is now not working when 'make run' is done. >>> The error is a bit too complicated for me to understand... >>> can anyone help? Am desperate to get things up and running >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/include/deal.II/base/convergence_table.h:21: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/include/deal.II/base/table_handler.h:31: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/serialization/map.hpp:24: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/archive/detail/basic_iarchive.hpp:23: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/scoped_ptr.hpp:14: >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/smart_ptr/scoped_ptr.hpp:74:31: >>> >>> **error: * >>> >>> * no template named 'auto_ptr' in namespace 'std'* >>> >>> explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( >>> p.release() ) >>> >>> * ~~~~~^* >>> >>> In file included from >>> /Users/janelee/Documents/fullmodel/full_solver/final/stokes.cc:7: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/include/deal.II/base/convergence_table.h:21: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/include/deal.II/base/table_handler.h:31: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/serialization/map.hpp:24: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/archive/detail/basic_iarchive.hpp:28: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/archive/detail/helper_collection.hpp:27: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/smart_ptr/shared_ptr.hpp:28: >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/smart_ptr/detail/shared_count.hpp:402:33: >>> >>> **error: * >>> >>> * no template named 'auto_ptr' in namespace 'std'* >>> >>> explicit shared_count( std::auto_ptr<Y> & r ): pi_( new >>> sp_counted_i... >>> >>> * ~~~~~^* >>> >>> In file included from >>> /Users/janelee/Documents/fullmodel/full_solver/final/stokes.cc:7: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/include/deal.II/base/convergence_table.h:21: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/include/deal.II/base/table_handler.h:31: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/serialization/map.hpp:24: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/archive/detail/basic_iarchive.hpp:28: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/archive/detail/helper_collection.hpp:27: >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/smart_ptr/shared_ptr.hpp:255:65: >>> >>> **error: * >>> >>> * no member named 'auto_ptr' in namespace 'std'* >>> >>> template< class T, class R > struct sp_enable_if_auto_ptr< >>> std::auto_ptr... >>> >>> * ~~~~~^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/smart_ptr/shared_ptr.hpp:255:75: >>> >>> **error: * >>> >>> * 'T' does not refer to a value* >>> >>> ...class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >>> >, R > >>> >>> * ^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/smart_ptr/shared_ptr.hpp:255:17: >>> >>> **note: * >>> >>> declared here >>> >>> template< class T, class R > struct sp_enable_if_auto_ptr< >>> std::auto_ptr... >>> >>> * ^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/smart_ptr/shared_ptr.hpp:255:81: >>> >>> **error: * >>> >>> * expected ';' at end of declaration* >>> >>> ...class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >>> >, R > >>> >>> * >>> ^* >>> >>> >>> ; >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/smart_ptr/shared_ptr.hpp:255:82: >>> >>> **error: * >>> >>> * expected unqualified-id* >>> >>> ...class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >>> >, R > >>> >>> * >>> ^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/smart_ptr/shared_ptr.hpp:454:31: >>> >>> **error: * >>> >>> * no template named 'auto_ptr' in namespace 'std'* >>> >>> explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn() >>> >>> * ~~~~~^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/smart_ptr/shared_ptr.hpp:467:22: >>> >>> **error: * >>> >>> * no template named 'auto_ptr' in namespace 'std'* >>> >>> shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn() >>> >>> * ~~~~~^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/smart_ptr/shared_ptr.hpp:544:34: >>> >>> **error: * >>> >>> * no template named 'auto_ptr' in namespace 'std'* >>> >>> shared_ptr & operator=( std::auto_ptr<Y> & r ) >>> >>> * ~~~~~^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/smart_ptr/shared_ptr.hpp:553:34: >>> >>> **error: * >>> >>> * no template named 'auto_ptr' in namespace 'std'* >>> >>> shared_ptr & operator=( std::auto_ptr<Y> && r ) >>> >>> * ~~~~~^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/smart_ptr/shared_ptr.hpp:555:38: >>> >>> **error: * >>> >>> * no template named 'auto_ptr' in namespace 'std'* >>> >>> this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( >>> *this ); >>> >>> * ~~~~~^* >>> >>> In file included from >>> /Users/janelee/Documents/fullmodel/full_solver/final/stokes.cc:7: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/include/deal.II/base/convergence_table.h:21: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/include/deal.II/base/table_handler.h:31: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/serialization/map.hpp:24: >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/archive/detail/basic_iarchive.hpp:63:16: >>> >>> **error: * >>> >>> * non-const lvalue reference to type* >>> >>> * 'boost::archive::detail::helper_collection' cannot bind to a >>> value of* >>> >>> * unrelated type 'boost::archive::detail::basic_iarchive'* >>> >>> return *this; >>> >>> * ^~~~~* >>> >>> In file included from >>> /Users/janelee/Documents/fullmodel/full_solver/final/stokes.cc:12: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/include/deal.II/grid/tria.h:30: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/signals2.hpp:19: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/signals2/signal.hpp:18: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/function.hpp:24: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/function/detail/prologue.hpp:18: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/mem_fn.hpp:22: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/bind/mem_fn.hpp:25: >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/get_pointer.hpp:48:23: >>> >>> **error: * >>> >>> * redefinition of 'get_pointer' as different kind of symbol* >>> >>> template<class T> T * get_pointer(std::auto_ptr<T> const& p) >>> >>> * ^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/get_pointer.hpp:20:23: >>> >>> **note: * >>> >>> previous definition is here >>> >>> template<class T> T * get_pointer(T * p) >>> >>> * ^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/get_pointer.hpp:48:40: >>> >>> **error: * >>> >>> * no member named 'auto_ptr' in namespace 'std'* >>> >>> template<class T> T * get_pointer(std::auto_ptr<T> const& p) >>> >>> * ~~~~~^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/get_pointer.hpp:48:49: >>> >>> **error: * >>> >>> * 'T' does not refer to a value* >>> >>> template<class T> T * get_pointer(std::auto_ptr<T> const& p) >>> >>> * ^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/get_pointer.hpp:48:16: >>> >>> **note: * >>> >>> declared here >>> >>> template<class T> T * get_pointer(std::auto_ptr<T> const& p) >>> >>> * ^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/get_pointer.hpp:48:52: >>> >>> **error: * >>> >>> * expected expression* >>> >>> template<class T> T * get_pointer(std::auto_ptr<T> const& p) >>> >>> * ^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/get_pointer.hpp:48:61: >>> >>> **error: * >>> >>> * expected ';' at end of declaration* >>> >>> template<class T> T * get_pointer(std::auto_ptr<T> const& p) >>> >>> * ^* >>> >>> ; >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/get_pointer.hpp:49:1: >>> >>> **error: * >>> >>> * expected unqualified-id* >>> >>> { >>> >>> *^* >>> >>> In file included from >>> /Users/janelee/Documents/fullmodel/full_solver/final/stokes.cc:12: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/include/deal.II/grid/tria.h:30: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/signals2.hpp:19: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/signals2/signal.hpp:22: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/signals2/connection.hpp:24: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/signals2/slot.hpp:22: >>> >>> In file included from >>> /Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/signals2/detail/tracked_objects_visitor.hpp:18: >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/signals2/slot_base.hpp:100:36: >>> >>> **error: * >>> >>> * no viable conversion from 'shared_ptr<void>' to* >>> >>> * >>> 'std::__1::vector<boost::variant<boost::weak_ptr<boost::signals2::detail::trackable_pointee>,* >>> >>> * boost::weak_ptr<void>, >>> boost::signals2::detail::foreign_void_weak_ptr>,* >>> >>> * >>> std::__1::allocator<boost::variant<boost::weak_ptr<boost::signals2::detail::trackable_pointee>,* >>> >>> * boost::weak_ptr<void>, >>> boost::signals2::detail::foreign_void_weak_ptr> >* >>> >>> * >::value_type' (aka* >>> >>> * >>> 'boost::variant<boost::weak_ptr<boost::signals2::detail::trackable_pointee>,* >>> >>> * boost::weak_ptr<void>, >>> boost::signals2::detail::foreign_void_weak_ptr>')* >>> >>> _tracked_objects.push_back(signal.lock_pimpl()); >>> >>> * ^~~~~~~~~~~~~~~~~~~* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/variant/variant.hpp:1782:5: >>> >>> **note: * >>> >>> candidate constructor [with T = boost::shared_ptr<void>] >>> >>> variant(T&& operand, >>> >>> * ^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/variant/variant.hpp:1758:5: >>> >>> **note: * >>> >>> candidate constructor [with T = boost::shared_ptr<void>] >>> >>> variant(const T& operand, >>> >>> * ^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/variant/variant.hpp:1768:5: >>> >>> **note: * >>> >>> candidate constructor [with T = boost::shared_ptr<void>] not >>> viable: >>> >>> expects an l-value for 1st argument >>> >>> variant( >>> >>> * ^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/variant/variant.hpp:1797:5: >>> >>> **note: * >>> >>> candidate constructor not viable: no known conversion from >>> >>> 'shared_ptr<void>' to 'const >>> >>> >>> boost::variant<boost::weak_ptr<boost::signals2::detail::trackable_pointee>, >>> >>> boost::weak_ptr<void>, >>> boost::signals2::detail::foreign_void_weak_ptr> &' >>> >>> for 1st argument >>> >>> variant(const variant& operand) >>> >>> * ^* >>> >>> */Applications/deal.II-9.0-spack.app/Contents/Resources/spack/view/include/boost/variant/variant.hpp:1808:5: >>> >>> **note: * >>> >>> candidate constructor not viable: no known conversion from >>> >>> 'shared_ptr<void>' to >>> >>> >>> 'boost::variant<boost::weak_ptr<boost::signals2::detail::trackable_pointee>, >>> >>> boost::weak_ptr<void>, >>> boost::signals2::detail::foreign_void_weak_ptr> &&' >>> >>> for 1st argument >>> >>> variant(variant&& operand) >>> BOOST_NOEXCEPT_IF(variant_move_noexcept_c... >>> >>> * ^* >>> >>> */Library/Developer/CommandLineTools/usr/include/c++/v1/vector:680:59: * >>> *note: * >>> >>> passing argument to parameter '__x' here >>> >>> _LIBCPP_INLINE_VISIBILITY void push_back(value_type&& __x); >>> >>> * ^* >>> >>> *fatal error: *too many errors emitted, stopping now [-ferror-limit=] >>> >>> 20 errors generated. >>> >> -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. 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