Unable to compile in ubuntu 22.04

[sabyasachi chatterjee]

Hello,

I recently upgraded to ubuntu 22.04 and the deal ii version I am using is 9.1.1. It used to compile fine in ubuntu 20.04. However, now I am seeing the following error:

***************************************************************************************

In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22,
                 from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23,
                 from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14,
                 from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42,
                 from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25,
                 from /usr/include/boost/smart_ptr/shared_ptr.hpp:29,
                 from /usr/include/boost/archive/detail/helper_collection.hpp:27,
                 from /usr/include/boost/archive/detail/basic_iarchive.hpp:28,
                 from /usr/include/boost/archive/detail/common_iarchive.hpp:21,
                 from /usr/include/boost/archive/basic_binary_iarchive.hpp:30,
                 from /usr/include/boost/archive/binary_iarchive_impl.hpp:21,
                 from /usr/include/boost/archive/binary_iarchive.hpp:20,
                 from /home/sabyasachi/Documents/dealii_libraries/dealii_setup/deal.II-v9.1.1/include/deal.II/base/utilities.h:45,
                 from /home/sabyasachi/Documents/dealii_libraries/dealii_setup/deal.II-v9.1.1/include/deal.II/base/tensor.h:26,
                 from /home/sabyasachi/Documents/dealii_libraries/dealii_setup/deal.II-v9.1.1/include/deal.II/base/point.h:23,
                 from /home/sabyasachi/Documents/dealii_libraries/dealii_setup/deal.II-v9.1.1/include/deal.II/base/quadrature.h:22,
                 from /home/sabyasachi/Documents/dealii_libraries/dealii_setup/deal.II-v9.1.1/include/deal.II/base/quadrature_lib.h:22,
                 from /home/sabyasachi/Documents/postdoc/irradiated_hardness_test_contact/main_hardness_contact.cc:1:
/usr/include/boost/detail/no_exceptions_support.hpp:17:1: note: ‘#pragma message: This header is deprecated. Use <boost/core/no_exceptions_support.hpp> instead.’
   17 | BOOST_HEADER_DEPRECATED("<boost/core/no_exceptions_support.hpp>")
      | ^~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/sabyasachi/Documents/dealii_libraries/dealii_setup/deal.II-v9.1.1/include/deal.II/grid/grid_tools.h:45,
                 from /home/sabyasachi/Documents/postdoc/irradiated_hardness_test_contact/main_hardness_contact.cc:33:
/usr/include/boost/geometry/index/detail/serialization.hpp: In static member function ‘static boost::geometry::index::detail::rtree::load<MembersHolder>::node_pointer boost::geometry::index::detail::rtree::load<MembersHolder>::raw_apply(Archive&, unsigned int, boost::geometry::index::detail::rtree::load<MembersHolder>::size_type, boost::geometry::index::detail::rtree::load<MembersHolder>::size_type&, const parameters_type&, const translator_type&, boost::geometry::index::detail::rtree::load<MembersHolder>::allocators_type&, boost::geometry::index::detail::rtree::load<MembersHolder>::size_type)’:
/usr/include/boost/geometry/index/detail/serialization.hpp:399:49: error: ‘Allocators’ was not declared in this scope; did you mean ‘allocators’?
  399 |             node_pointer n = rtree::create_node<Allocators, internal_node>::apply(allocators);              // MAY THROW (A)
      |                                                 ^~~~~~~~~~
      |                                                 allocators
/usr/include/boost/geometry/index/detail/serialization.hpp:399:74: error: template argument 1 is invalid
  399 |             node_pointer n = rtree::create_node<Allocators, internal_node>::apply(allocators);              // MAY THROW (A)
      |                                                                          ^
/usr/include/boost/geometry/index/detail/serialization.hpp:422:49: error: ‘Allocators’ was not declared in this scope; did you mean ‘allocators’?
  422 |             node_pointer n = rtree::create_node<Allocators, leaf>::apply(allocators);                       // MAY THROW (A)
      |                                                 ^~~~~~~~~~
      |                                                 allocators

********************************************************************************************

Probably it is something related to boost library. My code is an extension of Step 18 and I think it does not need the boost library. Please suggest how to resolve this. 

Thanks,

Sabyasachi

[Daniel Arndt]

Sabyasachi,

What is the boost version of the system-provided boost installation?

You should be able to work around this issue by forcing deal.II to use its bundled boost package via using `-DDEAL_II_FORCE_BUNDLED_BOOST=ON` when configuring deal.II.

Best,

Daniel

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[sabyasachi chatterjee]

Daniel,

Thanks for the suggestion. The boost version in ubuntu 22.04 by default is 1.74.0.

I tried reinstalling deal ii (version 9.1.1) using candi with DEAL_II_FORCE_BUNDLED_BOOST=ON in candi.cfg and received the following error:

*********************************************************************************************************

/usr/include/boost/detail/no_exceptions_support.hpp:17:1: note: ‘#pragma message: This header is deprecated. Use <boost/core/no_exceptions_support.hpp> instead.’

   17 | BOOST_HEADER_DEPRECATED("<boost/core/no_exceptions_support.hpp>")
      | ^~~~~~~~~~~~~~~~~~~~~~~

[ 44%] Built target obj_fe_release
make: *** [Makefile:136: all] Error 2
Failure with exit status: 2

Exit message: There was a problem building dealii v9.1.1.

*********************************************************************************************************'

I also tried to install without DEAL_II_FORCE_BUNDLED_BOOST=ON in candi.cfg and still it won't compile with the following error:

*********************************************************************************************************

/usr/include/boost/geometry/index/detail/serialization.hpp:579:79: error: expression list treated as compound expression in initializer [-fpermissive]
  579 |     subtree_destroyer remover(tree.members().root, tree.members().allocators());
      |                                                                               ^

make[2]: *** [source/base/CMakeFiles/obj_base_release.dir/build.make:496: source/base/CMakeFiles/obj_base_release.dir/parsed_convergence_table.cc.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [CMakeFiles/Makefile2:1841: source/base/CMakeFiles/obj_base_release.dir/all] Error 2
make: *** [Makefile:136: all] Error 2
Failure with exit status: 2

*********************************************************************************************************

However, when I install latest deal ii version (9.4.2), it installed successfully. So probably there is some compatibility issue of version 9.1.1 in ubuntu 22.04 related to the boost library version.

Best,

Sabyasachi