Your message dated Wed, 30 Dec 2020 10:23:08 +1100
with message-id <88ad98a38dc07ec8f0865b319beb7...@debian.org>
and subject line dolfin: FTBFS: MixedLinearVariationalSolver.cpp:240:23: error:
variable ‘dolfin::PETScNestMatrix A’ has initializer but incomplete type
has caused the Debian Bug report #978206,
regarding dolfin: FTBFS: MixedLinearVariationalSolver.cpp:240:23: error:
variable ‘dolfin::PETScNestMatrix A’ has initializer but incomplete type
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
978206: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=978206
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: dolfin
Version: 2019.2.0~git20200629.946dbd3+lfs-4
Severity: serious
Justification: FTBFS on amd64
Tags: bullseye sid ftbfs
Usertags: ftbfs-20201226 ftbfs-bullseye
Hi,
During a rebuild of all packages in sid, your package failed to build
on amd64.
Relevant part (hopefully):
> cd "/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu/dolfin" && /usr/bin/c++
> -DDOLFIN_VERSION=\"2019.2.0.dev0\" -DHAS_CHOLMOD -DHAS_HDF5 -DHAS_MPI
> -DHAS_UMFPACK -DHAS_ZLIB -DNDEBUG -Ddolfin_EXPORTS -I"/<<PKGBUILDDIR>>"
> -I"/<<PKGBUILDDIR>>/obj-x86_64-linux-gnu" -isystem
> /usr/lib/python3/dist-packages/ffc/backends/ufc -isystem /usr/include/eigen3
> -isystem /usr/include/hdf5/openmpi -isystem /usr/include/suitesparse -isystem
> /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem
> /usr/lib/x86_64-linux-gnu/openmpi/include -fpermissive -g -O2
> -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat
> -Werror=format-security -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=.
> -fstack-protector-strong -Wformat -Werror=format-security -O2 -g -DNDEBUG
> -fPIC -std=c++11 -o
> CMakeFiles/dolfin.dir/fem/MixedLinearVariationalSolver.cpp.o -c
> "/<<PKGBUILDDIR>>/dolfin/fem/MixedLinearVariationalSolver.cpp"
> /<<PKGBUILDDIR>>/dolfin/fem/MixedLinearVariationalSolver.cpp: In member
> function ‘void
> dolfin::MixedLinearVariationalSolver::solve(dolfin::MixedLinearVariationalSolver::assembled_system_type)’:
> /<<PKGBUILDDIR>>/dolfin/fem/MixedLinearVariationalSolver.cpp:240:23: error:
> variable ‘dolfin::PETScNestMatrix A’ has initializer but incomplete type
> 240 | PETScNestMatrix A(As);
> | ^
> /<<PKGBUILDDIR>>/dolfin/fem/MixedLinearVariationalSolver.cpp:281:5: error:
> ‘PETScLUSolver’ was not declared in this scope
> 281 | PETScLUSolver solver(comm, solver_type);
> | ^~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/dolfin/fem/MixedLinearVariationalSolver.cpp:285:5: error:
> ‘solver’ was not declared in this scope; did you mean ‘solve’?
> 285 | solver.set_operator(A);
> | ^~~~~~
> | solve
> /<<PKGBUILDDIR>>/dolfin/fem/MixedLinearVariationalSolver.cpp:290:5: error:
> ‘PETScKrylovSolver’ was not declared in this scope
> 290 | PETScKrylovSolver solver(comm, solver_type, pc_type);
> | ^~~~~~~~~~~~~~~~~
> /<<PKGBUILDDIR>>/dolfin/fem/MixedLinearVariationalSolver.cpp:291:5: error:
> ‘solver’ was not declared in this scope; did you mean ‘solve’?
> 291 | solver.parameters.update(parameters("krylov_solver"));
> | ^~~~~~
> | solve
> /<<PKGBUILDDIR>>/dolfin/fem/MixedLinearVariationalSolver.cpp:303:13: error:
> ‘PETScVector’ was not declared in this scope
> 303 | as_type<PETScVector>(u)->update_ghost_values();
> | ^~~~~~~~~~~
> /<<PKGBUILDDIR>>/dolfin/fem/MixedLinearVariationalSolver.cpp:303:27: error:
> no matching function for call to ‘as_type<<expression error>
> >(std::shared_ptr<dolfin::GenericVector>&)’
> 303 | as_type<PETScVector>(u)->update_ghost_values();
> | ^
> In file included from /<<PKGBUILDDIR>>/dolfin/la/GenericTensor.h:38,
> from /<<PKGBUILDDIR>>/dolfin/la/GenericMatrix.h:34,
> from
> /<<PKGBUILDDIR>>/dolfin/fem/MixedLinearVariationalSolver.cpp:27:
> /<<PKGBUILDDIR>>/dolfin/la/LinearAlgebraObject.h:64:8: note: candidate:
> ‘template<class Y, class X> Y& dolfin::as_type(X&)’
> 64 | Y& as_type(X& x)
> | ^~~~~~~
> /<<PKGBUILDDIR>>/dolfin/la/LinearAlgebraObject.h:64:8: note: template
> argument deduction/substitution failed:
> /<<PKGBUILDDIR>>/dolfin/fem/MixedLinearVariationalSolver.cpp:303:27: error:
> template argument 1 is invalid
> 303 | as_type<PETScVector>(u)->update_ghost_values();
> | ^
> In file included from /<<PKGBUILDDIR>>/dolfin/la/GenericTensor.h:38,
> from /<<PKGBUILDDIR>>/dolfin/la/GenericMatrix.h:34,
> from
> /<<PKGBUILDDIR>>/dolfin/fem/MixedLinearVariationalSolver.cpp:27:
> /<<PKGBUILDDIR>>/dolfin/la/LinearAlgebraObject.h:84:24: note: candidate:
> ‘template<class Y, class X> std::shared_ptr<_Tp>
> dolfin::as_type(std::shared_ptr<_Tp>)’
> 84 | std::shared_ptr<Y> as_type(std::shared_ptr<X> x)
> | ^~~~~~~
> /<<PKGBUILDDIR>>/dolfin/la/LinearAlgebraObject.h:84:24: note: template
> argument deduction/substitution failed:
> /<<PKGBUILDDIR>>/dolfin/fem/MixedLinearVariationalSolver.cpp:303:27: error:
> template argument 1 is invalid
> 303 | as_type<PETScVector>(u)->update_ghost_values();
> | ^
> make[4]: *** [dolfin/CMakeFiles/dolfin.dir/build.make:618:
> dolfin/CMakeFiles/dolfin.dir/fem/MixedLinearVariationalSolver.cpp.o] Error 1
The full build log is available from:
http://qa-logs.debian.net/2020/12/26/dolfin_2019.2.0~git20200629.946dbd3+lfs-4_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
If you reassign this bug to another package, please marking it as 'affects'-ing
this package. See https://www.debian.org/Bugs/server-control#affects
If you fail to reproduce this, please provide a build log and diff it with me
so that we can identify if something relevant changed in the meantime.
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
--- End Message ---
--- Begin Message ---
The bug is in openmpi, not dolfin (or petsc).
The clue is the cmake error, "Test PETSC_TEST_RUNS with shared library
linking - Failed"
openmpi 4.1.0 (+ pmix 4) caused all clients to fail with the same error,
Bug#978022.
Fixed now in openmpi 4.1.0-3.
--- End Message ---
