Your message dated Wed, 05 Jul 2017 19:00:12 +0000
with message-id <e1dspx2-0005qw...@fasolo.debian.org>
and subject line Bug#863828: fixed in dolfin 2016.2.0-4
has caused the Debian Bug report #863828,
regarding python3-instant: undefined symbol: PyClass_Type during interpolate
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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--
863828: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=863828
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: python3-instant
Version: 2016.2.0-2
Severity: normal
Testing the new python3 dolfin. It works fine on my own scripts. But
seems to fail when instant is invoked by interpolate.
$ instant-clean-3
$ ipython3
Python 3.5.3 (default, Jan 19 2017, 14:11:04)
In [1]: from fenics import * # dolfin module behaves the same
In [2]: mesh = UnitSquareMesh(2, 2)
In [3]: V = FunctionSpace(mesh, 'P', 1)
In [4]: u = interpolate(Expression('x[0] + x[1]', degree=1), V)
...
AssertionError: Failed to import module found in cache. Modulename:
'dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2';
Path:
'/home/user/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2';
ImportError:/home/user/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2/_dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2.so:
undefined symbol: PyClass_Type;
The full error report is:
In [4]: u = interpolate(Expression('x[0] + x[1]', degree=1), V)
Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
--- Instant: compiling ---
In instant.import_module_directly: Failed to import module
'dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2' from
'/home/user/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2';
ImportError:/home/user/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2/_dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2.so:
undefined symbol: PyClass_Type;
Failed to import module found in cache. Modulename:
'dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2';
Path:
'/home/user/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2';
ImportError:/home/user/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2/_dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2.so:
undefined symbol: PyClass_Type;
---------------------------------------------------------------------------
AssertionError Traceback (most recent call last)
<ipython-input-4-e06382777336> in <module>()
----> 1 u = interpolate(Expression('x[0] + x[1]', degree=1), V)
/usr/lib/python3/dist-packages/dolfin/functions/expression.py in __new__(cls,
cppcode, *args, **kwargs)
652 cpp_base, members = compile_expressions([cppcode],
653
[generic_function_members],
--> 654
mpi_comm=kwargs.get("mpi_comm"))
655 cpp_base, members = cpp_base[0], members[0]
656
/usr/lib/python3/dist-packages/dolfin/compilemodules/expressions.py in
compile_expressions(cppargs, generic_function_members, mpi_comm)
212 "\n\n".join(code_snippets), classnames,
213 additional_declarations="\n".join(additional_declarations),
--> 214 mpi_comm=mpi_comm)
215
216 return expression_classes, all_members
/usr/lib/python3/dist-packages/dolfin/compilemodules/expressions.py in
compile_expression_code(code, classnames, module_name, additional_declarations,
mpi_comm)
139 compiled_module = compile_extension_module(
140 code, additional_declarations=additional_declarations,
--> 141 mpi_comm=mpi_comm)
142
143 # Get the compiled class
/usr/lib/python3/dist-packages/dolfin/compilemodules/jit.py in mpi_jit(*args,
**kwargs)
66 # Just call JIT compiler when running in serial
67 if MPI.size(mpi_comm) == 1:
---> 68 return local_jit(*args, **kwargs)
69
70 # Compile first on process 0
/usr/lib/python3/dist-packages/dolfin/compilemodules/compilemodule.py in
compile_extension_module(code, module_name, additional_declarations,
additional_system_headers, mpi_comm, **instant_kwargs)
470 code=code,
471 additional_declarations=additional_declarations,
--> 472 **instant_kwargs)
473
474 sys.stdout.flush()
/usr/lib/python3/dist-packages/instant/build.py in build_module(modulename,
source_directory, code, init_code, additional_definitions,
additional_declarations, sources, wrap_headers, local_headers, system_headers,
include_dirs, library_dirs, libraries, swigargs, swig_include_dirs, cppargs,
lddargs, object_files, arrays, generate_interface, generate_setup,
cmake_packages, signature, cache_dir)
585
586 # Import module and place in memory cache
--> 587 module = import_and_cache_module(module_path, modulename,
moduleids)
588
589 if not module:
/usr/lib/python3/dist-packages/instant/cache.py in
import_and_cache_module(path, modulename, moduleids)
90 module, e = import_module_directly(path, modulename)
91 instant_assert(module is not None, "Failed to import module found
in cache. Modulename: '%s';\nPath: '%s';\n%s:%s;" % (modulename, path,
type(e).__name__,
---> 92
e))
93 for moduleid in moduleids:
94 place_module_in_memory_cache(moduleid, module)
/usr/lib/python3/dist-packages/instant/output.py in instant_assert(condition,
*message)
101 _log.error(*message)
102 text = message[0] % message[1:]
--> 103 raise AssertionError(text)
104
105
AssertionError: Failed to import module found in cache. Modulename:
'dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2';
Path:
'/home/user/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2';
ImportError:/home/user/.cache/instant/python3.5/cache/dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2/_dolfin_ee8f3791ac0426bc9e123d64557ccde25f2d90f2.so:
undefined symbol: PyClass_Type;
-- System Information:
Debian Release: 9.0
APT prefers unstable
APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64
(x86_64)
Foreign Architectures: i386
Kernel: Linux 4.9.0-3-amd64 (SMP w/4 CPU cores)
Locale: LANG=en_AU.UTF-8, LC_CTYPE=en_AU.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
Versions of packages python3-instant depends on:
ii build-essential 12.3
ii cmake 3.7.2-1
ii pkg-config 0.29-4+b1
ii python3-dev 3.5.3-1
ii python3-numpy 1:1.12.1-3
ii python3-six 1.10.0-4
pn python3:any <none>
ii swig 3.0.10-1.1
python3-instant recommends no packages.
python3-instant suggests no packages.
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: dolfin
Source-Version: 2016.2.0-4
We believe that the bug you reported is fixed in the latest version of
dolfin, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 863...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Drew Parsons <dpars...@debian.org> (supplier of updated dolfin package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 07 Jun 2017 12:14:40 +0800
Source: dolfin
Binary: libdolfin-dev libdolfin2016.2 libdolfin2016.2-dbg python-dolfin
python3-dolfin python-dolfin-dbg python3-dolfin-dbg dolfin-doc dolfin-bin
Architecture: source all amd64
Version: 2016.2.0-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Science Team
<debian-science-maintainers@lists.alioth.debian.org>
Changed-By: Drew Parsons <dpars...@debian.org>
Description:
dolfin-bin - Executable scripts for DOLFIN
dolfin-doc - Documentation and demo programs for DOLFIN
libdolfin-dev - Shared links and header files for DOLFIN
libdolfin2016.2 - Shared libraries for DOLFIN
libdolfin2016.2-dbg - Shared libraries with debugging symbols for DOLFIN
python-dolfin - Python interface for DOLFIN (Python 2)
python-dolfin-dbg - Python 2 extension modules for DOLFIN with debugging
symbols
python3-dolfin - Python interface for DOLFIN (Python 3)
python3-dolfin-dbg - Python 3 extension modules for DOLFIN with debugging
symbols
Closes: 863828 863829
Changes:
dolfin (2016.2.0-4) unstable; urgency=medium
.
[ Johannes Ring ]
* d/rules:
- Re-generate swig interface with correct Python version
before build and install. Closes: #863829.
- Build for Python 2 after Python 3 by switching the order in
PYVERS, since Python 2 is default.
* Add patch vtk-python2-only-cmake-usefile.patch that disables the
vtk section in UseDOLFIN.cmake for Python 3. Closes: #863828.
* d/control: Add python-ffc to Depends for binary package
libdolfin-dev (provides ufc.h).
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