Bug#895419: python3-dolfin: JIT compilation fails as python3-instant tries to includes petsc4py from python2
Fabrice
silva at lma.cnrs-mrs.fr
Wed Apr 11 12:14:05 BST 2018
Package: python3-dolfin
Version: 2017.2.0.post0-3
Severity: important
Dear Maintainer,
trying to run the simple following script:
-- test_fenics.py --
import fenics as fe
tmp = fe.Expression("1/x[0]")
-- end test_fenics.py --
the DOLFIN just-in-time compiler is called but fails.
stdout and stderr were captured (see attached files)
$ python3 test_fenics.py >> stdout.log 2>> stderr.log
Is also attached an archive with the .cache/instant folder containing in
particular the compile.log generated by fenics/dolfin.
The following lines are relevant
CMake Error in CMakeLists.txt:
Imported target "dolfin" includes non-existent path
"/usr/lib/python2.7/dist-packages/petsc4py/include"
python3-petsc4py is installed (3.8.1-3), while python-petsc4py is not (and
needs not to be installed)
It makes the package unusable, as no expression can be compiled and used in
finite elements computation
-- System Information:
Debian Release: buster/sid
APT prefers oldstable-updates
APT policy: (500, 'oldstable-updates'), (500, 'unstable'), (500, 'oldstable')
Architecture: amd64 (x86_64)
Kernel: Linux 4.15.0-2-amd64 (SMP w/8 CPU cores)
Locale: LANG=fr_FR.utf8, LC_CTYPE=fr_FR.utf8 (charmap=UTF-8), LANGUAGE=fr_FR.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
Versions of packages python3-dolfin depends on:
ii libboost-timer1.62.0 1.62.0+dfsg-5
ii libc6 2.27-3
ii libdolfin-dev 2017.2.0.post0-3
ii libdolfin2017.2 2017.2.0.post0-3
ii libgcc1 1:8-20180402-1
ii libhdf5-openmpi-100 1.10.0-patch1+docs-4
ii libopenmpi2 2.1.1-8
ii libpetsc-real3.8 3.8.4+dfsg1-1
ii libpython3.6 3.6.5-3
ii libslepc-real3.8 3.8.2+dfsg1-4
ii libstdc++6 8-20180402-1
ii libsz2 1.0.2-1
ii python3 3.6.5-2
ii python3-dijitso 2017.2.0.0-2
ii python3-ffc 2017.2.0.post0-2
ii python3-instant 2017.2.0.0-2
ii python3-numpy [python3-numpy-abi9] 1:1.13.3-2
ii python3-petsc4py 3.8.1-3
ii python3-ply 3.11-1
ii python3-six 1.11.0-2
ii python3-slepc4py 3.8.0-3
ii python3-sympy 1.1.1-5
ii python3-ufl 2017.2.0.0-2
ii zlib1g 1:1.2.8.dfsg-5
python3-dolfin recommends no packages.
Versions of packages python3-dolfin suggests:
pn dolfin-doc <none>
-- no debconf information
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Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
-------------- next part --------------
Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
--- Instant: compiling ---
In instant.recompile: The module did not compile with command 'cmake -DDEBUG=TRUE .', see '/home/fab/.cache/instant/python3.6/error/dolfin_4bedd8911ad2fa3696d85d184d02a288d3294659/compile.log'
Traceback (most recent call last):
File "test_fenics.py", line 57, in <module>
aux_invr = fe.Expression("1/x[0]")
File "/usr/lib/python3/dist-packages/dolfin/functions/expression.py", line 679, in __new__
mpi_comm=kwargs.get("mpi_comm"))
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/expressions.py", line 266, in compile_expressions
mpi_comm=mpi_comm)
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/expressions.py", line 183, in compile_expression_code
mpi_comm=mpi_comm)
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/jit.py", line 70, in mpi_jit
return local_jit(*args, **kwargs)
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/compilemodule.py", line 603, in compile_extension_module
**instant_kwargs)
File "/usr/lib/python3/dist-packages/instant/build.py", line 577, in build_module
build_system)
File "/usr/lib/python3/dist-packages/instant/build.py", line 158, in recompile
instant_error(msg % (cmd, compile_log_filename_dest))
File "/usr/lib/python3/dist-packages/instant/output.py", line 96, in instant_error
raise RuntimeError(text)
RuntimeError: In instant.recompile: The module did not compile with command 'cmake -DDEBUG=TRUE .', see '/home/fab/.cache/instant/python3.6/error/dolfin_4bedd8911ad2fa3696d85d184d02a288d3294659/compile.log'
--- Instant: compiling ---
In instant.recompile: The module did not compile with command 'cmake -DDEBUG=TRUE .', see '/home/fab/.cache/instant/python3.6/error/dolfin_4bedd8911ad2fa3696d85d184d02a288d3294659/compile.log'
Traceback (most recent call last):
File "bug_instant.py", line 9, in <module>
aux_invr = fe.Expression("1/x[0]")
File "/usr/lib/python3/dist-packages/dolfin/functions/expression.py", line 679, in __new__
mpi_comm=kwargs.get("mpi_comm"))
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/expressions.py", line 266, in compile_expressions
mpi_comm=mpi_comm)
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/expressions.py", line 183, in compile_expression_code
mpi_comm=mpi_comm)
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/jit.py", line 70, in mpi_jit
return local_jit(*args, **kwargs)
File "/usr/lib/python3/dist-packages/dolfin/compilemodules/compilemodule.py", line 603, in compile_extension_module
**instant_kwargs)
File "/usr/lib/python3/dist-packages/instant/build.py", line 577, in build_module
build_system)
File "/usr/lib/python3/dist-packages/instant/build.py", line 158, in recompile
instant_error(msg % (cmd, compile_log_filename_dest))
File "/usr/lib/python3/dist-packages/instant/output.py", line 96, in instant_error
raise RuntimeError(text)
RuntimeError: In instant.recompile: The module did not compile with command 'cmake -DDEBUG=TRUE .', see '/home/fab/.cache/instant/python3.6/error/dolfin_4bedd8911ad2fa3696d85d184d02a288d3294659/compile.log'
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