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
instant.tar.xz
Description: application/xz
Calling DOLFIN just-in-time (JIT) compiler, this may take some time. Calling DOLFIN just-in-time (JIT) compiler, this may take some time.
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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