Your message dated Mon, 16 Dec 2019 17:53:26 +0100 with message-id <CAK6Z60dcOWYX4+V5tDr8NFbxdKxT=tFYtXhnNmzx==q0nxk...@mail.gmail.com> and subject line has caused the Debian Bug report #946590, regarding python3-dolfin: cannot find -lmpi 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. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 946590: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=946590 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: python3-dolfin Version: 2019.1.0-7 Severity: normal I don't know if this is a bug in the package or in my system. With the simplest of python dolfin projects, I'm getting ``` ------------------- Start compiler output ------------------------ /usr/bin/ld: cannot find -lmpi collect2: error: ld returned 1 exit status ------------------- End compiler output ------------------------ Compilation failed! Sources, command, and errors have been written to: /tmp/jitfailure-dolfin_expression_0ca911efb98de95f0dd6d82a8f353384 Traceback (most recent call last): File "/usr/lib/python3/dist-packages/dolfin/jit/jit.py", line 167, in compile_class mpi_comm=mpi_comm) File "/usr/lib/python3/dist-packages/dolfin/jit/jit.py", line 47, in mpi_jit return local_jit(*args, **kwargs) File "/usr/lib/python3/dist-packages/dolfin/jit/jit.py", line 103, in dijitso_jit return dijitso.jit(*args, **kwargs) File "/usr/lib/python3/dist-packages/dijitso/jit.py", line 217, in jit % err_info['fail_dir'], err_info) dijitso.jit.DijitsoError: Dijitso JIT compilation failed, see '/tmp/jitfailure- dolfin_expression_0ca911efb98de95f0dd6d82a8f353384' for details During handling of the above exception, another exception occurred: Traceback (most recent call last): File "l.py", line 37, in <module> u0 = Expression("a*sin(2.5*pi*x[1])*x[0]", a=0.2, degree=5) File "/usr/lib/python3/dist-packages/dolfin/function/expression.py", line 400, in __init__ self._cpp_object = jit.compile_expression(cpp_code, params) File "/usr/lib/python3/dist-packages/dolfin/function/jit.py", line 158, in compile_expression expression = compile_class(cpp_data, mpi_comm=mpi_comm) File "/usr/lib/python3/dist-packages/dolfin/jit/jit.py", line 170, in compile_class raise RuntimeError("Unable to compile C++ code with dijitso") RuntimeError: Unable to compile C++ code with dijitso ``` Is there a missing dependency? MPI seems to be there: ``` $ ls /usr/lib/x86_64-linux-gnu/libmpi.so.40* /usr/lib/x86_64-linux-gnu/libmpi.so.40 /usr/lib/x86_64-linux-gnu/libmpi.so.40.20.2 ``` -- System Information: Debian Release: bullseye/sid APT prefers focal APT policy: (500, 'focal') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 5.3.0-19-generic (SMP w/8 CPU cores) Kernel taint flags: TAINT_PROPRIETARY_MODULE, TAINT_WARN, TAINT_OOT_MODULE Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8), LANGUAGE=en_US.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Init: systemd (via /run/systemd/system) LSM: AppArmor: enabled Versions of packages python3-dolfin depends on: ii libc6 2.30-0ubuntu2 ii libdolfin-dev 2019.1.0-7 ii libdolfin2019.1 2019.1.0-7 ii libgcc1 1:9.2.1-21ubuntu1 ii libopenmpi3 4.0.2-4 ii libpetsc-real3.11 3.11.4+dfsg1-3build1 ii libstdc++6 9.2.1-21ubuntu1 ii python3 3.7.5-1ubuntu1 ii python3-dijitso 2019.1.0-3 ii python3-ffc 2019.1.0.post0-2 ii python3-numpy [python3-numpy-abi9] 1:1.17.4-3ubuntu2 ii python3-petsc4py 3.11.0-4 ii python3-pkgconfig 1.5.1-3 ii python3-ply 3.11-3 ii python3-pybind11 2.3.0-2 ii python3-six 1.12.0-2build1 ii python3-slepc4py 3.11.0-2build1 ii python3-sympy 1.4-1 ii python3-ufl 2019.1.0-2 python3-dolfin recommends no packages. Versions of packages python3-dolfin suggests: pn dolfin-doc <none> -- no debconf information
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--- Begin Message ---Purging all of openmpi and reinstalling fixed the issue for me: ``` sudo apt purge *openmpi* ```
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