I am having a problem with a code I am running which uses a library called fenics. It runs fine on one machine but on another we get the following error:
I have no idea how to attempt to solve this and am looking for tips as to what might be going wrong here.
--- Instant: compiling ---
INFO:instant:--- Instant: compiling ---
In instant.import_module_directly: Failed to import module 'dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9' from '/scratch/ajs3g11/conda_envs/fenicsproject/.cache/instant/cache/dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9';
ImportError:/scratch/ajs3g11/conda_envs/fenicsproject/.cache/instant/cache/dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9/_dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9.so: undefined symbol: _ZN6dolfin10Expression12set_propertyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd;
WARNING:instant:In instant.import_module_directly: Failed to import module 'dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9' from '/scratch/ajs3g11/conda_envs/fenicsproject/.cache/instant/cache/dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9';
ImportError:/scratch/ajs3g11/conda_envs/fenicsproject/.cache/instant/cache/dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9/_dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9.so: undefined symbol: _ZN6dolfin10Expression12set_propertyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd;
Failed to import module found in cache. Modulename: 'dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9';
Path: '/scratch/ajs3g11/conda_envs/fenicsproject/.cache/instant/cache/dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9';
ImportError:/scratch/ajs3g11/conda_envs/fenicsproject/.cache/instant/cache/dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9/_dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9.so: undefined symbol: _ZN6dolfin10Expression12set_propertyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd;
ERROR:instant:Failed to import module found in cache. Modulename: 'dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9';
Path: '/scratch/ajs3g11/conda_envs/fenicsproject/.cache/instant/cache/dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9';
ImportError:/scratch/ajs3g11/conda_envs/fenicsproject/.cache/instant/cache/dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9/_dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9.so: undefined symbol: _ZN6dolfin10Expression12set_propertyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd;
---------------------------------------------------------------------------
AssertionError Traceback (most recent call last)
~/Minimal_Magnetic_Sims/ChrisExperiment_gmsh/Calc_Magnetic_Potential.py in <module>()
79 print('calculating U', flush=True)
80
---> 81 U = calc_U(params_arr, mesh, bc_markers)
82
83 print('done')
~/Minimal_Magnetic_Sims/ChrisExperiment_gmsh/Calc_Magnetic_Potential.py in calc_U(params, mesh, bc_markers)
38 M = [m*sin(theta)*cos(phi), m*sin(theta)*sin(phi), m*cos(theta)] # Magnetic Moment
39 vmag = [mag*sin(theta)*cos(phi), mag*sin(theta)*sin(phi), mag*cos(theta)]
---> 40 U = MagPotential(mesh,vmag,X,V,r,mu,bc_markers)
41 print('Done for {}'.format(X), flush=True)
42 return U
/scratch/ajs3g11/conda_envs/fenicsproject/lib/python3.6/site-packages/dolfin/functions/expression.py in __new__(cls, cppcode, *args, **kwargs)
677 [generic_function_members],
678 [mesh_function_members],
--> 679 mpi_comm=kwargs.get("mpi_comm"))
680 cpp_base, members = cpp_base[0], members[0]
681
/scratch/ajs3g11/conda_envs/fenicsproject/lib/python3.6/site-packages/dolfin/compilemodules/expressions.py in compile_expressions(cppargs, generic_function_members, mesh_function_members, mpi_comm)
264 "\n\n".join(code_snippets), classnames,
265 additional_declarations="\n".join(additional_declarations),
--> 266 mpi_comm=mpi_comm)
267
268 return expression_classes, all_members
/scratch/ajs3g11/conda_envs/fenicsproject/lib/python3.6/site-packages/dolfin/compilemodules/expressions.py in compile_expression_code(code, classnames, module_name, additional_declarations, mpi_comm)
181 compiled_module = compile_extension_module(
182 code, additional_declarations=additional_declarations,
--> 183 mpi_comm=mpi_comm)
184
185 # Get the compiled class
/scratch/ajs3g11/conda_envs/fenicsproject/lib/python3.6/site-packages/dolfin/compilemodules/jit.py in mpi_jit(*args, **kwargs)
68 # Just call JIT compiler when running in serial
69 if MPI.size(mpi_comm) == 1:
---> 70 return local_jit(*args, **kwargs)
71
72 # Default status (0 == ok, 1 == fail)
/scratch/ajs3g11/conda_envs/fenicsproject/lib/python3.6/site-packages/dolfin/compilemodules/compilemodule.py in compile_extension_module(code, module_name, additional_declarations, additional_system_headers, mpi_comm, **instant_kwargs)
601 code=code,
602 additional_declarations=additional_declarations,
--> 603 **instant_kwargs)
604
605 sys.stdout.flush()
/scratch/ajs3g11/conda_envs/fenicsproject/lib/python3.6/site-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)
584
585 # Import module and place in memory cache
--> 586 module = import_and_cache_module(module_path, modulename, moduleids)
587
588 if not module:
/scratch/ajs3g11/conda_envs/fenicsproject/lib/python3.6/site-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)
/scratch/ajs3g11/conda_envs/fenicsproject/lib/python3.6/site-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_2e958ba2ca5c864d398064d4f2a072e75125d7b9';
Path: '/scratch/ajs3g11/conda_envs/fenicsproject/.cache/instant/cache/dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9';
ImportError:/scratch/ajs3g11/conda_envs/fenicsproject/.cache/instant/cache/dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9/_dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9.so: undefined symbol: _ZN6dolfin10Expression12set_propertyENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd;
When I check the location the file exists and is in the correct location.
total 96
-rw------- 1 ajs3g11 mm 0 2019-04-02 12:48 dolfin_fbfc275cbcbd922aeeb604be688cc6206a71c594.lock
drwx------ 4 ajs3g11 mm 32768 2019-04-02 12:48 dolfin_fbfc275cbcbd922aeeb604be688cc6206a71c594
drwx------ 4 ajs3g11 mm 32768 2019-04-02 17:06 dolfin_abe903615e73dfd155bc3ce45776a118093f71ff
-rw------- 1 ajs3g11 mm 0 2019-04-02 17:07 dolfin_abe903615e73dfd155bc3ce45776a118093f71ff.lock
-rw------- 1 ajs3g11 mm 0 2019-04-08 13:44 dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9.lock
drwx------ 4 ajs3g11 mm 32768 2019-04-08 13:44 dolfin_2e958ba2ca5c864d398064d4f2a072e75125d7b9```
答案 0 :(得分：0)
I originally want to add comments, but I do not have enough reputations to do so. This is just a suggestion and a direction to solve the problem but not an answer to the problem. Also I am quite new to python, so there may be better ways.
You may try to debug the program using pdb https://docs.python.org/2/library/pdb.html
From your code, it is obviously that "import_module_directly" returns None and triggers the assertion
You may use your console to run pdb, set the breakpoint to the function "import_module_directly", then run by line and check what's wrong. You can check the local variables and function arguments using pdb.
答案 1 :(得分：0)
我仍然不知道问题是什么或引起问题的原因，但是将工作环境导出到.yml文件并从另一台计算机上安装它解决了问题。
答案 2 :(得分：0)
即使很晚，但我想在这里添加一些内容。
如果从pip安装fenics，则可能是因为您尚未安装cmake / gmp / mpfr软件包。您可以通过以下方式直接在Ubuntu中安装它们：
sudo apt install cmake gmp mpfr
您可能还需要安装boost / vtk / openmpi / eigen，具体取决于原始fenics软件包的构建方式。我通常是自己建造的，所以我知道需要哪些软件包。
大多数情况下，上述错误是由于系统中缺少某些工具/软件包引起的。