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FEniCS / dolfinx

Next generation FEniCS problem solving environment
https://fenicsproject.org
GNU Lesser General Public License v3.0
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[BUG]: can't create the form on parallel to solve for navier stokes equations using miniconda python dolfinx 0.6.0 #2675

Closed ruf10 closed 1 year ago

ruf10 commented 1 year ago

How to reproduce the bug

Hi guys,

Could anyone help me with the following problems? Thanks! I try to solve navier stokes on parallel, and when I define my form and solve for the assemble system: a = form([[((1.0 / dt) inner(u, v) + b(2 un - unMinus1, u, v) + 2.0 nu a_sym(u, v)) dx, -c(p, v) dx], [c(q, u) dx, None]]) L = form([(1.0 / dt) inner(un, v) * dx, None])

a = form((1./dt)inner(u,v) dx + b(2un-unMinus1,u,v)dx + 2.nua_sym(u,v) dx -c(p,v)dx + c(q,u) dx )

L = form((1./dt)(inner(un,v))*dx)x

unPlus1, pnPlus1 = solve_u(a,L,t) Where solve u is a function that takes care of solving the system.

Minimal Example (Python)

a = form([[((1.0 / dt) * inner(u, v) + b(2 * un - unMinus1, u, v) + 2.0 * nu * a_sym(u, v)) * dx, -c(p, v) * dx],
[c(q, u) * dx, None]])
L = form([(1.0 / dt) * inner(un, v) * dx, None])
#a = form((1./dt)inner(u,v) dx + b(2un-unMinus1,u,v)dx + 2.nua_sym(u,v) dx -c(p,v)dx + c(q,u) dx )
#L = form((1./dt)(inner(un,v))*dx)x
unPlus1, pnPlus1 = solve_u(a,L,t)

Output (Python)

Traceback (most recent call last):
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/setuptools/_distutils/unixccompiler.py", line 185, in _compile
    self.spawn(compiler_so + cc_args + [src, '-o', obj] + extra_postargs)
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/setuptools/_distutils/ccompiler.py", line 1041, in spawn
    spawn(cmd, dry_run=self.dry_run, **kwargs)
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/setuptools/_distutils/spawn.py", line 70, in spawn
    raise DistutilsExecError(
distutils.errors.DistutilsExecError: command '/ix/wlayton/rui/miniconda/envs/fenicsx-env/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/cffi/ffiplatform.py", line 51, in _build
    dist.run_command('build_ext')
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/setuptools/dist.py", line 1244, in run_command
    super().run_command(command)
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 988, in run_command
    cmd_obj.run()
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/setuptools/command/build_ext.py", line 84, in run
    _build_ext.run(self)
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 345, in run
    self.build_extensions()
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 467, in build_extensions
    self._build_extensions_serial()
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 493, in _build_extensions_serial
    self.build_extension(ext)
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/setuptools/command/build_ext.py", line 246, in build_extension
    _build_ext.build_extension(self, ext)
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 548, in build_extension
    objects = self.compiler.compile(
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/setuptools/_distutils/ccompiler.py", line 600, in compile
    self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/setuptools/_distutils/unixccompiler.py", line 187, in _compile
    raise CompileError(msg)
distutils.errors.CompileError: command '/ix/wlayton/rui/miniconda/envs/fenicsx-env/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/ix/wlayton/rui/para.py", line 404, in <module>
    a = form([[((1.0 / dt) * inner(u, v) + b(2 * un - unMinus1, u, v) + 2.0 * nu * a_sym(u, v)) * dx, -c(p, v) * dx],
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/dolfinx/fem/forms.py", line 176, in form
    return _create_form(form)
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/dolfinx/fem/forms.py", line 173, in _create_form
    return list(map(lambda sub_form: _create_form(sub_form), form))
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/dolfinx/fem/forms.py", line 173, in <lambda>
    return list(map(lambda sub_form: _create_form(sub_form), form))
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/dolfinx/fem/forms.py", line 173, in _create_form
    return list(map(lambda sub_form: _create_form(sub_form), form))
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/dolfinx/fem/forms.py", line 173, in <lambda>
    return list(map(lambda sub_form: _create_form(sub_form), form))
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/dolfinx/fem/forms.py", line 171, in _create_form
    return _form(form)
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/dolfinx/fem/forms.py", line 145, in _form
    ufcx_form, module, code = jit.ffcx_jit(mesh.comm, form,
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/dolfinx/jit.py", line 56, in mpi_jit
    return local_jit(*args, **kwargs)
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/dolfinx/jit.py", line 204, in ffcx_jit
    r = ffcx.codegeneration.jit.compile_forms([ufl_object], options=p_ffcx, **p_jit)
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/ffcx/codegeneration/jit.py", line 186, in compile_forms
    impl = _compile_objects(decl, forms, form_names, module_name, p, cache_dir,
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/ffcx/codegeneration/jit.py", line 270, in _compile_objects
    ffibuilder.compile(tmpdir=cache_dir, verbose=True, debug=cffi_debug)
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/cffi/api.py", line 725, in compile
    return recompile(self, module_name, source, tmpdir=tmpdir,
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/cffi/recompiler.py", line 1564, in recompile
    outputfilename = ffiplatform.compile('.', ext,
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/cffi/ffiplatform.py", line 22, in compile
    outputfilename = _build(tmpdir, ext, compiler_verbose, debug)
  File "/ix/wlayton/rui/miniconda/envs/fenicsx-env/lib/python3.10/site-packages/cffi/ffiplatform.py", line 58, in _build
    raise VerificationError('%s: %s' % (e.__class__.__name__, e))
cffi.VerificationError: CompileError: command '/ix/wlayton/rui/miniconda/envs/fenicsx-env/bin/x86_64-conda-linux-gnu-cc' failed with exit code 1

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garth-wells commented 1 year ago

Please post to https://fenicsproject.discourse.group/, and ensure to share the smallest possible complete code snippet.