# Unable to found JIT module **URL:** \ **Category:** mesh\ **Created:** [June 3, 2022, 11:15am UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454 "2022-06-03T11:15:44Z")\ **Posts on this page:** 19\ **Page:** 1
**Author:** ![MPenaR](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/mpenar/32/2985_2.png) [@MPenaR](https://fenicsproject.discourse.group/u/MPenaR)\ **Post date:** [June 3, 2022, 11:15am UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/1 "2022-06-03T11:15:44Z")
Well, the title is the message error. Basically I have dolfin-x 0.3.0 installed (it is the one that comes with debian testing right now as far as I know), and I was looking into the documentation for this version for the [poisson example](https://docs.fenicsproject.org/dolfinx/v0.3.0/python/demos/poisson/demo_poisson.py.html): I didn’t managed to replicate it as the command `V = FunctionSpace(mesh, ("Lagrange", 1))` fails giving the next error message: ```auto --------------------------------------------------------------------------- FileExistsError Traceback (most recent call last) /usr/lib/python3/dist-packages/ffcx/codegeneration/jit.py in get_cached_module(module_name, object_names, cache_dir, timeout) 61 # Create C file with exclusive access ---> 62 open(c_filename, "x") 63 return None, None FileExistsError: [Errno 17] File exists: '/home/manuel/.cache/fenics/libffcx_elements_0ba90af30174bac8aa16375eb5840f3f5018d54c.c' During handling of the above exception, another exception occurred: ModuleNotFoundError Traceback (most recent call last) /tmp/ipykernel_469262/3084727201.py in 5 CellType.triangle, dolfinx.cpp.mesh.GhostMode.none) 6 ----> 7 V = FunctionSpace(mesh, ("Lagrange", 1)) /usr/lib/petsc/lib/python3/dist-packages/dolfinx/fem/function.py in __init__ (self, mesh, element, cppV, form_compiler_parameters, jit_parameters) 383 384 # Compile dofmap and element and create DOLFIN objects --> 385 (self._ufc_element, self._ufc_dofmap), module, code = jit.ffcx_jit( 386 mesh.mpi_comm(), self.ufl_element(), form_compiler_parameters=form_compiler_parameters, 387 jit_parameters=jit_parameters) /usr/lib/petsc/lib/python3/dist-packages/dolfinx/jit.py in mpi_jit(comm, *args, **kwargs) 60 # Just call JIT compiler when running in serial 61 if comm.size == 1: ---> 62 return local_jit(*args, **kwargs) 63 64 # Default status (0 == ok, 1 == fail) /usr/lib/petsc/lib/python3/dist-packages/dolfinx/jit.py in ffcx_jit(ufl_object, form_compiler_parameters, jit_parameters) 216 r = ffcx.codegeneration.jit.compile_forms([ufl_object], parameters=p_ffcx, **p_jit) 217 elif isinstance(ufl_object, ufl.FiniteElementBase): --> 218 r = ffcx.codegeneration.jit.compile_elements([ufl_object], parameters=p_ffcx, **p_jit) 219 elif isinstance(ufl_object, ufl.Mesh): 220 r = ffcx.codegeneration.jit.compile_coordinate_maps( /usr/lib/python3/dist-packages/ffcx/codegeneration/jit.py in compile_elements(elements, parameters, cache_dir, timeout, cffi_extra_compile_args, cffi_verbose, cffi_debug, cffi_libraries) 105 if cache_dir is not None: 106 cache_dir = Path(cache_dir) --> 107 obj, mod = get_cached_module(module_name, names, cache_dir, timeout) 108 if obj is not None: 109 # Pair up elements with dofmaps /usr/lib/python3/dist-packages/ffcx/codegeneration/jit.py in get_cached_module(module_name, object_names, cache_dir, timeout) 73 spec = finder.find_spec(module_name) 74 if spec is None: ---> 75 raise ModuleNotFoundError("Unable to find JIT module.") 76 compiled_module = importlib.util.module_from_spec(spec) 77 spec.loader.exec_module(compiled_module) ModuleNotFoundError: Unable to find JIT module. ``` I don’t seem to find many people with this problem. PS: I would like to add that the [poisson example](https://fenics.readthedocs.io/projects/dolfin/en/2017.2.0/demos/poisson/python/demo_poisson.py.html) with dolfin (not the dolfin-x) seems to work properly. So for some reason I don’t understand dolfin finds the JIT but dolfin-x does not. ---
**Author:** ![dparsons](https://avatars.discourse-cdn.com/v4/letter/d/5e9695/32.png) [@dparsons](https://fenicsproject.discourse.group/u/dparsons)\ **Post date:** [June 3, 2022, 10:44pm UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/2 "2022-06-03T22:44:45Z")
> [@MPenaR](#): > > `FileExistsError: [Errno 17] File exists: '/home/manuel/.cache/fenics/libffcx_elements_0ba90af30174bac8aa16375eb5840f3f5018d54c.c'` Your cache is probably corrupted, possibly due to version upgrades. Try deleting `~/.cache/fenics` and try it again. ---
**Author:** ![MPenaR](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/mpenar/32/2985_2.png) [@MPenaR](https://fenicsproject.discourse.group/u/MPenaR)\ **Post date:** [June 3, 2022, 10:53pm UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/3 "2022-06-03T22:53:58Z")
Thanks, works fine now. Not sure if I understood the problem although. ---
**Author:** ![dparsons](https://avatars.discourse-cdn.com/v4/letter/d/5e9695/32.png) [@dparsons](https://fenicsproject.discourse.group/u/dparsons)\ **Post date:** [June 4, 2022, 8:08am UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/4 "2022-06-04T08:08:15Z")
The hash in the file name is intended to established uniqueness of the jit file within the context of the build environment. i.e. to mark whether it needs to be regenerated or not (the fenics run is faster if it doesn’t). But the hash signature doesn’t yet capture every nuance in the build environment, leading to the problem you experienced. cf. [increasing the entropy of the jit hash · Issue #290 · FEniCS/ffcx · GitHub](https://github.com/FEniCS/ffcx/issues/290) ---
**Author:** ![MPenaR](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/mpenar/32/2985_2.png) [@MPenaR](https://fenicsproject.discourse.group/u/MPenaR)\ **Post date:** [June 5, 2022, 8:44pm UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/5 "2022-06-05T20:44:30Z")
I understand, thank you very much! ---
**Author:** ![Pasuta](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/pasuta/32/6517_2.png) [@Pasuta](https://fenicsproject.discourse.group/u/Pasuta)\ **Post date:** [February 7, 2024, 10:18am UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/6 "2024-02-07T10:18:49Z")
Could you please explain me in detail how to delete the cache, i couldn’t find where is cache located ---
**Author:** ![dparsons](https://avatars.discourse-cdn.com/v4/letter/d/5e9695/32.png) [@dparsons](https://fenicsproject.discourse.group/u/dparsons)\ **Post date:** [February 7, 2024, 10:21am UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/7 "2024-02-07T10:21:58Z")
With dolfinx (ffcx), it’s now usually located at `~/.cache/fenics/`. With older versions you might find it at `~/.ffcx_cache/` (or maybe that’s just my setup). You can configure the location via the `jit_options` argument in `LinearProblem` or `NonlinearProblem`, which takes a dict of values (the cache location has keyname `"cache_dir"`) cf. [Set JIT cache directory](https://fenicsproject.discourse.group/t/set-jit-cache-directory/5047) ---
**Author:** ![Pasuta](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/pasuta/32/6517_2.png) [@Pasuta](https://fenicsproject.discourse.group/u/Pasuta)\ **Post date:** [February 13, 2024, 7:19am UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/8 "2024-02-13T07:19:37Z")
I coudn’t find those files. I don’t know if everyone is like me but mine is coded on the Jupiter Lab website. And I can’t save those codes on my computer. I must save and export notebook as… and whenever i closed the Jupiter Lab i had to copy those code and patse it again. ---
**Author:** ![Pasuta](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/pasuta/32/6517_2.png) [@Pasuta](https://fenicsproject.discourse.group/u/Pasuta)\ **Post date:** [February 13, 2024, 7:38am UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/9 "2024-02-13T07:38:10Z")
this might be requesting too much but I will greatly appreciate it If you can show me how to do it and record the screen for me (forgot to mention that I ran it on Docker.) Another thing is that coding is something very new for me and I might be asking a lot.Thank you. ---
**Author:** ![dparsons](https://avatars.discourse-cdn.com/v4/letter/d/5e9695/32.png) [@dparsons](https://fenicsproject.discourse.group/u/dparsons)\ **Post date:** [February 13, 2024, 9:40am UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/10 "2024-02-13T09:40:09Z")
I don’t use Jupyter or docker myself. I use a Linux environment. ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [February 13, 2024, 3:08pm UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/11 "2024-02-13T15:08:00Z")
If you run jupyterlab with docker, you should be able to open the terminal inside jupyter lab (it has a terminal option), and call dijitso clean. ---
**Author:** ![Pasuta](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/pasuta/32/6517_2.png) [@Pasuta](https://fenicsproject.discourse.group/u/Pasuta)\ **Post date:** [February 14, 2024, 3:42am UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/12 "2024-02-14T03:42:47Z")
I put the first line in terminal Jupyterlab. It says Permission denied. ```auto ~/.cache/fenics/libffcx_forms_5eb899f22d9b05f26c47e06ab454b4561b19ac5a.c ``` ![Screenshot 2024-02-14 102317](https://global.discourse-cdn.com/free1/uploads/fenicsproject1/original/2X/0/0d51c2c2c90e70fe345a9bc0f78f385fa4415d59.png) and when i call dijitso clean. ```auto bash: dijitso: command not found ``` ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [February 14, 2024, 4:44am UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/13 "2024-02-14T04:44:25Z")
What docker image are you using and what commands are you using to launch Jupyterlab with docker? ---
**Author:** ![Pasuta](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/pasuta/32/6517_2.png) [@Pasuta](https://fenicsproject.discourse.group/u/Pasuta)\ **Post date:** [February 14, 2024, 6:10am UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/14 "2024-02-14T06:10:21Z")
![Screenshot 2024-02-14 130056](https://global.discourse-cdn.com/free1/uploads/fenicsproject1/original/2X/e/e76d6ccf7eea331b8422fde414a549101afab55b.png) I run with this command on window powershell, the command is from [GitHub - FEniCS/dolfinx: Next generation FEniCS problem solving environment](https://github.com/FEniCS/dolfinx) > docker run --init -ti -p 8888:8888 dolfinx/lab:stable then i copy the URL after run ‘docker run’ command and paste it on google chrome to open it > [http://127.0.0.1:8888/lab?token=95fb25d4089f88d63894dd83345d8d018b7c80fad1aad8b4](http://127.0.0.1:8888/lab?token=95fb25d4089f88d63894dd83345d8d018b7c80fad1aad8b4) ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [February 14, 2024, 6:51am UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/15 "2024-02-14T06:51:45Z")
then it is no Wonder dijitso isn’t there, as dolfinx doesn’t use dijitso. > [@Pasuta](#): > > `~/.cache/fenics` Did you try `rm -rf /root/.cache/fenics`? ---
**Author:** ![Pasuta](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/pasuta/32/6517_2.png) [@Pasuta](https://fenicsproject.discourse.group/u/Pasuta)\ **Post date:** [February 14, 2024, 7:08am UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/16 "2024-02-14T07:08:04Z")
nothing happen 🥲 ![Screenshot 2024-02-14 14062222](https://global.discourse-cdn.com/free1/uploads/fenicsproject1/original/2X/2/2d25702a777ec40bd0e95fb446ef298dea79e605.png) ---
**Author:** ![Pasuta](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/pasuta/32/6517_2.png) [@Pasuta](https://fenicsproject.discourse.group/u/Pasuta)\ **Post date:** [February 14, 2024, 7:18am UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/17 "2024-02-14T07:18:31Z")
but the error is change from (you can see my problem from [Calculate sensitivity equation of reaction-diffusion systems with dolfinx](https://fenicsproject.discourse.group/t/calculate-sensitivity-equation-of-reaction-diffusion-systems-with-dolfinx/13545)) ```auto "TimeoutError: JIT compilation timed out, probably due to a failed previous compile.Try cleaning cache (e.g. remove /root/.cache/fenics/libffcx_forms_5eb899f22d9b05f26c47e06ab454b4561b19ac5a.c) or increase timeout option." ``` to this ```auto --------------------------------------------------------------------------- ArityMismatch Traceback (most recent call last) Cell In[121], line 1 ----> 1 dJdm_form = dolfinx.fem.form(ufl.derivative(J, eps)) File /usr/local/dolfinx-complex/lib/python3.10/dist-packages/dolfinx/fem/forms.py:188, in form(form, dtype, form_compiler_options, jit_options) 185 return list(map(lambda sub_form: _create_form(sub_form), form)) 186 return form --> 188 return _create_form(form) File /usr/local/dolfinx-complex/lib/python3.10/dist-packages/dolfinx/fem/forms.py:183, in form.._create_form(form) 180 """Recursively convert ufl.Forms to dolfinx.fem.Form, otherwise 181 return form argument""" 182 if isinstance(form, ufl.Form): --> 183 return _form(form) 184 elif isinstance(form, collections.abc.Iterable): 185 return list(map(lambda sub_form: _create_form(sub_form), form)) File /usr/local/dolfinx-complex/lib/python3.10/dist-packages/dolfinx/fem/forms.py:141, in form.._form(form) 139 if mesh is None: 140 raise RuntimeError("Expecting to find a Mesh in the form.") --> 141 ufcx_form, module, code = jit.ffcx_jit(mesh.comm, form, 142 form_compiler_options=form_compiler_options, 143 jit_options=jit_options) 145 # For each argument in form extract its function space 146 V = [arg.ufl_function_space()._cpp_object for arg in form.arguments()] File /usr/local/dolfinx-complex/lib/python3.10/dist-packages/dolfinx/jit.py:56, in mpi_jit_decorator..mpi_jit(comm, *args, **kwargs) 51 @functools.wraps(local_jit) 52 def mpi_jit(comm, *args, **kwargs): 53 54 # Just call JIT compiler when running in serial 55 if comm.size == 1: ---> 56 return local_jit(*args, **kwargs) 58 # Default status (0 == ok, 1 == fail) 59 status = 0 File /usr/local/dolfinx-complex/lib/python3.10/dist-packages/dolfinx/jit.py:204, in ffcx_jit(ufl_object, form_compiler_options, jit_options) 202 # Switch on type and compile, returning cffi object 203 if isinstance(ufl_object, ufl.Form): --> 204 r = ffcx.codegeneration.jit.compile_forms([ufl_object], options=p_ffcx, **p_jit) 205 elif isinstance(ufl_object, ufl.FiniteElementBase): 206 r = ffcx.codegeneration.jit.compile_elements([ufl_object], options=p_ffcx, **p_jit) File /usr/local/lib/python3.10/dist-packages/ffcx/codegeneration/jit.py:190, in compile_forms(forms, options, cache_dir, timeout, cffi_extra_compile_args, cffi_verbose, cffi_debug, cffi_libraries) 187 for name in form_names: 188 decl += form_template.format(name=name) --> 190 impl = _compile_objects(decl, forms, form_names, module_name, p, cache_dir, 191 cffi_extra_compile_args, cffi_verbose, cffi_debug, cffi_libraries) 192 except Exception as e: 193 try: 194 # remove c file so that it will not timeout next time File /usr/local/lib/python3.10/dist-packages/ffcx/codegeneration/jit.py:260, in _compile_objects(decl, ufl_objects, object_names, module_name, options, cache_dir, cffi_extra_compile_args, cffi_verbose, cffi_debug, cffi_libraries) 256 import ffcx.compiler 258 # JIT uses module_name as prefix, which is needed to make names of all struct/function 259 # unique across modules --> 260 _, code_body = ffcx.compiler.compile_ufl_objects(ufl_objects, prefix=module_name, options=options) 262 ffibuilder = cffi.FFI() 263 ffibuilder.set_source(module_name, code_body, include_dirs=[ffcx.codegeneration.get_include_path()], 264 extra_compile_args=cffi_extra_compile_args, libraries=cffi_libraries) File /usr/local/lib/python3.10/dist-packages/ffcx/compiler.py:97, in compile_ufl_objects(ufl_objects, object_names, prefix, options, visualise) 95 # Stage 1: analysis 96 cpu_time = time() ---> 97 analysis = analyze_ufl_objects(ufl_objects, options) 98 _print_timing(1, time() - cpu_time) 100 # Stage 2: intermediate representation File /usr/local/lib/python3.10/dist-packages/ffcx/analysis.py:88, in analyze_ufl_objects(ufl_objects, options) 85 else: 86 raise TypeError("UFL objects not recognised.") ---> 88 form_data = tuple(_analyze_form(form, options) for form in forms) 89 for data in form_data: 90 elements += [convert_element(e) for e in data.unique_sub_elements] File /usr/local/lib/python3.10/dist-packages/ffcx/analysis.py:88, in (.0) 85 else: 86 raise TypeError("UFL objects not recognised.") ---> 88 form_data = tuple(_analyze_form(form, options) for form in forms) 89 for data in form_data: 90 elements += [convert_element(e) for e in data.unique_sub_elements] File /usr/local/lib/python3.10/dist-packages/ffcx/analysis.py:163, in _analyze_form(form, options) 160 complex_mode = "_Complex" in options["scalar_type"] 162 # Compute form metadata --> 163 form_data = ufl.algorithms.compute_form_data( 164 form, 165 do_apply_function_pullbacks=True, 166 do_apply_integral_scaling=True, 167 do_apply_geometry_lowering=True, 168 preserve_geometry_types=(ufl.classes.Jacobian,), 169 do_apply_restrictions=True, 170 do_append_everywhere_integrals=False, # do not add dx integrals to dx(i) in UFL 171 complex_mode=complex_mode) 173 # If form contains a quadrature element, use the custom quadrature scheme 174 custom_q = None File /usr/local/lib/python3.10/dist-packages/ufl/algorithms/compute_form_data.py:415, in compute_form_data(form, do_apply_function_pullbacks, do_apply_integral_scaling, do_apply_geometry_lowering, preserve_geometry_types, do_apply_default_restrictions, do_apply_restrictions, do_estimate_degrees, do_append_everywhere_integrals, complex_mode) 412 preprocessed_form = reconstruct_form_from_integral_data(self.integral_data) 414 # TODO: Test how fast this is --> 415 check_form_arity(preprocessed_form, self.original_form.arguments(), complex_mode) 417 # TODO: This member is used by unit tests, change the tests to 418 # remove this! 419 self.preprocessed_form = preprocessed_form File /usr/local/lib/python3.10/dist-packages/ufl/algorithms/check_arities.py:198, in check_form_arity(form, arguments, complex_mode) 196 """Check the arity of a form.""" 197 for itg in form.integrals(): --> 198 check_integrand_arity(itg.integrand(), arguments, complex_mode) File /usr/local/lib/python3.10/dist-packages/ufl/algorithms/check_arities.py:190, in check_integrand_arity(expr, arguments, complex_mode) 188 for arg, conj in arg_tuples: 189 if arg.number() == 0 and not conj: --> 190 raise ArityMismatch("Failure to conjugate test function in complex Form") 191 elif arg.number() > 0 and conj: 192 raise ArityMismatch(f"Argument {arg} is spuriously conjugated in complex Form") ArityMismatch: Failure to conjugate test function in complex Form ``` ---
**Author:** ![dokken](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/dokken/32/1560_2.png) [@dokken](https://fenicsproject.discourse.group/u/dokken)\ **Post date:** [February 14, 2024, 8:25am UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/18 "2024-02-14T08:25:22Z")
Well, so this changes things. The issue is with how one differentiates a complex valued problem. I would try: `dJdm = dolfinx.fem.form(ufl.derivative(J, eps, ufl.conj(ufl.TestFunction(eps.function_space))` given that `eps` is a function in some functionspace. ---
**Author:** ![Pasuta](https://yyz2.discourse-cdn.com/free1/user_avatar/fenicsproject.discourse.group/pasuta/32/6517_2.png) [@Pasuta](https://fenicsproject.discourse.group/u/Pasuta)\ **Post date:** [February 14, 2024, 10:00am UTC](https://fenicsproject.discourse.group/t/unable-to-found-jit-module/8454/19 "2024-02-14T10:00:23Z")
It worked now, Thank you so much! It’s very useful.😃 😃