accessing external files on docker

[dlorod55]

Im currently using turtle fsi on docker and microsoft visual studio and have trouble accessing external filed and when i execute moving cylinder i get fenics@df3ab8a8010e:~/local/turtleFSI$ turtleFSI --problem MovingCylinder
{'A_ratio': 0.25,
'D': 0.1,
'F_r': 1.0,
'Re': 500,
'St': 0.228,
'T': 5,
'Um': 0.8,
'atol': 1e-07,
'bc_ids': [],
'c_s': 0.0,
'checkpoint_step': 500,
'compiler_parameters': {'add_tabulate_tensor_timing': False,
'cache_dir': '',
'convert_exceptions_to_warnings': False,
'cpp_optimize': True,
'cpp_optimize_flags': '-O2',
'epsilon': 1e-14,
'error_control': False,
'external_include_dirs': '',
'external_includes': '',
'external_libraries': '',
'external_library_dirs': '',
'form_postfix': False,
'format': 'ufc',
'generate_dummy_tabulate_tensor': False,
'log_level': 25,
'log_prefix': '',
'max_signature_length': 0,
'no-evaluate_basis_derivatives': True,
'optimize': True,
'output_dir': '.',
'precision': None,
'quadrature_degree': 4,
'quadrature_rule': None,
'representation': 'auto',
'split': False},
'counter': 0,
'd_deg': 1,
'ds_s_id': None,
'dt': 0.000125,
'dx_f_id': 1,
'dx_s_id': 2,
'extrapolation': 'laplace',
'extrapolation_sub_type': 'constant',
'factor': 50.0,
'fluid': 'fluid',
'fluid_properties': [],
'folder': 'results_moving_cylinder',
'gravity': None,
'k_s': 0.0,
'killtime': None,
'lambda_s': 450000.0,
'linear_solver': 'mumps',
'lmbda': 1.0,
'loglevel': 20,
'material_model': 'StVenantKirchoff',
'max_it': 50,
'mu_f': 0.2,
'mu_s': 50000.0,
'nu_s': 0.45,
'p_deg': 1,
'problem': 'MovingCylinder',
'recompute': 25,
'recompute_tstep': 100,
'restart_folder': None,
'rho_f': 1000,
'rho_s': 1000.0,
'robin_bc': False,
'rtol': 1e-07,
'save_deg': 1,
'save_step': 100,
'solid': 'no_solid',
'solid_properties': [],
'solver': 'newtonsolver',
'sub_folder': None,
't': 0,
'theta': 0.500125,
'u_inf': 1.0,
'v_deg': 1,
'verbose': True}
Traceback (most recent call last):
File "/usr/local/bin/turtleFSI", line 11, in
load_entry_point('turtleFSI', 'console_scripts', 'turtleFSI')()
File "/home/fenics/local/turtleFSI/turtleFSI/run_turtle.py", line 18, in main
from turtleFSI import monolithic
File "/home/fenics/local/turtleFSI/turtleFSI/monolithic.py", line 63, in
mesh, domains, boundaries = get_mesh_domain_and_boundaries(**vars())
File "/home/fenics/local/turtleFSI/turtleFSI/problems/MovingCylinder.py", line 81, in get_mesh_domain_and_boundaries
infile.read(mesh)
RuntimeError:

*** -------------------------------------------------------------------------
*** DOLFIN encountered an error. If you are not able to resolve this issue
*** using the information listed below, you can ask for help at

---

*** fenics-support@googlegroups.com

---

*** Remember to include the error message listed below and, if possible,
*** include a minimal running example to reproduce the error.

---

*** -------------------------------------------------------------------------
*** Error: Unable to open XDMF file.
*** Reason: XDMF file "mesh/MovingCylinder/mesh4.xdmf" does not exist.
*** Where: This error was encountered inside XDMFFile.cpp.
*** Process: 0

---

*** DOLFIN version: 2019.1.0
*** Git changeset: 74d7efe1e84d65e9433fd96c50f1d278fa3e3f3f
*** -------------------------------------------------------------------------

fenics@df3ab8a8010e:~/local/turtleFSI$

Help me please

[dlorod55]

This is really important as im using it for my masters

[keiyamamo]

Hi @dlorod55,

mesh can be downloaded from here. Note that you need to place the mesh at correct path or modify the problem file so that path to the mesh is correct.

[dlorod55]

Just to confirm what would be the ideal way to install turtleFSI on windows

[jorgensd]

Just to confirm what would be the ideal way to install turtleFSI on windows

Using docker, as petsc, the LA backend of dolfin and turtleFSI is not easily installed on Windows

[dlorod55]

so whats the best way to use turtleFSI because im struggling lol

[keiyamamo]

As @jorgensd answered, docker is good. For further questions, please specify the exact problem you have.

[dlorod55]

As in general if you were going to buy a laptop or pc to just run turtleFSI what and how would u do it. Like the best case scenario.

[jorgensd]

As in general if you were going to buy a laptop or pc to just run turtleFSI what and how would u do it. Like the best case scenario.

If you can buy a new laptop, I would either:

1. Familiarize yourself with how docker works
2. Familiarize yourself with how subsystem for Linux (WSL2) works on Windows
3. Buy a Linux based system.

[dlorod55]

i put file in right place but still staying not found. do i have to do anything after placing it into to the right directory
/

[keiyamamo]

No, you shouldn't need do anything for that. You can go to the folder where you have mesh4.xdmf and run pwd command and then replace the path to the mesh inside the problem file.

[dlorod55]

fenics@6b4451a874e7:/local/turtleFSI$ pwd
/home/fenics/local/turtleFSI
fenics@6b4451a874e7:/local/turtleFSI$ turtleFSI --problem MovingCylinder
{'A_ratio': 0.25,
'D': 0.1,
'F_r': 1.0,
'Re': 500,
'St': 0.228,
'T': 5,
'Um': 0.8,
'atol': 1e-07,
'bc_ids': [],
'c_s': 0.0,
'checkpoint_step': 500,
'compiler_parameters': {'add_tabulate_tensor_timing': False,
'cache_dir': '',
'convert_exceptions_to_warnings': False,
'cpp_optimize': True,
'cpp_optimize_flags': '-O2',
'epsilon': 1e-14,
'error_control': False,
'external_include_dirs': '',
'external_includes': '',
'external_libraries': '',
'external_library_dirs': '',
'form_postfix': False,
'format': 'ufc',
'generate_dummy_tabulate_tensor': False,
'log_level': 25,
'log_prefix': '',
'max_signature_length': 0,
'no-evaluate_basis_derivatives': True,
'optimize': True,
'output_dir': '.',
'precision': None,
'quadrature_degree': 4,
'quadrature_rule': None,
'representation': 'auto',
'split': False},
'counter': 0,
'd_deg': 1,
'ds_s_id': None,
'dt': 0.000125,
'dx_f_id': 1,
'dx_s_id': 2,
'extrapolation': 'laplace',
'extrapolation_sub_type': 'constant',
'factor': 50.0,
'fluid': 'fluid',
'fluid_properties': [],
'folder': 'results_moving_cylinder',
'gravity': None,
'k_s': 0.0,
'killtime': None,
'lambda_s': 450000.0,
'linear_solver': 'mumps',
'lmbda': 1.0,
'loglevel': 20,
'material_model': 'StVenantKirchoff',
'max_it': 50,
'mu_f': 0.2,
'mu_s': 50000.0,
'nu_s': 0.45,
'p_deg': 1,
'problem': 'MovingCylinder',
'recompute': 25,
'recompute_tstep': 100,
'restart_folder': None,
'rho_f': 1000,
'rho_s': 1000.0,
'robin_bc': False,
'rtol': 1e-07,
'save_deg': 1,
'save_step': 100,
'solid': 'no_solid',
'solid_properties': [],
'solver': 'newtonsolver',
'sub_folder': None,
't': 0,
'theta': 0.500125,
'u_inf': 1.0,
'v_deg': 1,
'verbose': True}
Traceback (most recent call last):
File "/usr/local/bin/turtleFSI", line 11, in
load_entry_point('turtleFSI', 'console_scripts', 'turtleFSI')()
File "/home/fenics/local/turtleFSI/turtleFSI/run_turtle.py", line 18, in main
from turtleFSI import monolithic
File "/home/fenics/local/turtleFSI/turtleFSI/monolithic.py", line 63, in
mesh, domains, boundaries = get_mesh_domain_and_boundaries(**vars())
File "/home/fenics/local/turtleFSI/turtleFSI/problems/MovingCylinder.py", line 81, in get_mesh_domain_and_boundaries
infile.read(mesh)
RuntimeError:

*** -------------------------------------------------------------------------
*** DOLFIN encountered an error. If you are not able to resolve this issue
*** using the information listed below, you can ask for help at

---

*** fenics-support@googlegroups.com

---

*** Remember to include the error message listed below and, if possible,
*** include a minimal running example to reproduce the error.

---

*** -------------------------------------------------------------------------
*** Error: Unable to open XDMF file.
*** Reason: XDMF file "/home/fenics/local/turtleFSI/mesh/MovingCylinder/mesh4.xdmf" does not exist.
*** Where: This error was encountered inside XDMFFile.cpp.
*** Process: 0

---

*** DOLFIN version: 2019.1.0
*** Git changeset: 74d7efe1e84d65e9433fd96c50f1d278fa3e3f3f
*** -------------------------------------------------------------------------

fenics@6b4451a874e7:~/local/turtleFSI$

[dlorod55]

can u see where im going wrong

[keiyamamo]

What's the result of pwd inside the folder mesh? What if you run the turtleFSI command where there's folder mesh and monolithic.py?

[dlorod55]

Hi, rather than doing a moving cylinder my airflow around a circle then an ellipse then an aerofoil. I'm confused how to start thats why i tried moving cylinder to see how that workeed.

[keiyamamo]

I’m not sure what you’re asking here and don’t have time to guide you step by step for all the details. As the error message is indicating, you don’t either have mesh in a correct place or your path to the mesh is wrong inside problem file.

[keiyamamo]

Closing for now. Feel free to reopen if you have more questions @dlorod55