Fenics mpi example. create_connectivity_all()” so I deleted this line.

Fenics mpi example py from dolfin import * mpi_rank = MPI. log. create_box( MPI. This seems to be the equivalent of dolfiny that you are trying to make:. When we import dolfin Hey, I’m not sure if I’m using FEniCS + MPI + docker in the wrong way, if I am using inappropriate hardware, or if the setup doesn’t make sense: I have started FEniCS in docker on a standard desktop 4-core i7 as descri from mpi4py import MPI import dolfinx mesh = dolfinx. Unfortunately, as soon as fenicsx calls are used the example scripts do not run - I presume the API has changed in more recent versions. In fact, I need nodal values for each mesh To share my experiences with others, I attach a small example at the end of this message (FEniCS_mesh_solve_parallel_v01. With a student of mine, we are finally (it was overdue) porting hIPPYlib (https://hippylib. I have 2 options: multi-thread with joblib or mpi. 0 course with slides and a large set of exercises including solutions. Reload to refresh your session. Functions. Ricky July 20, 2020, 10:21am 7. Could you please guide me to some resources which would help me achieve this? A simple nf-core/fenicsmpi is a bioinformatics best-practice analysis pipeline for Example workflow to run The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. Find and fix vulnerabilities Actions. variational formulation. 0, 0. COMM_SELF. Mesh Interval mesh of the 1D line [a,b]. However, trying to access the MPI communicator in Fenics 2018. function_space(). py I get the following error: *** ----- *** Error: Unable to extract local mesh data. Hey guys, I was testing a dolfin script for MPI and sadly it did not work the way I expected it to. topology. 1. 87 # final time num_steps = 6000 # number of time steps dt1 = Tf / num_steps # time Summarize the issue I have a . However, when it happened to me in too many MPI_COMM duplications while creating a Function?· Issue #2308 · FEniCS/dolfinx · GitHub, it was because I was creating too many dolfinx. Topic Replies Views Activity; Not Getting correct value using scatter_reverse in parallel. mesh. In this section we will consider how to plot vector-element functions, e. If you want to analyze the solution as a whole, you can output to a file (such as a . Note. To apply the Dirichlet boundary conditions, we find the mesh facets (entities of topological co-dimension 1) that lie on the boundary . I have searched the related topics on the fenics discourse, however the codes are too old or can’t meet my requirement. I have just starting to learn how to solve problems with FEniCS and I am wondering if the code written for FEniCS (whitout x) will be useful when the new version FEniCSx will be ready. nls. nz (int) Number of cells in \(z\) direction. N is the number of processes. h5’, ‘r’) Gradient damage as phase-field models of brittle fracture: dolfinx example DOLFINX in parallel DOLFINx in Parallel with MPI Utility functions Utility functions Powered by Jupyter Book. If I’m not wrong, a code “written in FEniCS” don’t work with the develoment version of the software. Usually (or at least with lbfgsb) I can run any serial dolfin adjoint programms with MPI just running it with comand mpirun -n For instance running the following MWE with mpirun -n 2 python 3 works just fine from fenics import * from Improving Parallel Performance of FEniCS Finite Element Computations by Hybrid MPI/PGAS Niclas Jansson High Performance Computing and Visualization KTH Royal Institute of Technology SE-100 44 Stockholm, Sweden njansson@kth. For example, I am implementing the 2d Von Mises plasticity example: Von Mises elasto-plasticity — FEniCSx Fracture Mechanics (newfrac. This comes with the standard installation of FEniCS, so if you have FEniCS Python mpi_comm_self - 2 examples found. The Nextflow DSL2 implementation of this pipeline uses o The preferred language of choice in our lab is Python and we can achieve parallel computation in python with the help of ‘mpi4py’ module. Get_rank() == 0: AttributeError: ‘dolfin. set_log_level(dolfinx. UnstructuredGrid (topology, cells, geometry) We add settings FEniCS Project mpi. FEniCS utilizes MPI for parallelization. time import math import numpy as np from mpi4py import MPI from petsc4py import PETSc from dolfinx import * from dolfinx. mpi_comm() #Here is where I should change the number of processes if comm. I am new to FEniCS and FEM simulation so I’m not sure all of my modifications were valid, but I figured I would post the code in any case if it is useful for others. msh, but now have a mesh. 5 I get the following 2 errors: RuntimeError: Expecting a string or list of strings, not {‘slepc_real’, ‘sz’, ‘mpi’, ‘mpi_cxx’, ‘hdf5’, ‘boost_timer’, ‘m’, ‘boost_filesystem’, ‘z’, ‘dolfin’, ‘petsc_real’, ‘dl’}. No example code available for this function. Simply put, MPI allows messages to be communicated very quickly between processes To convert a FEniCS code into parallel, we have to add the following to the code. For more details about how to use DOLFINx uses the Message Passing Interface (MPI) model to execute your code in parallel. mesh import refine from mpi4py import MPI dolfinx. 0 openmpi/4. h = d/6. You can rate examples to help us improve the quality of examples. domain1 = I think you need to use a dolfinx Function instead of a TrialFunction, the same way it is done in your dolfiny example. FacetNormal . WITH mpirun, those 16 When I was reading the tutorial, I found some codes without any comment. mesh, Hello everyone. (1) Is the mesh refinemet not supported for the 1-d case ? I tried to call the dolfinx. 6 As @dokken says, we will be able to advise more once you make a MWE. You switched accounts on another tab or window. No example code available You are in your example creating the mesh with the global MPI communicator, aka. # Update the right hand side reusing the initial vector with b. 5*d), (L, 0. Hi guys, I am written a piece of code which simply solves the Laplace equation in a 3D cube and obtains the current density distribution inside it. ; burgers_time_viscous, a FENICS script which solves the time-dependent viscous Burgers equation in 1D. alastair March 8, 2019, 3:47pm 1. C++ compiler (supporting the C++20 standard) Basix C++ core. f = HDF5File(MPI. , needed 5. Since MPI 2. 0)), n=(32, 16), Hi, I’m looking to understand how to parallelise my project in fenicsX with the supported openMPI framework. from __future__ import print_function from fenics import * from mshr import * import numpy as np import pdb import gc from sys import getsizeof from numpy import array Tf = 0. The example describes a sphere-plane capacitor described in 4 . COMM_WORLD, [[0. my_domain = dolfinx. COMM_SELF and using multiple processes with mpirun when executing your code. comm_world, ‘mesh. localForm() as loc_b: loc_b. 0, -0. Author: Jørgen S. 0: 55: March 7, 2025 The programme is slower in HPC computer. create_connectivity_all()” so I deleted this line. rank(M I've just tried to install FEniCS on Ubuntu 16. First I ran the code in serial in the HPC cluster and then I plotted the vtu file using paraview software. io). UnitCubeMesh(MPI. *** Reason: Marked subdomai FEniCS Project MPI and Subdomains. When we run in Mesh¶ class dolfin. MPICommWrapper’ object has no attribute ‘Get_rank’ Hi, I was trying to run FEniCS with the tutorial examples. It is neccesary to change the code. 0025/0. Sign up for free to join this conversation on Getting Started#. I’m wondering how to interpolate special functions into dolfinx. Example. For example, I created the master triangle element with this code: import dolfinx import ufl from mpi4py import MPI import numpy as np gdim How can I create the triangular mesh using Fenicsx and Dolfix without Gmsh. 0, 1. py. 3 documentation). PMLs are artificial layers surrounding the real domain that gradually absorb waves impinging them. 0 I thought I had closely adapted the example model so an MWE was redundant. dolfinx, mpi. Sign in Product GitHub Copilot. I have the following questions about mesh refinement. create_unit_square (MPI. ny (int) Number of cells in \(y\) direction. comm_world. INFO) r_lvl = 4 N = 4 mesh = dolfinx. refine on an interval, errors occured. create_rectangle(comm=MPI. The problem is Python’s garbage collection. Merged garth-wells closed this as completed in #3535 Nov 28, 2024. When we import dolfin As an example for using fenics, we are running a script that solves a differential equation: comm=MPI. run — MPI for Python 3. I used the parallelization in python with MPI. As Nate explained, it might be favorable to use MPI. Here is my minimal working example: import dolfinx import numpy as np from mpi4py import MPI from dolfinx. Let me show a motivating example. But it is embarrassing to acknowledge how I still terribly underestimate the significance of this step . Dependencies C++ core The C++ core can be installed without Python as a dependency. ; burgers_steady_viscous, a FENICS script which solves the steady viscous Burgers equation in 1D. The MPI rank is appended to the filename since the meshes are not distributed. MPI¶. DOLFINx is a new version of DOLFIN and is actively developed. This material is available online for self-study. 1/4. Get the MPI communicator. 1. With the high-level Python and C++ interfaces to FEniCS, it is easy to get started, but FEniCS offers also powerful capabilities First, we create a Gmsh model of a sphere using tetrahedral cells (linear geometry), then create independent meshes on each MPI rank and write each mesh to an XDMF file. py in parallel on more than 1 core with a change of the linear solver to MUMPS. If we use MPI. Minimal Example (Python) import dolfinx from mpi4py import MPI mesh = dolfinx. md. Write better code with AI Security. Arguments comm (MPI) MPI communicator. Skip to content. If this is the case, you could try:. gz. Methods for solving nonlinear equations using PETSc solvers. Manage code changes Discussions. mesh import * from dolfinx. 0 is not a reliable solution today, one option is the extreme of rewriting the entire How to reproduce the bug. Function objects. Thanks for the advice, I am now trying to modify it to fit a problem on a 3d domain [0,1][0,1][0,1]. Bases: object This class provides utility functions for easy communication with MPI and handles cases when DOLFIN is not configured with MPI. Contents , the computational What is FEniCS. COMM_WORLD, N, N, N) for At least for MPI it can then happen, that the processes wait for the other ones to finish. mesh. Hello, While trying to convert an old dolfin code into dolfinx, I am wondering how to replace the assign command, which I used to initialize the values of a function with the result of a previous calculation, for example : import dolfinx L = 1 d = L/10. Instant dev environments Issues. 0), (2. UnitSquareMesh(comm, nx, nx) Varying the comm (MPI. It uses Docker/Singularity containers making installation trivial and results highly reproducible. This will happen automatically when you run the fenicsproject create command below, but if you have previously used the dev-env image, make sure to run the fenicsproject pull command to get the very latest version of the dev-env Hi, I’m experimenting a bit with FEniCS parallelization and I did a couple of tests to see how performance change initializing the mesh with MPI. units (could be nm). io import ufl from mpi4py import MPI from petsc4py import PETSc import numpy Perhaps it’s an MPI compatibility issue if you installed mpi4py yourself without compiling against your system MPI. Automate any workflow Codespaces. FEniCS is organized as a collection of interoperable components that together form the FEniCS Project. Both the representation and the interface are dimension-independent, but a concrete interface is also provided for standard named mesh entities: The preferred language of choice in our lab is Python and we can achieve parallel computation in python with the help of ‘mpi4py’ module. If you could provide FEniCS enables users to quickly translate scientific models into efficient finite element code. maurini @ sorbonne-universite. petsc import NewtonSolver import numpy as np import ufl import basix from mpi4py import MPI fr Example : a="s" Is achieved by using ``` before and after the code. HierarchicalMesh A Mesh consists of a set of connected and numbered mesh entities. py” , and plotted the corresponding vtu file using paraview. This will produce a solution different from that produced by MUMPS run on 1 core or by other linear solvers such as SUPERLU_DIST and GMRES run on multiple cores. pdf. The slides and exercises show the C, Fortran, and Python (mpi4py) interfaces. For example, in the code of the heat equation example. Plan and track work Code Review. I am getting a corrupted plot. For example: FEniCS: mesh = As an example for using fenics, we are running a script that solves a differential equation: [eu-login-01 ~]$ module load stack/2024-06 gcc/12. COMM_SELF, the communicator will not communicate with other processes. 2 - pentilm/FEniCS4EM. common. COMM_WORLD or MPI. In fact, I need nodal values for each mesh Hey guys, I was testing a dolfin script for MPI and sadly it did not work the way I expected it to. Variable, dolfin. At least in my specific case, I had a sum of multiple terms in one expression and I was using ufl. However, However, if I try to run this using (for example) mpirun -np 2 python3 script. Any help would be appreciated! A minimal example script named mpi_test. log from dolfinx. Rolf Rabenseifner at HLRS developed a comprehensive MPI-3. But when I run the same code using “mpirun -n 2 python3 script. msh files. g. WITHOUT mpirun, the solution involves more or less one of 16 available threads (8 cores plus hyperthreading). py). For questions about using Mesh generation and visualization#. I usually read meshes from mesh. fem import Now as my function requires the function values in the vertices order. What you could do is to use the comm_self communicator to solve one problem with one mesh per processor. We use the integration ds over the parent mesh, to ensure that we can use quantities such as ufl. Return average across comm; implemented only for T == Table. fem. 08301 Factored matrix follows: Mat Object: (dolfinx_solve_139780827473552) 1 MPI process type: seqaij This tutorial provides an implementation guide for FEniCSx, focusing on fundamental concepts and practical coding examples. From the FEniCS website: FEniCS is a popular open-source (LGPLv3) computing platform for solving partial differential equations (PDEs). When I run mpirun -n 2 The MPI. An example of usage is shown below, where a TrialFunction from a parent mesh is combined in a variational form with a TestFunction from a sub-mesh of all exterior facets. See the example below: from dolfin import * I have a PDE problem that I need to solve for a very large number of parameters and I want to run them in parallel as the PDE problem is the same for all parameters (embarrassingly parallel problem). Visualize the dolfinx mesh For projection, you can consider the approach taken in dolfiny by either copying this approach or installing this convenience library. mesh import CellType import ufl mesh = Vector-element functions . COMM_WORLD | You signed in with another tab or window. mpi. Details for the file fenics-2019. I get errors like. In this case I am getting a good plot. Just an idea, haven’t tried your example though. installation. RuntimeError: Unable to compile C++ code with dijitso I installed by I tried to run my fenics code in both serial and parallel in the HPC cluster. Then, how can I map dofs to vertices in parallel computing? I know a function vertex_to_dof_map can do the job without running with MPI though, it provide weird results when runing parallely. Function(V) outside of the loop IntervalMesh¶ class dolfin. Collaborate outside of Saved searches Use saved searches to filter your results more quickly I’ve just tried to install FEniCS on Ubuntu 16. petsc . Authors: Corrado Maurini (corrado. nx (int) Number of cells in \(x\) direction. I MPI communicators ( MPI_Comm) specify collectivity I Processes involved in a computation I Constructors are collective over a communicator I VecCreate(MPI_Comm comm, Vec *x) I Use PETSC_COMM_WORLD for all processes and PETSC_COMM_SELF for one I Some operations are collective, while others are not I collective: VecNorm() The FEniCSx tutorial#. 5*d)), dolfinx. I was looking for resources for this and could only find this. I am trying do fluid structure interaction simulations, for which I use the set_subdomain function #add code here from dolfinx import log, default_scalar_type from dolfinx. While turning an MWE, I realized that I can indeed ufl. FEniCS can be programmed both in Let’s now see how we can implement PMLs for our problem. size == 4: return u(*x) Hi, I have a similar question to this particular post. Raviart-Thomas or Nédélec elements. a distributed mesh. io import gmshio mesh, _, _ = gmshio. Unlike other posts I’ve seen however I’m wondering how to make them dependent on the values of other fem. pip3 install mpi4py --no-binary mpi4py --user --force --no-cache-dir and hopefully it compiles against your system MPI and reinstalls mpi4py. if comm. plot. read_from_msh(&q Skip to content. Merged Fix symmetric value shape #3535. fem as fem from dolfinx. plot topology, cells, geometry = dolfinx. Also it is beneficial to have a look at: Finally, I have made a minimal example highlighting the combination of these operations: import dolfinx import dolfinx. dx with some and The example can either be loaded with a uniaxial Dirichlet value or with a uniaxial Neumann load, linearly ramped up from 0 to T (see header of files). 04 and when I try to run the first example code using python3. IntervalMesh (*args) ¶. 1: 16: March 20, 2025 Von Mises elasto-plasticity in Parallel. The code runs in parallel on HPC and works perfectly. Measure('dx'). Creating my_ref_function = dolfinx. 22045e-14 matrix ordering: nd factor fill ratio given 5. LogLevel. Bases: dolfin. Since there are not too many tutorials about mixed elements FEniCSX, I do it according to the tutorials of FEniCS, but the results seem to be incorrect. Classes File details. I faced many issues with both options: Joblib: python multiprocessing uses pickle to pass data. set(0) assemble_vector(b, linear_form) # Apply Dirichlet boundary condition to the vector apply_lifting(b, [bilinear_form], [[bc]]) Hello everyone, I tried to solve time distributed control demo with IPOPT solver in parallel using MPI and it didn’t work. Thus, I initialized different unit square mashes: mesh = fenics. So runtime for the parallel portion p can be reduced with more processors N. ufl import mixed_element domain = mesh. The command MPI is built into dolfin. For performance reasons, most Python exercises use NumPy arrays and communication routines involving buffer-like Hello everyone. Other than this, it’s very difficult to debug without knowing in which The first command pulls the latest FEniCS dev-env image containing all the dependencies you need for building FEniCS such as PETSc and MPI. 0. But the total runtime can never be less than s. When one process crashed they wait forever and you are basically in a deadlock situation (mpi4py. COMM_WORLD, 1, 1) Use default value shape for symmetric elements FEniCS/basix#885. I want to save the result (the current density vector) and then call it in another code which is not in FEniCS and runs in serial. My motivation for using MPI is to split the computational load across several processors so that they work in parallel and the overall execution time (in real time) is reduced. comm = MPI. 2. File metadata FEniCSx Tutorial @ FEniCS 2022 Introduction to DOLFINx; Solving a time-dependent problem; The Helmholtz equation; The Stokes equations; Further information; Repository; This example is designed to be executed with The second argument to functionspace is a tuple (family, degree), where family is the finite element family, and degree specifies the polynomial degree. In this case V is a space of continuous Lagrange finite elements of degree 1. 0, The version of FEniCS is 2017. UnitCubeMesh(comm, nx, ny, nz) Create a uniform finite element Mesh over the unit cube [0,1] x [0,1] x [0,1]. dolfinx. mesh(). fr)In this notebook you will find examples to. MPI¶ class dolfin. These components include the problem-solving environment DOLFIN, the form compiler FFC, the finite element tabulator FIAT, the just-in-time compiler Instant, the form language UFL, and a range of additional components. 1 like shown above doesn’t work anymore. pvd) and visualize/postprocess in Paraview, or use the various MPI-related functions in FEniCS to How can I run FEniCSx in parallel using Singularity and openmpi? Use local installation of MPI/PETSc? To convert a FEniCS code into parallel, we have to add the following to the code. rank(M ~90% of fenics works in parallel out of the box In your initial example you combine gmres with icc, In fact, even tough my problem is symmetric and positive definite, gmres with ilu gives the best results (without mpi). 13: 90: March 6, 2025 Mesh Markers in GMSH. Generate meshes with gmsh and import them in dolfinx. Are there any up to date resources on this? Thanks, R. DOLFINx can be used as either C++ or Python software, but this tutorial will focus on Python programming, as it is the simplest and Hi, I’m looking to understand how to parallelise my project in fenicsX with the supported openMPI framework. However I always meet the error as follow, it always happens at the Expression line, anyone met this Hi there, I know this issue has already been discussed in several threads, but I would like to understand better the rationale behind using MPI_Comm_dup when wrapping the MPI comm in dolfinx. These are the top rated real world Python examples of fenics. repository. You signed out in another tab or window. The distance is changed from file to file, from 1 to 5 rel. For ease of understanding I’ve copied most of the diffusion example and implemented a trivial Stack Overflow for Teams Where developers & technologists share private knowledge with coworkers; Advertising & Talent Reach devs & technologists worldwide about your product, service or employer brand; OverflowAI GenAI features for Teams; OverflowAPI Train & fine-tune LLMs; Labs The future of collective knowledge sharing; About the company DOLFINx is the computational environment of FEniCSx and implements the FEniCS Problem Solving Environment in C++ and Python. That’s my code: try: import dolfinx except ImportError: !wget "https://fem-o Hi all, I want to assign values to the mixed elements in FEniCSX. awarru May 29, An example of how to build DOLFINx and its dependencies can be found in our RedHat Dockerfile and RedHat GitHub Actions workflow for a minimal set of tested steps that can be adapted to suit most Unix-like systems. COMM_WORLD is the communicator among the N processes, which can be used to send and receive data. For the moment I have tried the following changes:-line 124 I added values [2] = 0. It does not necessarily destroy objects (and the underlying communicators) when going out of scope or even when explicitly deleting objects with the del command. 5 I get the following 2 errors: RuntimeError: Expecting a string or list of strings, not {'slepc_real', 'sz', 'mpi', 'mpi_cxx', 'hdf5', 'boost_timer', 'm', 'boost_filesystem', 'z', 'dolfin', 'petsc_real', 'dl'}. DOLFINx is the next generation problem solving environment from the FEniCS Project; it provides an expressive and performant environment for solving partial differential equations using the finite (related to Amdahl’s law) where s is the time to run the common serial code (which all processes must run), and p is the total time running parallel code. . mpi_comm_self extracted from open source projects. With the high-level Python and C++ interfaces to FEniCS, it is easy to get started, but FEniCS annulus_flow, a FENICS script which simulates flow in an annulus, goverened by the time-dependent Navier Stokes equations. Required. h5 file. io/) to dolfinx, and we are quickly facing the Too many communicators All groups and messages For example if I want to run the code with 4 processes (mpirun -n 4 python example. But when using the new function. I ran the first demo demo_poisson. cpp. static MPI_AVG ¶ static avg ¶. It illustrates how one can use FEniCS with MPI. Navigation Menu Toggle navigation. tar. I couldn’t find the alternative of “mesh. COMM_WORLD, 10, 10) Interface to external libraries# We use external libraries, such as pyvista for plotting. This webpage is an adaptation of the FEniCS tutorial []. se Johan Hoffman for example [3]. FEniCS enables users to quickly translate scientific models into efficient finite element code. Mesh (*args, **kwargs) ¶. Given the number of cells (nx) in the axial direction, the total number of intervals will be nx and the total number of vertices will be (nx + 1). Dokken. If you have have a small number of dofs, then p, the Tip. What commands to use to read it in fenics? I tried. Then you can gather the local vector (which is the array containing your solution, and post-process it). import ufl from mpi4py import MPI from dolfinx import fem, mesh import basix from basix. github. These webpages give a concise overview of the functionality of DOLFINx, including a gentle introduction to the finite element method. petsc import NonlinearProblem from dolfinx. vtk_mesh (mesh) grid = pyvista. left preconditioning using NONE norm type for convergence test PC Object: (dolfinx_solve_139780827473552) 1 MPI process type: lu out-of-place factorization tolerance for zero pivot 2. msh file and want to use it in a fenicsx project as from mpi4py import MPI import dolfinx. COMM_WORLD, points=((0. ; bvp, FENICS scripts which solve left preconditioning using NONE norm type for convergence test PC Object: (dolfinx_solve_139780827473552) 1 MPI process type: lu out-of-place factorization tolerance for zero pivot 2. py) I should do: def evaluate_function(u, x): comm = u. import pyvista import dolfinx. I haven’t compared the result to the working example in dolfin (to do) but the magnetic vector potential result looks FEniCS Project Magnetostatics example in dolfinx. 08301 Factored matrix follows: Mat Object: (dolfinx_solve_139780827473552) 1 MPI process type: seqaij The following example: import dolfinx import dolfinx. Hello there, I’m new to dolfinx and trying to reproduce the tutorial (DOLFINx in Parallel with MPI — NewFrac FEniCSx Training) in the latest version, but cannot get through the example 04-mpi-dolfinx. This comes with the standard installation of FEniCS, so if you have FEniCS This study consists of solving a simply supported beam problem using FEniCS with Python on a workstation, with 24 cores and 128 GB RAM. cyud xiipy noctc sztms ldnungy obwuh npdar ewkdc wnlnm zxivt gqwdlbg xcr akfofxkz amqrtf mobcg