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Linux Environment Setup
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Linux Environment Setup

Simulations are most reliably executed in a Linux environment. Many of the required tools (compilers, MPI libraries, FEBio builds, scripting workflows) are designed with Linux-based systems in mind.

This page outlines three common approaches to set up a Linux environment:

  • Installing Linux as your primary operating system
  • Running Linux inside a virtual machine
  • Using a remote high-performance computing (HPC) cluster

Choose the option that best matches your experience level, hardware access, and computational needs.

Option 1 — Native Linux Operating System
Click to expand.

Overview

Installing Linux directly on your machine provides the most stable and highest-performance environment. This is recommended for users who plan to run simulations regularly or compile custom plugins.

Recommended Distributions

  • Ubuntu (most common and well-supported)

Installation Approaches

  1. Full Installation
    Replace your current OS with Linux.

  2. Dual Boot
    Install Linux alongside Windows or macOS.

  3. Separate Workstation
    Use a dedicated Linux machine for simulations.

Advantages

  • Best performance
  • Full control over compilers and dependencies
  • Simplest path for building FEBio from source
  • Most consistent with HPC cluster environments
Option 2 — Linux Virtual Machine
Click to expand.

Overview

A virtual machine (VM) allows you to run Linux inside your existing operating system. This is a good option if you cannot replace your OS but want a stable Linux environment.

VM Software Options

  • VirtualBox (free)
  • VMware Workstation / Fusion
  • UTM (macOS Apple Silicon)

Install a Linux ISO (Ubuntu) inside the VM.

Recommended VM Configuration

  • At least 8 GB RAM allocated (if available)
  • 2–4 CPU cores (allows testing parallelization)
  • 40+ GB storage

Advantages

  • No need to modify your primary OS
  • Safe sandbox environment for learning workflows, testing small changes to code, and developing scripts
  • Can run most MBE simulations

Limitations

  • Slower than native Linux
  • Limited memory and CPU availability
  • Not ideal for large-scale simulations (e.g., for large FSG simulations, an HPC cluster is preferred)
Option 3 — High-Performance Computing Cluster
Click to expand.

Overview

Clusters provide scalable computational power for large simulations, parameteric sweeps, and optimization studies. Most research institutions provide access to an HPC system. Commonly used clusters:

  • Yale Grace Cluster
    Documentation: https://docs.ycrc.yale.edu/clusters/grace/
    To request access, follow the instructions under “Access the Cluster.”

  • Expanse (SDSC)
    Access and documentation: [link to be added]
    (Instructions to be added.)

Typical Workflow

  1. Connect via SSH:
ssh username@cluster.address.edu
  1. Load required modules:
module load gcc
module load cmake
module load mpi
  1. Compile or run simulations (specifics under simulation tutorials), first on debug node and then submitted through scheduler (e.g., SLURM):
sbatch run_simulation.sh

Advantages

  • Massive parallelization
  • Large memory nodes
  • Ideal for long running simulations or large meshes

Limitations

  • Requires learning job schedulers and file management via command line
  • Often no graphical interface

Suggestion: Use a local machine to develop code and workflow, then use clusters for scaling to final study.

Typical Software Stack

After establishing your Linux environment, you will typically install:

sudo apt update
sudo apt install build-essential cmake git python3 python3-pip

Additional tools may include:

  • GCC (modern version)
  • OpenMPI
  • MKL (if required)
  • ParaView
  • PyVista/NumPy/SciPy

This setup provides a reproducible computational environment.

Linux Terminal/Command Line Cheat Sheet

  • pwd — Print the current working directory.
  • ls — List files.
  • cd <dir> — Change directory.
  • cd .. — Move up one level.
  • mkdir — Create a directory.
  • cp <src> <dst> — Copy files.
  • mv <src> <dst> — Move or rename files and directories.
  • rm <file> — Delete a file.
  • cat file.txt — View file contents.
  • head -n 20 file.txt — View the first 20 lines of a file.
  • tail -n 20 file.txt — View the last 20 lines of a file.
  • less file.txt — View large text files (press q to quit).
  • vim file.txt — Edit a file in Vim.
  • emacs file.txt — Edit a file in Emacs.