AvidaMT

Installing AvidaMT

macOS (Homebrew)

These instructions cover a native macOS install using Homebrew and the modern CMake-based build system.

These instructions have been verified on:

Component Version
macOS Ventura 13.7.8 (Intel x86_64)
Xcode 15.2 (Apple Clang 15.0.0)
Homebrew Boost 1.87.0
CMake 4.3.0

Step 1: Prerequisites

Install the Xcode Command Line Tools (skip if already installed):

xcode-select --install

Install Homebrew, then use it to install CMake and Boost:

brew install cmake boost

This installs a modern Boost (1.87.0 or later) and CMake. No manual Boost configuration is needed — CMake finds it automatically.

Step 2 — Clone the repositories

AvidaMT depends on ealib-modern, which must be cloned as a sibling directory (both repos live inside the same parent folder).

mkdir Avida && cd Avida
git clone https://github.com/kgskocelas/ealib-modern.git ealib-modern
git clone https://github.com/kgskocelas/AvidaMT.git AvidaMT

Confirm the layout looks like this:

Avida/
├── ealib-modern/
└── AvidaMT/

Why side by side? AvidaMT’s CMakeLists.txt pulls in ealib-modern via add_subdirectory(../ealib-modern …), so the relative path must be correct.

Step 3 — Configure

cd AvidaMT
cmake -B build -S .

Step 4 — Build

cmake --build build --parallel

All four executables will be compiled into build/:

Executable Description
avida-logic9 Logic-9 baseline experiment
mt_lr_gls Major transitions (GLS)
mt_lr_gls_dol_control Major transitions (DOL control)
ts_mt Task-switching experiment

Step 5 — Verify

Run all commands from inside AvidaMT/. Each test runs in its own subdirectory so output files don’t overwrite each other.

mkdir -p verify/logic9
(cd verify/logic9 && ../../build/avida-logic9 -c ../../etc/logic9.cfg --ea.run.updates=5 --ea.rng.seed=42)
echo $?   # should print 0

mkdir -p verify/mt_lr_gls
(cd verify/mt_lr_gls && ../../build/mt_lr_gls -c ../../etc/major_transitions.cfg --ea.run.updates=100 --ea.rng.seed=42)
echo $?   # should print 0; creates tasks.dat, mt_gls.dat, dol.dat

mkdir -p verify/mt_lr_gls_dol_control
(cd verify/mt_lr_gls_dol_control && ../../build/mt_lr_gls_dol_control -c ../../etc/major_transitions.cfg --ea.run.updates=100 --ea.rng.seed=42)
echo $?   # should print 0; creates tasks.dat, mt_gls.dat

mkdir -p verify/ts_mt
(cd verify/ts_mt && ../../build/ts_mt -c ../../etc/ts_mt.cfg --ea.run.updates=100 --ea.rng.seed=42)
echo $?   # should print 0; creates tasks.dat, ts.dat, mt.dat

Troubleshooting

Boost not found If CMake cannot locate Boost, set BOOST_ROOT explicitly:

cmake -B build -S . -DBOOST_ROOT=$(brew --prefix boost)

ealib-modern not found Verify that ealib-modern/ and AvidaMT/ are in the same parent directory. The relative path ../ealib-modern in CMakeLists.txt must resolve correctly.

Compiler errors about C++ standard library headers Make sure Xcode Command Line Tools are up to date:

xcode-select --install

MSU HPCC

These instructions are for the Michigan State University High Performance Computing Center (HPCC), which uses the Lmod module system. CMake and Boost are available as pre-built modules — no manual Boost compilation is needed.

You need an HPCC account. If you do not have one, request access through ICER at https://icer.msu.edu before starting.

Step 1 — Connect and move to a development node

Log in to the HPCC and request a development node so that compilation does not run on the shared login node:

Step 2 — Check available Boost modules

module spider Boost

Look for a result like Boost/1.83.0-GCC-13.2.0 (a full Boost library, not Boost.Python/). Note the exact version string — you will need it in the next step.

Step 3 — Load modules

Load a compatible set of GCC, CMake, and Boost. Use the version numbers you found in Step 2. For example:

module purge
module load GCC/13.2.0
module load CMake/3.27.6-GCCcore-13.2.0
module load Boost/1.83.0-GCC-13.2.0

module purge clears any previously loaded modules to avoid version conflicts.

Verify:

cmake --version   # should print 3.14 or newer

Step 4 — Clone the repositories

AvidaMT and ealib-modern must be cloned as sibling directories inside the same parent folder.

cd $HOME
mkdir Avida && cd Avida
git clone https://github.com/kgskocelas/ealib-modern.git ealib-modern
git clone https://github.com/kgskocelas/AvidaMT.git AvidaMT

Confirm the layout:

$HOME/
├── Avida
├──── ealib-modern/
└──── AvidaMT/

Step 5 — Configure and build

cd $HOME/Avida/AvidaMT
cmake -B build -S .
cmake --build build --parallel

The build will take a few minutes. When it finishes, the four executables are in build/:

Executable Description
avida-logic9 Logic-9 baseline experiment
mt_lr_gls Major transitions (GLS)
mt_lr_gls_dol_control Major transitions (DOL control)
ts_mt Task-switching experiment

Step 6 — Verify

Run from inside $HOME/Avida/AvidaMT/. Use the same verification steps as local installation.

Step 7 — Save your module setup

Modules are reset at the end of each login session. Save the current setup so you can restore it quickly:

module save avidamt

In future sessions, restore it before building or running experiments:

module restore avidamt

Running experiments via SLURM

Full AvidaMT experiments are computationally expensive and must be submitted as batch jobs, not run on a login or development node. A minimal SLURM job script looks like:

#!/bin/bash
#SBATCH --job-name=mt_lr_gls
#SBATCH --time=24:00:00
#SBATCH --mem=4G
#SBATCH --cpus-per-task=1
#SBATCH --output=slurm-%j.out

module restore avidamt
cd $HOME/AvidaMT
./build/mt_lr_gls -c etc/major_transitions.cfg --ea.rng.seed=$SLURM_ARRAY_TASK_ID

Troubleshooting (HPCC)

Boost not found at configure time Make sure the Boost module is loaded (module list). If it is loaded but CMake still cannot find it, set BOOST_ROOT explicitly:

cmake -B build -S . -DBOOST_ROOT=$EBROOTBOOST

$EBROOTBOOST is set automatically by the Lmod Boost module.

ealib-modern not found Verify that ealib-modern/ and AvidaMT/ share the same parent directory. The relative path ../ealib-modern in CMakeLists.txt must resolve correctly.

This site is open source. Improve this page.