Fwdpy11

Introduction

Fwdpy11 is a Python package for forward-time population genetic simulation.

For more information, please check:

Docker hub: https://hub.docker.com/r/molpopgen/fwdpy11

Home page: https://github.com/molpopgen/fwdpy11

Versions

• 0.18.1

Commands

• python3

• python

Module

You can load the modules by:

module load biocontainers
module load fwdpy11

Interactive job

To run fwdpy11 interactively on our clusters:

(base) UserID@bell-fe00:~ $ sinteractive -N1 -n12 -t4:00:00 -A myallocation
salloc: Granted job allocation 12345869
salloc: Waiting for resource configuration
salloc: Nodes bell-a008 are ready for job
(base) UserID@bell-a008:~ $ module load biocontainers fwdpy11
(base) UserID@bell-a008:~ $ python
Python 3.8.10 (default, Mar 15 2022, 12:22:08)
[GCC 9.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import fwdpy11
>>> pop = fwdpy11.DiploidPopulation(100, 1000.0)
>>> print(f"N = {pop.N}, L = {pop.tables.genome_length}")

Batch job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run fwdpy11 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=fwdpy11
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers fwdpy11

python script.py