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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

CLUMPP

CLUMPP (CLUster Matching and Permutation Program) deals with label switching and multimodality in the output of population-structure clustering programs such as Structure. It permutes the cluster labels of replicate runs so that they match up as closely as possible.

License

CLUMPP is freely downloadable and free to use; no specific open-source license is specified. See the CLUMPP home page for terms.

Available

  • Roihu: 1.1.2, via the bio-apps module.

Usage

CLUMPP is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the CLUMPP module:

module load bio-apps/v202603
module load clumpp/1.1.2

CLUMPP is driven by a parameter file (paramfile) that specifies the input, output and options. Run it with:

CLUMPP paramfile

CLUMPP is often used as part of an automated Structure workflow — see StrAuto, which runs CLUMPP as part of its post-processing.

Example batch script

#!/bin/bash
#SBATCH --job-name=clumpp
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=2G

module load bio-apps/v202603
module load clumpp/1.1.2

CLUMPP paramfile

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

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