DMU

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Description

DMU is a package of tools for analysing multivariate mixed models.

The package consists of the following modules:

  • DMU1 -- Initial program that always must be used; the program reads a driver file containing descriptions of data, model and variance structure, prior variances and covariances and auxiliary input to the other modules.
  • DMU4 -- This module can be used to predict future outcomes of random effects (e.g. breeding values) and to estimate fixed effects.
  • DMU5 -- This module can be used to solve the multiple trait mixed model equations based on iteration on data.
  • DMUAI -- This module can be used for estimation of (co)variance components using Average Information REstricted Maximum Likelihood (AI-REML) (Jensen et al. 1997).
  • RJMC -- Description to come (the module is still under development).

Availability

DMU is available in the version 6, release 5.0.

Use

Batch use:

  • prepare the job description script -- use a general skeleton supplemented by the following lines:
...
# load the module into the environment
module add dmu-6.5
 
# run the computation
# general format: PROGRAM <INPUT_FILE.DIR >OUTPUT_FILE
# available programs: dmu1, dmu4, dmu5, dmuai, rjmc
# e.g.:
dmu1 <my_input_file.DIR >my_output_file
...
  • pass the job description file to the scheduler together with the request for a single processor and the requested amount of memory:
$ qsub -l nodes=1:ppn=1 -l mem=XXXg mydescriptionfile.sh

Interactive use:

  • ask the scheduler for an interactive job having a single node and a single processor reserved:
$ qsub -I -l nodes=1:ppn=1 -l mem=XXXg
Note: Do not forget to apppropriately set the amount of requested memory (mem attribute) and/or another job requirements.
  • load the DMU module into the environment:
$ module add dmu-6.5
  • to run the computations provided by the module, use the wrapping scripts (named r_dmu4, r_dmu5, r_dmuai and r_rjmc) followed by a file specifying the computation to be done (so-called driver file):
$ r_dmu4 my_computation    # the DIR suffix will be added automatically
$ r_dmu5 my_computation    # the DIR suffix will be added automatically
$ r_dmuai my_computation   # the DIR suffix will be added automatically
$ r_rjmc my_computation    # the DIR suffix will be added automatically
Note: Even though the wrapping scripts exist, one can also run the provided tools (dmu1, dmu4, dmu5, dmuai, rjmc) directly.

Documentation

The documentation is available on the producer's WWW server or locally in the /software/dmu-6.5/doc/ directory.

License

The program is free of charge for research purposes, but the use should be acknowledged in publications by reference to its manual.

Supported platforms

Linux

Program administrator

meta@cesnet.cz

Homepage

URL: http://www.dmu.agrsci.dk/