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Terry edited this page Apr 20, 2017 · 25 revisions

LSDTM

Location-Specific Disease Transmission Models -related scripts

About

The LSDTM project is a collection of scripts (named after the primary script, lsdtm.sh) for running the MIDAS-ISG version of the Public Health Dynamics Laboratory branch of FRED on the Olympus cluster of the Pittsburgh Supercomputing Center through Portable Batch System (PBS). Currently, only Synthia-formatted synthetic populations are supported.

LSDTM Dependencies

Ensure fred/fred-phdl2.12.0-isg1.0 and fred_populations/spew2synthia-1.2.0 modules are available in working environment. Run module avail on command-line prompt to see a list of available modules

How to Load LSDTM

  1. Clone or download LSDTM project
  2. Determine population ID ('spew_1.2.0_mng' is the population ID for Mongolia in Synthia-formatted SPEW v1.2.0)
  3. Run [path]/LSDTM/lsdtm.sh -p <synthetic_population_ID> -o <output_directory>

Home

User Guide

Script Usage Reference

Appendix A: Available SPEW 1.2.0 Populations

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