Parallel computation of genetic likelihoods using CRI-MAP, PVM, and a network of distributed workstations
- Univ. of Pittsburgh, PA (United States); and others
We have developed a version of the CRI-MAP computer program for genetic likelihood computations that runs CRI-MAP`s, FLIPS and ALL functions in parallel on a distributed network of workstations. We used the Parallel Virtual Machine (PVM) software to control communication between machines, and employed a simple load balancing algorithm to maximize speedup and efficiency and to reduce overhead incurred through parallelization. The performance of CRI-MAP-PVM was assessed in several linkage analyses using the FLIPS option of CRI-MAP on a map of 85 microsatellite markers for human chromosome 1. The performance was tested on a heterogeneous collection of two to twenty-five machines, comprised of up to 6 different types of workstations, including Suns, HPs (Hewlett Packard), and DECs (Digital Electronics Corporation). These analyses showed excellent speedup and efficiency and low distribution overhead. In addition, we have adapted the MultiMap program for automated construction of linkage maps to use CRI-MAP-PVM. These improvements significantly reduce the time required to compare likelihoods of different marker orders. Thus, the construction of linkage maps can proceed in a much more timely fashion, in keeping with recent advances in genotyping technology.
- OSTI ID:
- 134073
- Report Number(s):
- CONF-941009--
- Journal Information:
- American Journal of Human Genetics, Journal Name: American Journal of Human Genetics Journal Issue: Suppl.3 Vol. 55; ISSN AJHGAG; ISSN 0002-9297
- Country of Publication:
- United States
- Language:
- English
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