Difference between revisions of "Team:FAU Erlangen/Tour25"
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<li> Cutting down to solve the specific problem at hand | <li> Cutting down to solve the specific problem at hand | ||
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| + | <h4>Brute force optimization</h4> | ||
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| + | As the first attempt at brute force was not feasible, we tried to make better use of the computing power at hand. The first try used only one CPU core, which was a really slow way of doing things, since the problem was mainly CPU-bound. The code was designed to be executed in as many processes as there are cores in the current system, meaning an effective division of the time needed by that number. The system we used has 64 cores and the change greatly increased | ||
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Revision as of 13:31, 13 September 2015
The struggle to be unique
In order to execute our project, we first needed unique sequences, which are not common or do not appear at all in the yeast stems we use. We needed 10 basepairs that are not present. The first brute force attempt turned out to take approximately 40 days, counting all 4194304 possible combinations throughout the chromosomes. As that was not an option, we needed a faster program that could tell us which sequences are the least common. There were 2 different approaches.
- Brute force optimization
- Cutting down to solve the specific problem at hand
Brute force optimization
As the first attempt at brute force was not feasible, we tried to make better use of the computing power at hand. The first try used only one CPU core, which was a really slow way of doing things, since the problem was mainly CPU-bound. The code was designed to be executed in as many processes as there are cores in the current system, meaning an effective division of the time needed by that number. The system we used has 64 cores and the change greatly increased