running structure in parallel

[Sanndes Serestaa]

Hello,

I want to run structure in parallel. I have unix server with 32 cores and 64 G ram. I tried frontend but uses just one core. I want to run all cores.

It is taking so much time to run the analysis (already 3 days not even finished k1).

Please let me know how can I find Strauto to run in parallel.

Thanks

Sandesh

[Vikram Chhatre]

Google: ParalleleStructure R package.

V

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[zeamne T]

Hi Sanndes,

Just curious, how many markers do you have, and how long are your run parameters? Perhaps you can lower your run parameters, or if you have too many markers, it might be difficult to run using Structure and you may have to use fastSTRUCTURE instead.

Cheers,
yujie

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yujie

[Sanndes Serestaa]

I tried parallelstructure but not able to figure out how to make job file.

I have 8000 SNPs.

I was running 100k burn in 100k MCMC k1-10 with 10 replicates.

Thanks

Sandesh

[Ramesh krishnan Ramasamy]

Here (http://www.molecularecologist.com/2013/09/using-r-to-run-parallel-analyses-of-population-genetic-data-in-structure-parallelstructure/) is an excellent tutorial on parallel structure.

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[Sanndes Serestaa]

Ramesh:

Is there any simple way to figure out how to make jobfile with required parameters and data file with PS.

I was able to run example data in PS but not able to modify my data to run and set jobfile.

Thank you

Sandesh 

[Ramesh krishnan Ramasamy]

Sorry, I don't have enough experience in parallel structure to help you.

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