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stevemussmann / BayesAss3-SNPs

Modification of BayesAss 3.0.4 to allow handling of large SNP datasets
GNU General Public License v3.0
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Parallelization #16

Closed githubgig closed 1 year ago

githubgig commented 1 year ago

Hello,

I'm running BA3 using parallel, but it is using only 2 threads even when I specify -j 20. Is there a better way to parallelize?

Thank you.

stevemussmann commented 1 year ago

Each instance of BA3 will run on a single core, so the number of threads in use will be determined by the number of instances of BA3 that are submitted to parallel simultaneously.

githubgig commented 1 year ago

Hi Steve,

Thanks for the reply. I see. I'm guessing each instance is one run correct? I'm currently doing just one test run (10M iterations using a single command in the ba3_commands.txt). I was wondering if there is a way to parallelize within each run?

Thanks again.

stevemussmann commented 1 year ago

That is correct - each instance is one run. There is currently no way to parallelize within a run. It's on my 'to do' list but will require a significant code overhaul.

githubgig commented 1 year ago

I see. Thanks for your replies though.

stevemussmann commented 1 year ago

No problem. I'm going to close this issue but please feel free to open a new one if you run into problems.