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I think it does depend on the problem. Genetic stuff always seemed not easily parallelizable like my field (physics simulation) is. That said, the culture here
by noobermin 4y ago
I think it does depend on the problem. Genetic stuff always seemed not easily parallelizable like my field (physics simulation) is. That said, the culture here is that MPI works and thus cray still builds computers that work better with it, so we use MPI so it works...etc etc.
- krab 4y ago> Genetic stuff always seemed not easily parallelizable Not really. Processing one sample may take a few hours but if you have hundreds or more samples, it's an obvious axis for independent parallelization. The cool kids use Nextflow or CWL these days. It's something like `make` - it remembers what you've already computed and what the dependencies are - but it uses a batch engine like SGE/Condor/AWS Batch to actually execute the jobs.