Parallelize Tasks

SEISMIC-RNA can use multiple CPU cores to speed up processing.

--num-cpus N

Pass --num-cpus N to any command to use up to N cores simultaneously. By default, SEISMIC-RNA uses all available cores on your machine.

SEISMIC-RNA parallelizes across independent inputs: each core processes a different sample, reference, or batch at the same time. The speedup is roughly proportional to N, up to the number of independent inputs. For example, if you have 4 references and set --num-cpus 4, all four are processed simultaneously.

On a shared computing cluster, set --num-cpus to your allocated core count rather than leaving it at the default.

To watch how many of the inputs have been processed, see the progress bar, which counts every input as it finishes, however many are being processed at once.

Batches

The IDmut step divides each dataset into batches of reads, controlled by --batch-size N (number of reads per batch, default 65,536). Downstream steps (Filter, Cluster) reuse those same batches, so --batch-size is set only on IDmut (or on seismic wf, which passes it through).

Batches serve two purposes:

  • Speed: multiple batches can be processed simultaneously.

  • Memory: only one batch needs to fit in RAM at a time. Reducing --batch-size lowers peak memory usage at the cost of more output files and slightly more overhead.

Recommendations

  • Start with the defaults (all CPUs, batch size 65,536).

  • If a step runs out of memory, reduce --num-cpus or --batch-size.

  • If you have many small inputs, set --num-cpus to match the number of inputs for maximum utilization.

See also

  • Branches — run multiple analyses in parallel with different settings

  • Log Messages — progress bars and log messages while a command runs