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.

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