[hansvm]

Is there any particular reason you wouldn't want to wrap that workload in a function/module/... and call it in a loop? Is the problem that your commonly used tools are exposed only as command line interfaces and not as libraries?

[clavigne]

Yeah that's what I mean. This is the case for both commercial software (eg Q-Chem) and free software.

This is not to say that the boot time is always a problem, there are plenty of applications in which it doesn't matter at all (as you point out). However that's not always the case (by a long shot) which is why tools like GNU Parallel and snakemake exist.