A Run is generated from a Setup using setup_run. Application setup_run does not allow any options that would change how the structure calculation is performed by Rosetta. Instead setup_run allows to specify how running the structure calculation is implemented on the particular platform. Thus, using the same Setup one can generate runs using, e.g., the “mpi.linuxgccrelease”, or “default.linuxiccrelease” versions of Rosetta applications. One can further change which type of job-script is generated catering thus to different queuing systems. A user having accounts on different computer-centers can thus easily switch between platforms without the need for further manual editing of script files. Moreover, one can prepare a large set of targets and subsequently run equivalent setups, e.g., in a terminal running bash one would enter
for i in $( cat my_benchmark_targets); do setup_run -method abrelax -label with_rdc -target $i -dir ~/run_benchmark_with_rdc -jobs slurm; done
for multiple targets as required for benchmarking.
Job-scripts are generated from templates provided in csrosetta3/flag_library/jobtemplates. Users can easily edit existing templates to match their specific queuing systems and add additional templates in this directory. Templates should be called production.<JOBTYPE>.job and test.JOBTYPE.job for production and test jobs respectively. The name JOBTYPE can be chosen freely and will appear as a choice for option -job JOBTYPE in the help setup_run -h.