Here is a list of common/useful run options. Please see the full option list and the particular application you are using for more.
-run:batches flag1 flag2 flag3 Run a batch. in flag1 .. flag3 you have those flags that differ from batch to batch. All the other flags can go onto the cmd-line like normal (Oliver Lange). Works with MPI. -run:maxruntime Maximum runtime in seconds.JobDistributor will signal end if time is exceeded no matter how many jobs were finished. Default='-1'. [Integer] -run:maxruntime_bufferfactor If set, the JobDistributor will attempt to stop if there doesn't appear to be enough time for `maxruntime_bufferfactor` more jobs before maxruntime occurs. [Real] -run:constant_seed Use a constant seed (1111111 unless specified). [Boolean] -run:jran Specify seed (requires -constant_seed). Used for non-MPI parellel runs Default='1111111'. [Integer] -run:use_time_as_seed Use time as random number seed instead of default rng seed device. [Boolean] Used for non-MPI parellel runs -run:seed_offset This value will be added to the random number seed. Useful when using time as seed and submitting many jobs to clusters.Using the condor job id will force jobs that are started in the same second to still have different initial seeds. Default='0'. [Integer] Used for non-MPI parellel runs -run:delay Wait N seconds before doing anything at all. Useful for cluster job staggering. Default='0'. [String] -run:nodelay Do not delay launch of Rosetta [Boolean] -run:random_delay Wait a random amount of 0..N seconds before doing anything at all. Useful for cluster job staggering. Default='0'. [Integer] -run:rng Random number generation algorithm: Currently only mt19937 is a accepted here. Default='mt19937'. legal=['mt19937']. [String] -run:rng_seed_device Obtain random number seed from specified device. Default='/dev/urandom'. [String] -run:shuffle Shuffle job order. Default='false'. [Boolean]