missing wait argument in submitJobs

[kerschke]

Is there something like a wait argument within submitJobs (as within its BatchJobs-version)? And can I somewhere set the max. number of concurrent jobs within batchtools? Currently, I always get the following error message when exceeding the max. number of concurrent jobs:

> submitJobs(findNotSubmitted(ids), resources = list(walltime = 8L * 3600L))
Submitting 30 jobs in 30 chunks using cluster functions 'TORQUE' ...
Submitting [======================-----------------------------]  43% eta:  3s
Error in submitJobs(ids, resources = list(walltime = 8L *  : 
  Fatal error occurred: 101. Command 'qsub' produced exit code 226. Output: 'qsub: Maximum number of jobs already in queue for user MSG=total number of current user's jobs exceeds the queue limit: user [abc], queue [def]

Also, I now have to manually submit new jobs once some of my jobs are done.

And do you have any suggestions for a convenient fix to that -- except for a loop that checks every couple of minutes whether I can submit new jobs and then submits the amount of jobs that is accepted by the cluster?

[mllg]

• You can wait for submitted jobs to terminate with waitForJobs()
• Max concurrent jobs can be controlled via reg$max.concurrent.jobs. Just add a line like max.concurrent.jobs = 500 to your config file. See ?Registry.

Re-open if you need more flexibility or encounter any problems.