Question: passing submitJobs parameters from BatchJobsParam
1
3.5 years ago by
Alejandro Reyes1.7k
Dana-Farber Cancer Institute, Boston, USA
Alejandro Reyes1.7k wrote:

Hi,

I was using BiocParallel with BatchJobsParam and kept getting an error described here ( https://github.com/tudo-r/BatchJobs/issues/58 ). To avoid that error, I needed to pass the parameter job.delay from the function submitJobs (defined in BatchJobs), but I could not find a way pass this parameter to submitJobs when creating my BatchJobsParam object. By looking at the code, the only parameter that is passed to submitJobs from BatchJobsParam is 'resources':

submit.pars <- Filter(not_null, list(resources=resources))

So, what I end up doing was to manually modify my BatchJobsParam object:

cf <- makeClusterFunctionsLSF("/home/reyes/lsf.tmpl") bjp <- BatchJobsParam( nCores,     conffile="/g/huber/users/reyes/CLL/org/BatchJobs_config.R",     cluster.functions=cf,resources = list("queue" = "medium_priority", "memory"="8000", "cpus"="1" ))

bjp$submit.pars$job.delay <- function(n,i) runif(1,1,3)

This works, but I think it would be nicer to have full control of the submitJobs parameters when creating the BatchJobsParam object, as well as to have documentation of how to do this in ?BatchJobsParam

Alejandro

biocparallel • 487 views
modified 3.5 years ago by Martin Morgan ♦♦ 23k • written 3.5 years ago by Alejandro Reyes1.7k
Answer: passing submitJobs parameters from BatchJobsParam
2
3.5 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

I added conf.pars, reg.pars, and submit.pars arguments to the BatchJobs constructor as an alternative way to communicate with BatchJobs in BiocParallel version 1.5.18. Please let me know if there are problems; I'm not in the habit of using BatchJobs.