Question: passing submitJobs parameters from BatchJobsParam
1
gravatar for Alejandro Reyes
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
ADD COMMENTlink 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
gravatar for Martin Morgan
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.

ADD COMMENTlink written 3.5 years ago by Martin Morgan ♦♦ 23k
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