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Making a series of similar, but modified .r files for simulation experiment - suggested method(s)?
3 messages · Laura S, Glen A Sargeant, Lars Westerberg
1 day later
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Laura, Since you are submitting to a Linux cluster you probably use the SGE queuing system. If so, there is a trick you can use if submitting several tasks in one job (i.e. array job, see info on flag "-t": qsub ... -t 1-20:1). A colleague of mine have written a rudimentary how-to for our project group: http://tinyurl.com/35u2fxf In the shell script that you submit to the cluster, you can use $SGE_TASK_ID as argument when calling your main R-function. This parameter will be one of values that is defined by the "-t"-flag. You can use the task-id directly to modify your for-loop, or you use it to specify a row in a look-up table holding the values you are after. HTH /Lars
Laura S wrote:
Dear all: Any suggestions are much appreciated. I am looking for a way to make a series of similar, but slightly modified, .r files. My issue is automating making 320 .r files that change the for(i in 1:x) in my base .r file (as well as other elements, e.g., the load(...), setwd(...)). For smaller jobs running on a single computer with batch files, I have been manually changing the for(i in 1:x) line, etc.. Why does this matter to me? I am planning on running a simulation experiment on a linux cluster as a serial job. Although not elegant, it has been suggested I make 320 .r files so qsub runs one .r file and then selects other jobs. Thus, the manual route I am currently using would take a very long time (given multiple runs of 320 .r files, given experimental replication). Thank you, Laura