Dear all, I have some questions about how to submit Rmpi Parallel Job with LSF.


I'd like to use LSF command bsub to submit Rmpi parallel job directly, for example, use the command line

$bsub -W 10 -a openmpi -n 16 -q x64_dbg -o result.Rout -e err mpijob.openmpi 'R --no-save -q < prog.R > Output' 

to submit Rmpi parallel job, using 16 remote CPUs.

However, some errors appear:     
.......................
 29 The output (if any) follows:
 30
 31 ARGUMENT '<' __ignored__
 32
 33 ARGUMENT 'prog.R' __ignored__
 34
 35 ARGUMENT '>' __ignored__
 36
 37 ARGUMENT 'Output' __ignored__
.......................
How can I implement this process--use LSF to submit Rmpi parallel jobs directly?

Using Rlsf seems to be able to solve this problem, but the user submits R jobs in R environment, not as convenient as bsub.

Furthermore, based on the webpage http://rc.partners.org/node/241 , the user can directly use bsub to submit Rmpi jobs.


Thank you for your time!

2010-07-23 



hongxu 

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