[R-sig-hpc] [R-sig-HPC]Problems of submitting Rmpi Parallel Job with LSF

[Dirk Eddelbuettel]

On 23 July 2010 at 10:17, hongxu wrote:
| 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?

Looks like your problem is with your shell indirection. I *much* prefer to
work with r (ie /usr/bin/r from the littler project) when I launch Rmpi jobs.
You could also use Rscript.

Examples for r and Rmpi are in my 'Intro to High-Performance Computing with
R' slides at http://dirk.eddelbuettel.com/presentations.html.

I can't help with lsf as I don't access to it -- but slurm works quite nicely
with Rmpi via r.

Hope this helps.

Dirk


| 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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| 
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-- 
Dirk Eddelbuettel | edd at debian.org | http://dirk.eddelbuettel.com