[R-sig-hpc] A question about Cores vs. tasks using Slurm for R

[Hodgess, Erin]

Hello!

This was my fault...my max was 16, not 32 on SLURM.
Sorry for submitting and wasting air time.

Sincerely,
Erin

________________________________________
From: Norm Matloff [nsmatloff at ucdavis.edu]
Sent: Saturday, September 26, 2015 7:23 PM
To: Hodgess, Erin; R-sig-hpc at r-project.org
Subject: Re: [R-sig-hpc] A question about Cores vs. tasks using Slurm for R

(Apologies if this message is circulated twice.)

Erin, specifically, what machine (and not machineS, plural, as in a
cluster) are you running this on, and what specific OS?  The number of
cores that are sensed here could depend on either or both.  See R's
online help for 'detectCores' for a brief discussion, as well as the
material on hyperthreading in my book (Ch.1).

In addition, there are probably definitional issues regarding SLURM
here.  I'm not a SLURM user, but I'm sure others on this list can
comment on that.

Norm

On Sat, Sep 26, 2015 at 11:02:25PM +0000, Hodgess, Erin wrote:
> Hello!
>
> I'm experimenting with some of the very interesting code in Prof. Matloff's new book "Parallel Computing for Data Science with Examples in R, C++ and CUDA".
>
> I have access to a supercomputer and am using SLURM to run my batch jobs in R.
>
> Here is what I have in my SBATCH file:
>
>
> !/bin/bash
>
> #SBATCH -t 00:05:00
>
> #SBATCH -n 32
>
> #SBATCH -p development
>
> #SBATCH -J myparb
>
> #SBATCH -o myparb.%j.out
>
> #SBATCH -e myparb.%j.err
>
>
>
>
> module load intel/15.0.2 Rstats/3.2.1
>
>
> source ~/.profile_user
>
>
> R CMD BATCH --slave ~/MutLinkPar2.R parb.txt
>
>
> Fair enough.  Here is a little section of my R file:
>
>
> cores <- detectCores()
>
> cls <- initmc(cores)
>
> cat("cores",cores,"\n")
>
> sim(500,500,cls)
>
>
>
> However, the output for the "cat" statement shows the number of cores to be 16.
>
> Why is this, please?  Shouldn't it be 32, please?
>
> Thank you in advance for any help!
>
> Note:  This is R version 3.2.1.
>
> Sincerely,
> Erin Hodgess
>
>
>
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>
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