[R-sig-hpc] RFC: Checkpoint-Restart for R/HPC (DMTCP)Qaqaoi

Roger rkoenker at illinois.edu
Fri Jan 29 15:26:09 CET 2016


cats w

Sent from my iPhone

> On Jan 25, 2016, at 6:54 PM, Gene Cooperman <gene at ccs.neu.edu> wrote:
> 
> Hi Bjorn-Helge,
> 
> I'd be very happy to package DMTCP as an R package.  However,
> DMTCP is a package written in C/C++ for Linux.  We usually build it as:
> 
>  tar zxvf dmtcp.tar.gz
>  cd dmtcp && ./configure && make -j
> 
> After that, we would invoke it as:
> 
>  path_to_dmtcp_root/bin/dmtcp_launch Rscript myscript.R
> 
> or something similar.  In another window, we can then type:
> 
>  path_to_dmtcp_root/bin/dmtcp_command --checkpoint
> 
> So we're using DMTCP from the outside of R.  If it's easier for
> users to invoke DMTCP from inside R, I'm happy to collaborate,
> but I'm not an expert in R, and would appreciate advice.
> 
> Best,
> - Gene
> 
>> Date: Thu, 21 Jan 2016 10:05:55 +0100
>> From: Bj?rn-Helge Mevik <b.h.mevik at usit.uio.no>
>> To: r-sig-hpc at r-project.org
>> Subject: Re: [R-sig-hpc] RFC:  Checkpoint-Restart for R/HPC (DMTCP)
>> Message-ID: <s3s8u3jz4i4.fsf at varelg.uio.no>
>> Content-Type: text/plain; charset=utf-8
>> 
>> As an administrator for an HPC cluster, I'd say dmtcp for R would be
>> very useful.  Some HPC clusters (including our :) implement a
>> "lowpri"/"opportunistic" queue, where jobs can be requeued any time a
>> higher priority job needs the resources.
>> 
>> An R package that implemented dmtcp integration would be very usable
>> also for many users not using BioConductor, so I would suggest creating
>> a package that is uploaded to CRAN, so one wouldn't have to install
>> BioConductor to use it.
>> 
>> -- 
>> Regards,
>> Bj?rn-Helge Mevik
> 
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