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

Gene Cooperman gene at ccs.neu.edu
Tue Jan 26 01:54:35 CET 2016


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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