Anyone using or has access to ParallelR? I was looking at the page and found nothing really useful! http://www.revolution-computing.com/sitegenius/topic.php?id=195 I want to see if I can run R on a cluster of workstation, and use batch systems like Grid Engine or Xgrid: http://gridengine.sunsource.net/ http://ww.apple.com/acg/xgrid/ --Chi
Hi! Have you looked at snow, snowfall, Rmpi, or rparallel, please? Hope this helps, Sincerely, Erin On Wed, Oct 8, 2008 at 10:14 AM, Chi Chan <chichan2008 at gmail.com> wrote:> Anyone using or has access to ParallelR? I was looking at the page and > found nothing really useful! > > http://www.revolution-computing.com/sitegenius/topic.php?id=195 > > I want to see if I can run R on a cluster of workstation, and use > batch systems like Grid Engine or Xgrid: > > http://gridengine.sunsource.net/ > http://ww.apple.com/acg/xgrid/ > > --Chi > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodgess at gmail.com
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Chi, ParallelR is a commercial software to run R in parallel. It is working very well. We tested it at a small linux cluster. You also can use R and the parallel packages (snow, Rmpi, nws, ...) packages. All Open Source and for free. You probably will have some more work installing the complete system, but the same results. You also can use a batch system with R. We are using Sun Grid Engine! (this should be even possible for parallelR) Best Markus Chi Chan wrote:> Anyone using or has access to ParallelR? I was looking at the page and > found nothing really useful! > > http://www.revolution-computing.com/sitegenius/topic.php?id=195 > > I want to see if I can run R on a cluster of workstation, and use > batch systems like Grid Engine or Xgrid: > > http://gridengine.sunsource.net/ > http://ww.apple.com/acg/xgrid/ > > --Chi > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.-----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.4-svn0 (GNU/Linux) Comment: Using GnuPG with SUSE - http://enigmail.mozdev.org iD8DBQFI7SGUwxqyUctZsggRAjInAJ9Cw7cy97nVa57lokaWFx7VJk2iwwCeOuwO KHcLP7HUUMSmfak+oLrQjXU=fPMX -----END PGP SIGNATURE-----
Hi, I wonder if there are any parallel package which do not rely on mpi or pvm? On Wed, Oct 8, 2008 at 5:09 PM, Markus Schmidberger <schmidb at ibe.med.uni-muenchen.de> wrote:> -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > Hi Chi, > > ParallelR is a commercial software to run R in parallel. It is working > very well. We tested it at a small linux cluster. > > You also can use R and the parallel packages (snow, Rmpi, nws, ...) > packages. All Open Source and for free. You probably will have some more > work installing the complete system, but the same results. > > You also can use a batch system with R. We are using Sun Grid Engine! > (this should be even possible for parallelR) > > Best > Markus > > > Chi Chan wrote: >> Anyone using or has access to ParallelR? I was looking at the page and >> found nothing really useful! >> >> http://www.revolution-computing.com/sitegenius/topic.php?id=195 >> >> I want to see if I can run R on a cluster of workstation, and use >> batch systems like Grid Engine or Xgrid: >> >> http://gridengine.sunsource.net/ >> http://ww.apple.com/acg/xgrid/ >> >> --Chi >> >> ______________________________________________ >> R-help at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v2.0.4-svn0 (GNU/Linux) > Comment: Using GnuPG with SUSE - http://enigmail.mozdev.org > > iD8DBQFI7SGUwxqyUctZsggRAjInAJ9Cw7cy97nVa57lokaWFx7VJk2iwwCeOuwO > KHcLP7HUUMSmfak+oLrQjXU> =fPMX > -----END PGP SIGNATURE----- > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- ??? Hesen Peng http://hesen.peng.googlepages.com/
But when I use the function makeSOCKmpi I am required to input my password to local computer, right? I haven't figured out how to do that when using a Sun Grid Engine. Do you have any suggestions? Thanks a lot. 2008/10/9 Martin Morgan <mtmorgan at fhcrc.org>:> snow can use native sockets, i.e., no additional dependencies. Martin > > "Hesen Peng" <hesen.peng at gmail.com> writes: > >> Hi, >> >> I wonder if there are any parallel package which do not rely on mpi or pvm? >> >> On Wed, Oct 8, 2008 at 5:09 PM, Markus Schmidberger >> <schmidb at ibe.med.uni-muenchen.de> wrote: >>> -----BEGIN PGP SIGNED MESSAGE----- >>> Hash: SHA1 >>> >>> Hi Chi, >>> >>> ParallelR is a commercial software to run R in parallel. It is working >>> very well. We tested it at a small linux cluster. >>> >>> You also can use R and the parallel packages (snow, Rmpi, nws, ...) >>> packages. All Open Source and for free. You probably will have some more >>> work installing the complete system, but the same results. >>> >>> You also can use a batch system with R. We are using Sun Grid Engine! >>> (this should be even possible for parallelR) >>> >>> Best >>> Markus >>> >>> >>> Chi Chan wrote: >>>> Anyone using or has access to ParallelR? I was looking at the page and >>>> found nothing really useful! >>>> >>>> http://www.revolution-computing.com/sitegenius/topic.php?id=195 >>>> >>>> I want to see if I can run R on a cluster of workstation, and use >>>> batch systems like Grid Engine or Xgrid: >>>> >>>> http://gridengine.sunsource.net/ >>>> http://ww.apple.com/acg/xgrid/ >>>> >>>> --Chi >>>> >>>> ______________________________________________ >>>> R-help at r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/r-help >>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >>>> and provide commented, minimal, self-contained, reproducible code. >>> >>> -----BEGIN PGP SIGNATURE----- >>> Version: GnuPG v2.0.4-svn0 (GNU/Linux) >>> Comment: Using GnuPG with SUSE - http://enigmail.mozdev.org >>> >>> iD8DBQFI7SGUwxqyUctZsggRAjInAJ9Cw7cy97nVa57lokaWFx7VJk2iwwCeOuwO >>> KHcLP7HUUMSmfak+oLrQjXU>>> =fPMX >>> -----END PGP SIGNATURE----- >>> >>> ______________________________________________ >>> R-help at r-project.org mailing list >>> https://stat.ethz.ch/mailman/listinfo/r-help >>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >>> and provide commented, minimal, self-contained, reproducible code. >>> >> >> >> >> -- >> ??? Hesen Peng >> http://hesen.peng.googlepages.com/ >> ______________________________________________ >> R-help at r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M2 B169 > Phone: (206) 667-2793 >-- ??? Hesen Peng http://hesen.peng.googlepages.com/
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, mpi is probably the mostly used standard for parallel computing. It was especially developed for message passing. Therefore most packages are based on MPI. Using "snow" you can choose between socket, mpi, pvm and (in the newest version) nws. I think actually there are no other communication ports. To avoid entering your password you should use ssh-keys! Best Markus Hesen Peng wrote:> Hi, > > I wonder if there are any parallel package which do not rely on mpi or pvm? > > On Wed, Oct 8, 2008 at 5:09 PM, Markus Schmidberger > <schmidb at ibe.med.uni-muenchen.de> wrote: > Hi Chi, > > ParallelR is a commercial software to run R in parallel. It is working > very well. We tested it at a small linux cluster. > > You also can use R and the parallel packages (snow, Rmpi, nws, ...) > packages. All Open Source and for free. You probably will have some more > work installing the complete system, but the same results. > > You also can use a batch system with R. We are using Sun Grid Engine! > (this should be even possible for parallelR) > > Best > Markus > > > Chi Chan wrote: >>>> Anyone using or has access to ParallelR? I was looking at the page and >>>> found nothing really useful! >>>> >>>> http://www.revolution-computing.com/sitegenius/topic.php?id=195 >>>> >>>> I want to see if I can run R on a cluster of workstation, and use >>>> batch systems like Grid Engine or Xgrid: >>>> >>>> http://gridengine.sunsource.net/ >>>> http://ww.apple.com/acg/xgrid/ >>>> >>>> --Chi >>>> >>>> ______________________________________________ >>>> R-help at r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/r-help >>>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >>>> and provide commented, minimal, self-contained, reproducible code. >>______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.>>- -- Dipl.-Tech. Math. Markus Schmidberger Ludwig-Maximilians-Universit?t M?nchen IBE - Institut f?r medizinische Informationsverarbeitung, Biometrie und Epidemiologie Marchioninistr. 15, D-81377 Muenchen URL: http://www.ibe.med.uni-muenchen.de Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de Tel: +49 (089) 7095 - 4599 -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.4-svn0 (GNU/Linux) Comment: Using GnuPG with SUSE - http://enigmail.mozdev.org iD8DBQFI7jNowxqyUctZsggRAqiSAKCz4c3IYw4JRrIMCgVaFDQH/QZqQQCaAsFE 7JzsNIzkdm1A8gLnevHNsTo=p8Xk -----END PGP SIGNATURE-----