similar to: Using the Sun Grid Engine with R-3.0

In principle, I'd like to be able to do something like this: sge.parLapply(seq(10), function(x) parLapply(seq(x), function(x) x^2)) In practice, however, I have to resort to acrobatics like this: sge.options(sge.remove.files=FALSE) sge.options(sge.qsub.options='-cwd -V') sge.parLapply(seq(10), function(x) { sge.options(sge.save.global=TRUE)

Hi - I'm trying to set up a parallelized batch job that is run under rmpi and managed by sge, using qsub, but it reports that it can't load RMySQL because it can't find the libmysqlclient.so.15 file. Note, when I run R interactively, and manually load the RMySQL library, it works without a hitch, however, when I have qsub launch R, it reports the following error: Error in

In pvec(list(1, 2), FUN, mc.cores=2) FUN sees integer() arguments whereas pvec(list(1, 2, 3), FUN, mc.cores=2) FUN sees list() arguments; the latter seems consistent with pvec's description. This came up in a complicated Bioconductor thread about generics and parallel evaluation https://stat.ethz.ch/pipermail/bioc-devel/2012-October/003745.html One relevant point is that a

Hi, The problem is most likely, you need to call a R CMD BATCH with your arguments and the R-script inside of a shell script that you submit to your qsub. Unfortunately we don't use qsub anymore so can't test it, but it should be as follows: R-script eg. test.R: > ##First read in the arguments listed at the command line > args=(commandArgs(TRUE)) > > ##args is now a list of

Dear all: Any suggestions are much appreciated. I am looking for a way to make a series of similar, but slightly modified, .r files. My issue is automating making 320 .r files that change the for(i in 1:x) in my base .r file (as well as other elements, e.g., the load(...), setwd(...)). For smaller jobs running on a single computer with batch files, I have been manually changing the for(i in 1:x)

Hi: I'm using RSPerl_0.6-3 calling R from Perl under UNIX system. My perl programs with the RSPerl work well in my computer. If submitting these programs to a UNIX system by 'ssh' or to GNQS system by 'qsub', these programs do not work even though both systems can run R. Details are following. Any suggestion will be highly appreciated. Xiao My perl program 'tt.pl'

Hi - I saw your posting on the R-help mailing list. Were you ever able to get this working? did you end up switching to use the rsge library? I'm trying to do the same, and not having very much luck getting it going. Thanks! Peter Waltman [[alternative HTML version deleted]]

Commit-ID: f81d1584a063044567d4e530fdc4aa242e907637 Gitweb: http://git.kernel.org/?p=libs/klibc/klibc.git;a=commit;h=f81d1584a063044567d4e530fdc4aa242e907637 Author: Harald van Dijk <harald at gigawatt.nl> AuthorDate: Fri, 26 Sep 2014 22:27:13 +0800 Committer: Ben Hutchings <ben at decadent.org.uk> CommitDate: Fri, 25 Jan 2019 02:57:21 +0000 [klibc] [JOBS] Fix off-by-one

Commit-ID: 5f90510fbb7e11f5d4fccb6178a2f6e684b7ce64 Gitweb: http://git.kernel.org/?p=libs/klibc/klibc.git;a=commit;h=5f90510fbb7e11f5d4fccb6178a2f6e684b7ce64 Author: Tobias Klauser <tklauser at distanz.ch> AuthorDate: Thu, 10 Dec 2015 08:59:34 +0100 Committer: Ben Hutchings <ben at decadent.org.uk> CommitDate: Fri, 25 Jan 2019 02:57:21 +0000 [klibc] jobs: Don't attempt

Commit-ID: 4e8511b9af7387ed958094485407e636cd06dcc8 Gitweb: http://git.kernel.org/?p=libs/klibc/klibc.git;a=commit;h=4e8511b9af7387ed958094485407e636cd06dcc8 Author: Tobias Klauser <tklauser at distanz.ch> AuthorDate: Thu, 10 Dec 2015 08:59:34 +0100 Committer: Ben Hutchings <ben at decadent.org.uk> CommitDate: Sat, 28 Mar 2020 21:42:54 +0000 [klibc] dash: jobs: Don't

Commit-ID: 8e4ecd111d7e780e24830ef28093677b30180f4e Gitweb: http://git.kernel.org/?p=libs/klibc/klibc.git;a=commit;h=8e4ecd111d7e780e24830ef28093677b30180f4e Author: Harald van Dijk <harald at gigawatt.nl> AuthorDate: Fri, 26 Sep 2014 22:27:13 +0800 Committer: Ben Hutchings <ben at decadent.org.uk> CommitDate: Sat, 28 Mar 2020 21:42:54 +0000 [klibc] dash: [JOBS] Fix

NAME rq v2.3.2 SYNOPSIS rq (queue | export RQ_Q=q) mode [mode_args]* [options]* URIS http://raa.ruby-lang.org/project/rq/ http://www.linuxjournal.com/article/7922 DESCRIPTION ruby queue (rq) is a zero-admin zero-configuration tool used to create instant linux clusters. rq requires only a central nfs filesystem in order to manage a simple sqlite database as a distributed

HISTORY --- 2.3.3: - fixed bug in updater related to io files (see tmp_stdin in jobqueue.rb) - [IMPORTANT] removed feature where stdin jobs could contain comments (''#''). input lines are now taken literally __except__ blank lines, which are still ignored. - added ability to dump stdin/stdout/stderr for any job rq q stdout 42

I've some trouble with installing numpy in python 3.3 on Centos 6.8 as installation request a different python version... [root at sge ~]$ yum install python33 python33-python-tools [root at sge ~]$ scl enable python33 bash ===== *this load Python 3.3.2* === [root at sge ~]$ easy_install pip [root at sge ~]$ pip install numpy Collecting numpy Using cached numpy-1.12.0.zip

Hi there, I want to run an R script on a cluster with qsub. Obviously I don't want to display any X window, but I want use png() or something else to write out images. Unfortunately I get the following error message: > png(filename = " ALL.png", width = 480, height = 480, pointsize = 12, bg = "white", res = NA) Error in X11(paste("png::", filename,

http://bugzilla.mindrot.org/show_bug.cgi?id=1070 Summary: Enchancement: Integration with GridEngine Product: Portable OpenSSH Version: 4.1p1 Platform: All OS/Version: All Status: NEW Severity: enhancement Priority: P2 Component: sshd AssignedTo: bitbucket at mindrot.org ReportedBy:

Hi all, I've been writing a package and I've run into a problem that I'm unsure how to solve. I am looking to pass a C++ class object to R so that it may be passed back to another C++ function later on to be used. I'm quite new to R and this is my first time writing a package, so I hope you can bear with me. The following is how I create the class and use

This sounds like an operating system specific question, in that "submit the R script to a PBS HPC scheduler" would be the kind of action that would run R with very different environment variables and possibly different access credentials than your usual interactive terminal. A thorough reading of the "Installation and Administration Guide" and some study of your HPC

Hi, GridEngine (http://gridengine.sunsource.net, aka. SGE) is an opensource batch system for clusters. They have an integration with SSH: http://gridengine.sunsource.net/project/gridengine/howto/qrsh_ssh.html The idea is that instead of using a modified rsh/rshd, they wanted to OpenSSH. However, in order to provide full job control, they need to add a few hooks in OpenSSH. Question: - Is it OK

On Mon, 2017-02-06 at 13:07 +0100, Patrick Begou wrote: > I've some trouble with installing numpy in python 3.3 on Centos 6.8 as > installation request a different python version... > > [root at sge ~]$ yum install python33 python33-python-tools > [root at sge ~]$ scl enable python33 bash > ===== *this load Python 3.3.2* === > [root at sge ~]$ easy_install