search for: pbs

Hi R users, Working from a PC, I am trying to install the spatstat package on a Unix cluster. I created the following PBS file to send a job array: #!/bin/bash -ue #PBS -m ae #PBS -M my email #PBS -J 1-45 #PBS -A my username #PBS -N job name #PBS -l resources #PBS -l walltime cd $PBS_O_WORKDIR module load R/2.14.1 R CMD INSTALL -l /path/to/library spatstat R CMD BATCH /path/to/folder/Script_$PBS_ARRAY_INDEX.R O...

Hi R-users, I have a problem running my R code on a Linux cluster. What I did was write a .pbs file to instruct the cluster on what to do and how: #!/bin/sh #PBS -m ae #PBS -M uqlcatta@uq.edu.au #PBS -A uq-CSER #PBS -N job1_lollo #PBS -l select=1:ncpus=1:NodeType=fast:mem=8GB #PBS -l walltime=999:00:00 cd $PBS_O_WORKDIR source /usr/share/modules/init/bash module...

Hello: Anybody knows how to run Rmpi through PBS (Portable Batch System) on a cluster computer. I'm using a supercomputer which require to submit jobs to PBS queue for dispatching. I tried use mpirun in my PBS script. But all my Rslaves are spawned to the same node. This is not desired. Any suggestions are welcome! Thanks in advance. =====...

Dear all, please could you advise me on the following : I've written a R script that reads 3 arguments from the command line, i.e. : " args <- commandArgs(TRUE) TUMOR <- args[1] GERMLINE <- args[2] CHR <- args[3] ". when I submit the R script to a PBS HPC scheduler, I do the following (below), but ... I am getting an error message. (I am not posting the error message, because the R script I wrote works fine when it is run from a regular terminal ..) Please may I ask, how do you usually submit the R scripts with command line arguments to PBS HPC...

Please remove me from the mailing list -----Original Message----- From: r-help-bounces at stat.math.ethz.ch To: Shengqiao Li Cc: r-help Sent: 24/03/2004 10:10 AM Subject: Re: [R] Rmpi and PBS On Tue, 2003-12-30 at 08:39, Shengqiao Li wrote: > Hello: > > Anybody knows how to run Rmpi through PBS (Portable Batch System) on a > cluster computer. I'm using a supercomputer which require to submit jobs > to PBS queue for dispatching. I tried use mpirun in my PBS script. B...

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 document...

Dear Experts, I know there are many HPC (high performance computing) experts on this list. I'd like to ask your advise. Almost two decades ago I chose to go with OpenPBS (turned down condor and other alternatives for whatever reason) for clusters and number crunchers I support for the Department at the university. It turned out to be not bad, long lived choice. At some point I smoothly migrated to torque which was advertised as open source project (based on PBS...

...ou submit with a qsub with all the options you specified the test.sh qsub .... test.sh cheers Peter > On 12. Jul 2017, at 03:01, Jeff Newmiller <jdnewmil at dcn.davis.ca.us> wrote: > > 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 document...

I'm new to R so forgive me if this seems like a simple question: So I have table where the row titles are string variables. When I plot the data with rows along the x-axis, the data is ordered alphabetically as opposed to the order of the table. How can I preserve the row order of the table in the plot? Thanks in advance. -- View this message in context:

...01.jpg and here is the code I am using: RN<-read.csv("N:/data.dat",header=T) DATA<-RN[is.element(RN$age,0:3),] #select data on age ogmod1<-glm(mig~age+length,family=binomial(link="logit"),data=DATA) design1<-expand.grid(age=c(0:3),length=seq(30,300,by=10)) design1$pbs<-predict(ogmod1,new=design1,type="response") design1$migr<-round(design1$pbs) library(lattice) wireframe(pbs~age*length,data=design1,aspect=c(1,1),main="Probability Surface", drape=T,scale=list(arrows=FALSE),screen=list(z=45,x=-75), colorkey=list(space=...

CentOS 6.6 I've got two servers, server1 and hbs (honkin' big server). Both are running munge, and torque... *separately*. My problem is that I've got users who want to be able to submit from server1 to hbs. I see that munged can be pointed to an alternate keyfile... but is there any way to tell qsub what to use? (And yes, I got on the torque users' list, and I'm trying

Hi, I use R 1.6.2 under Mandrake9.0. I've got a problem with the postscript files I try to creat. When I look to the file with ghostview it's ok. When I want to print it, I've got a blank page or a black page (fill of black encre) I changed the printer (guessing it was my driver printer), it was the same. Does anyone had the same problem and resolved it ? -- Cordialy

Hi everybody, I m a newbie with Wine, but I tried to launch Maple, NotePad, etc... and it works ! Great ! My problem is that I can t launch MS Office (Winword 2000, etc...). The output is the picture of Word2000 (the logo), and then the program is stopped... Here is the output : ***** fixme:system:SystemParametersInfo16 Unknown option 70. fixme:system:SystemParametersInfoA SPI_GETHIGHCONTRAST

Hi, I am trying to use datas written in the stdin to run scriptindex, (I am working with Windows and not Unix). And Scriptindex does not work, the database is created but the datas are not indexed. Thanks by advance Stephane

Hi all! At my university, we use for compatibility reasons a windows shared printer running samba server. The main thing is that I can't get smbprint to send pages to the printer. And, more amazing, I get this message: "Unable to connect to SAMBA host, will retry in 60 seconds...ERROR: Connection failed with error NT_STATUS_WRONG_PASSWORD" only when I give the GOOD password! :-/

...eciate it. Alex Here was your post: http://lists.samba.org/archive/rsync/2005-September/013566.html Alex Loker Senior UNIX Administrator, Enterprise Platforms Public Broadcasting Service 1310 Braddock Place, Alexandria, VA 22314 Office: 703-739-5080 Cell: 703-856-3514 arloker@pbs.org ___________________________________________________________________ Big Big Friends are coming your way for Big Big Friend Day on PBS KIDS! On November 25th, join pals from CLIFFORD and DRAGON TALES For fun, surprises, and a peek at some brand new friends! pbskids.org __________________...

...;do_mul". The script file "do_mul" " #!/bin/bash export var for var in $(seq 1 5) do qsub -v var do_test done exit 0 " Through "do_mul", 5 "do_test" script files are submitted to the cluster. The script file "do_test": " #!/bin/bash -l #PBS -l ncpus=1 #PBS -l walltime=0:05:00 cd $PBS_O_WORKDIR mkdir test$var cd test$var module load R/2.5.0 R --vanilla< test exit 0 " The content in R file "test" is : "rm(list=ls(all=TRUE)) sample(10) " I expect to have different samples each time. However, for these 5 repl...

...Valeri Galtsev Sent: Friday, April 17, 2020 10:28 To: centos at centos.org Subject: [CentOS] HPC question: torques replacement Dear Experts, I know there are many HPC (high performance computing) experts on this list. I'd like to ask your advise. Almost two decades ago I chose to go with OpenPBS (turned down condor and other alternatives for whatever reason) for clusters and number crunchers I support for the Department at the university. It turned out to be not bad, long lived choice. At some point I smoothly migrated to torque which was advertised as open source project (based on PBS, bu...

I use ssh in a batch environment (www.pbspro.com) and am using host based authentication to allow sshes between some resources. When I converted from openssh 3.1 to newer versions (up to an including 3.8 where ssh-keysign was moved to a standalone binary) I had issues with ssh-keysign failing with the error "bad fd". A litt...

Hi, The first (maybe) LLVM social in Beijing will happen on May 19th, 2018. Everyone interested in LLVM related projects is invited to join. Event details is at https://github.com/hellollvm/website/blob/master/README.md Presentations are welcome :-) Looking forward to meet you ! -- Best wishes, Wei Wu (吴伟)