search for: qsub

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 dyn.load(file, DLLp...

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 character vectors > ## First check to see if argume...

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...

...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 schedulers ? qsub -d $PWD -l nodes=1:ppn=4 -l vmem=10gb -m bea -M tanasa at gmail.com \ -v TUMOR="tumor.bam",GERMLINE="germline.bam",CHR="chr22" \ -e script.efile.chr22 \ -o script.ofile.chr22 \ script.R Thank you very very much ! -- bogdan [[alternative HTML version deleted]]

...... 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 schedulers ? > >qsub -d $PWD -l nodes=1:ppn=4 -l vmem=10gb -m bea -M tanasa at gmail.com \ >-v TUMOR="tumor.bam",GERMLINE="germline.bam",CHR="chr22" \ >-e script.efile.chr22 \ >-o script.ofile.chr22 \ >script.R > >Thank you very very much ! > >-- bogdan > > [...

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' #!/usr/bin/perl -w use R; use RReferences; &R::initR("--silent"); &R::setDebug(0); &amp...

...maller jobs running on a single computer with batch files, I have been manually changing the for(i in 1:x) line, etc.. Why does this matter to me? I am planning on running a simulation experiment on a linux cluster as a serial job. Although not elegant, it has been suggested I make 320 .r files so qsub runs one .r file and then selects other jobs. Thus, the manual route I am currently using would take a very long time (given multiple runs of 320 .r files, given experimental replication). Thank you, Laura -- " Genius is the summed production of the many with the names of the few attached...

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) sge.options(sge.remove.files=FALSE) sge.parLapply(seq(x), function(x) x^2,...

Dear sir, I want to submit R batch jobs (e.g. 5) under the linux cluster by the script file "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 --van...

...l_Data/Experiment_1/" "/home/jpura/Desktop/FDA_Trial_Data/testscript.RData" It runs just fine (i.e. I get the right output file, which is testscript.RData) when I type the lines in the shell script file directly into the command prompt. However, when I try to submit the file using: qsub "path/to/testscript.sh", I don't get the desired output file. Any insights to this is be greatly appreciated. Thanks, John -- View this message in context: http://r.789695.n4.nabble.com/Running-Shell-Script-with-R-tp4115734p4115734.html Sent from the R help mailing list archive at...

I've looked through all of the posts about this issue (and there are plenty!) but I am still unable to solve the error. ERROR: cannot allocate vector of size 455 Mb I am using R 2.6.2 - x86_64 on a Linux x86_64 Redhat cluster system. When I log in, based on the specs I provide [qsub -I -X -l arch=x86_64] I am randomly assigned to a x86_64 node. I am using package GenABEL. My data (~ 650,000 SNPs, 3,000 people) loads in okay and I am able to look at the data using basic commands [nids, nsnps, names(phdata)] The problem occurs when I try to run the extended analysis: xs <-...

Hello, I have several systems which I recently updated with yum -y update to all the latest packages. These systems use yum-priorities and use the CentOS (priority 1) EPEL (priority 5) and rpmforge (priority 10) repositories. After the updates, dhcpd stopped working with a SIGPIPE error which occurs shortly after it attempts to fork into the background. I worked around that problem by building

Hello All, Attached is a patch for the ARM target. The ARM v7M profile does not have the signed most-significant-word multiply instruction so SMMUL, for instance, is not valid on Cortex-M3 and Cortex-M4. The attached patch adds an additional attribute, +mmul, which controls most-significant word multiplies on v6T2+ targets. This is especially important for me now that I've

...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 there, too). mark "really needs to solve this tomorrow"

...With the R-3.0 release, the package Rsge has been discontinued. What would be the equivalent way of running jobs on the cluster using current packages? I understand that the parallel package has been updated. What would be the equivalent to the lines below: require(Rsge) sge.options("sge.qsub.options"="-cwd -q GT -pe smp 8 -l C=2") sge.options("sge.save.global"=TRUE) sge.options("sge.remove.files"=TRUE) jobList = list( ....) myJobFunc = function(x) {....} result = sge.parLapply(jobList, myJobFunc, njobs=length(jobList)) Many thanks Hubert Rehrauer

We have spent some time setting up Sun Grid Engine and OpenMPI on a group of linux boxes. I have created a parallel environment and everything seems to be working. I have Rmpi 0.5.5-5 installed on all machines. I would like to start an interactive R session using, say, 8 processors and then start the Rmpi cluster. I haven't been able to find what needs to be done in order to accomplish

...a, opus_int32 b) +{ + int res; + __asm__( + "qadd %0, %1, %2;\n" + : "=&r"(res) + : "r"(a), "r"(b) + ); + return res; +} + +static inline opus_int32 silk_SUB_SAT32(opus_int32 a, opus_int32 b) +{ + int res; + __asm__( + "qsub %0, %1, %2;\n" + : "=&r"(res) + : "r"(a), "r"(b) + ); + return res; +} + +static inline opus_int32 silk_CLZ16(opus_int16 in16) +{ + opus_int32 res; + __asm__( + "clz %0, %1;\n" + "subs %0, %0, #16;\n" + &quo...