similar to: Condor and R

Hello dear R-help group (and David Smith from REvolution), I would like to perform parallel computing using R with Condor (hopefully using foreach or other recommended solutions, if available) for some "Embarrassingly parallel" problem. I will start by listing what I found so far, and then go on asking for help. So far I found the a manual by Xianhong Xie from Rnews_2005-2 (see page

Hello, I would be extremely grateful if anyone is able to provide any (rather obscure) advice on using R with Condor. I think I'm following Xianhong Xie's instructions (R News 5(2) 13-15) correctly, but my job just stays held in the queue (for days / months). I've checked condor_status to make sure there are plenty of machines available, but can't see any way to attack the

Hello all, Recently I started playing with running R scripts on the Condor system in my institute. (For more on this, have a look at: Running Long R Jobs with Condor DAG by Xianhong Xie link: http://cran.r-project.org/doc/Rnews/Rnews_2005-2.pdf ) Might someone advice me about the following question: How should I handle the RNG (random number generation) in the running of parallel instances of R

Hi, I'm having trouble with glmmPQL from the MASS package. I'm trying to fit a model with a binary response variable, two fixed and two random variables (nested), with a sample of about 200,000 data points. Unfortunately, I'm getting an error message that is difficult to understand without knowing the internals of the glmmPQL function. > model <- glmmPQL(primed ~

After upgrading to R 2.6.0, I'm having trouble running lmer: model <- lmer(primed ~ log(dist.time)*role + 1|target.utt, data=data.utts) Error in UseMethod("as.logical") : no applicable method for "as.logical" So I thought I'd upgrade lme4 to the latest version, but unfortunately the compilation fails - perhaps there's a missing #include: R CMD INSTALL

Dear Experts, Could someone recommend some "quick and dirty" HOWTO on condor based cluster? A did a bunch of cluster setups, I always used PBS (or torque lately). But my professor wants his to be Condor. I started reading Condor documentation, and it is vast. And quick route, like: architecture chart, and parameters I need to configure on master/submit, and compute nodes - somehow

I've got a problem with "mcmcsamp" used with glmer objects produced with "lmer" from the lme4 package. When calling mcmcsamp, I get the error Error in if (var(y) == 0) { : missing value where TRUE/FALSE needed This does not occur with all models, but I can't find anything wrong with the dataset. If the error is in my data, can someone tell me what I am looking

I've discussed this a little with Ian off list, but relating to: https://fedoraproject.org/wiki/Features/Condor_Cloud Condor Cloud aims at setting up a bunch of Fedora nodes to act as a mini-cloud managed via the Condor grid infrastructure. So the natural question was... Why not use oVirt Node for this rather than a full Fedora OS install? Pulling condor-cloud and condor RPMs into the core

Hi Everyone, I have group of R jobs that should be submitted to the condor when I submit the jobs to the condor, they don't run and when I checked the Sched Log files the jobs are exiting with status code 10. Previously, the jobs ran well on condor but now when I submit the jobs on condor they aren't running.Can anyone explain the meaning of this? Here is my submit file: # Submit file

Full_Name: Juergen Rose Version: 2.8.0 (2008-10-20) OS: Linux 2.6.27.4 x86_64 Intel Submission from: (NULL) (87.185.220.122) If I start as ordinary user rose R and help.start(), the help is displayed in emacs. If I do as the user root, file:///tmp/Rtmpyzlc7Y/.R/doc/html/index.html is shown as expected in a firefox windows. So it seems to be connected with my private configuration. But I can not

Full_Name: david Reitter Version: 1.9.1 OS: Mac OS X 10.3 Submission from: (NULL) (18.85.44.174) The installer package seems to change the permissions on the /Applications folder (and probably on other folders as well), which means that a normal user (that does not happen to have user id 501) cannot open the Applications folder anymore. Both group and user are changed to id '501' (which

My master is running 12.04 Version: 2.7.11-1ubuntu2 Depends: ruby1.8, puppetmaster-common (= 2.7.11-1ubuntu2) My client is 10.04 Version: 2.6.3-0ubuntu1~lucid1 Depends: puppet-common (= 2.6.3-0ubuntu1~lucid1), ruby1.8 I followed this tutorial to install Puppet on the client: http://shapeshed.com/setting-up-puppet-on-ubuntu-10-04/ (I didn''t need that tar ball because the "best

--Apple-Mail-44--797532055 Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Content-Transfer-Encoding: 7bit I believe read.table may report misleading errors. In this example, where a header line in a file has an incorrect number of row names (28 instead of 29), I get the error message "duplicate row.names are not allowed". However, I cannot not find any

Hello.. When i use the command Smbpasswd ?a carguillo. It adds this entry in LDAP. # carguello,Personas,NOVA dn: uid=carguello,ou=Personas,o=NOVA uid: carguello sambaSID: S-1-5-21-2532083711-3846753250-2864659012-2328 sambaPrimaryGroupSID: S-1-5-21-2532083711-3846753250-2864659012-513 sambaPwdCanChange: 1075936258 sambaPwdMustChange: 2147483647 sambaLMPassword:

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

It's probably a beginner's question: How do I show text in boxes? That is, can I specify a background color for text output with text() ? The following doesn't work as I would expect: text(labels="123", 50, 0.5, bg="green") I've experimented with legend(),which will make the box too wide, and also with rect(), which doesn't know the extent of the text

> From: Ross Boylan <ross at biostat.ucsf.edu> > > In answer to the other question about using OS checkpointing > facilities, I haven't tried them since the application will be running > on a cluster. More precisely, the optimization will be driven from a > single machine, but the calculation of the objective function will be > distributed. So checkpointing at the

Hi all, Note: selinux was in permissive prior to error Got this with a yum update: abrt_version: 2.0.8 cgroup: cmdline: semodule -n -r oracle-port -b base.pp.bz2 -i accountsd.pp.bz2 ada.pp.bz2 cachefilesd.pp.bz2 cpufreqselector.pp.bz2 chrome.pp.bz2 awstats.pp.bz2 abrt.pp.bz2 aiccu.pp.bz2 amanda.pp.bz2 afs.pp.bz2 apache.pp.bz2 arpwatch.pp.bz2 audioentropy.pp.bz2 asterisk.pp.bz2

I need to serialize computing job requests for two different multicore machines, and in some near future, for a cluster. I have worked with SGE but it requires NFS and other administrative steps, plus it seems a bit overkill for my needs. I guess some simpler queue managing engine may have been developed, possibly over SSH. Any pointers? TIA. -- Eduardo Grosclaude Universidad Nacional del

I suspect I've found a bug buried somewhere deep inside the SMBmv code; I have an application, Archicad, which will not allow you to file->save over the top of an existing file, unless you happen to be the (unix) owner of that file. Unix permissions are mode 664, users can otherwise manipulate the files as expected. I've attempted various combinations/ permutations of