R

pbdR Available on H2P

Dear R users of CRC,

Packages from pbdR (programming in big data with R) are now available to use over the h2p Omnipath cluster. The packages will allow R users to write MPI enabled parallel code in R. An example code and slurm job definition are available at “/ihome/crc/how_to_run/pbdr” on the cluster. To know more about pbdR see [1,2]. Do not hesitate to contact us should you face difficulties with using these packages.

[1] https://www.hpcwire.com/off-the-wire/ornl-researchers-bridge-gap-r-hpc-c...

[2] https://rbigdata.github.io

R module, "phytools"

We want to run jobs using the R environment, and so we load the R module. Within this module, there is a particular R-module we need called "phytools". Could it be added to the R module? Or is there another way that we could load it?

Many thanks.

Please install R64, the 64-bit version of R.

We have an R program that uses a lot of memory, so we were wondering if you could please install the 64-bit version of R?

I searched for R64 after loading the 'genomics' module, and while I found R, I did not find R64.

Thank you, Dan Weeks

Using R on Cluster

Hello,

I am trying to submit a .PBS_script file on the cluster running R but I keep getting an error. I wanted to see if you could let me know what the command line would be to access R? I have only used plink before on the cluster... also it is giving me an error say the load option is not available. What should I use to open or get the cluster to access the workspace/dataset I had uploaded. If you could help me, I would greatly appreciate it.

Thank you in advance!

R command not found

I’m attempting to run some jobs with an R script in them but they are failing. the error returned is “R: command not found”. See below ...

[rminster@login0 rs114920405]$ qsub -I -q shared

qsub: waiting for job 1539310.headnode.localdomain to start

qsub: job 1539310.headnode.localdomain ready

[rminster@n4 ~]$ module load r

[rminster@n4 ~]$ R

-bash: R: command not found

R process killed

Hi,

I'm running some R simulations, in this case on a single node.

I keep getting an error message in the .err file that says:

/pan/genomics/src/R/2.15.2/gcc/lib64/R/bin/BATCH: line 60: 9517 Killed ${R_HOME}/bin/R -f ${in} ${opts} ${R_BATCH_OPTIONS} > ${out} 2>&1

The 4-digit number immediately after "line 60:" is changes, but the rest is the same each time. I've looked online in various places, but can't figure out why this process keeps getting killed. The R commands work on my terminal.

Any advice is much appreciated, Stephen

how to submit multiple jobs simultaneously?

Dear manager,

I want to know how to submit multiple R progams to nodes with at least 64GB RAM. Could you help me?

Thanks! Xingbin

Running R locally to display data on Frank

Hello,

Is there a way to view data that resides on Frank in a local installation of R (i.e. my desktop)? I'm trying to avoid copying data from Frank to my local computer and then viewing the data in R. It is cumbersome and keeps two copies of the same data.

Thank you,

Paul

Executation Halted on a Script Using R

I’m puzzled by a sudden change in the behavior of my a script using R I’ve been running without problem until last night.

I’m not getting an error in the .Rout shortly after starting:

Error: error reading from connection Execution halted

--Ryan

Install New R package

Hi,Dear manager.

I need to install three R package on Frank. Could you help me to install them?

"Biobase" "doSNOW" "lme4"

Thanks a lot!

Rui

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