Question: R slow, using all physical memory and 20GB Virt
0
gravatar for guilherme
4.4 years ago by
guilherme0
guilherme0 wrote:

Hello,

we are running a script in Linux Ubuntu 64bit, that should be very simple. We have 1TB HD, 16GB RAM and a Xeon with 4 CPUs.  The script is pasted in the final of file.

We just started the job yesterday, and it seems to be running yet, however, I can see CPUs in "waiting" mode, while the memory is 90% allocated to R, but, as a newbie, I canot see details of what the script is doing, what step it is now, etc...

Do you have any suggestions to help me to monitor the current status of the job?  Not only what I can see in top/htop?

Or maybe to increase speed of this job?

Current JOB status:

===============

22903  1.6 84.2 21042208 13826372 pts/16 D<+ Jun30  25:29 /usr/lib/R/bin/exec/R --slave --no-restore --file=script_andre.r --args

 

========SCRIPT=========

#INSTALAR PACOTES

#install.packages("ape")
#install.packages("betapart")

#ABRIR PACOTES
library(ape)
library(betapart)

#IMPORTAR ARQUIVOS
tree<-read.tree("/home/XXXX/pruned_tree.txt")
comm<-read.table("/home/XXXX/matriz_andre.txt")

#CALCULAR PHYLOBETADIVERSIDADE SORENSEN

pbd<-phylo.beta.pair(comm, tree, index.family="sorensen")

#EXPORTAR ARQUIVO QUANDO TERMINAR

write.table(pbd, "/home/gf7brasil/pbd.txt")

 

 

ADD COMMENTlink modified 4.4 years ago by Hervé Pagès ♦♦ 14k • written 4.4 years ago by guilherme0
Answer: R slow, using all physical memory and 20GB Virt
0
gravatar for Hervé Pagès
4.4 years ago by
Hervé Pagès ♦♦ 14k
United States
Hervé Pagès ♦♦ 14k wrote:

Hi,

This is not a Bioconductor question. I would suggest you ask on the R-help mailing list or to the authors of the ape package directly. They will probably need more information in order to be able to help you. Note that going from 16GB to 32GB is really cheap these days (we start to see laptops sold with 32GB as the default).

Cheers,

H.

ADD COMMENTlink written 4.4 years ago by Hervé Pagès ♦♦ 14k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 380 users visited in the last hour