R slow, using all physical memory and 20GB Virt
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guilherme • 0
@guilherme-8315
Last seen 6.1 years ago

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")

 

 

linux r phylogenetic computational biology • 782 views
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Entering edit mode
@herve-pages-1542
Last seen 14 hours ago
Seattle, WA, United States

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.

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