Question

I have a bash script that tracks memory usage over time as a command is run. It spawns the desired command and then writes a log with column1 = “memory in use by program (gigs)” and column 2 is the time elapsed so far in seconds. e.g.

31.282 1470
31.565 1480
31.848 1490
31.989 1500
32.273 1510
32.414 1520
32.697 1530
32.980 1540
33.122 1550
33.405 1560
6.511 1570
6.935 1580
7.502 1590
7.926 1600
8.351 1610
8.775 1620
9.059 1630
9.483 1640
9.908 1650
10.333 1660

What I want to do is wait until the process is complete and then use R to plot a graph of memory usage over time and save it in the current directory. I was playing around with R and I know exactly what commands I need to use:

> heisenberg <- read.csv(file="4644.log",head=FALSE,sep=" ")
> plot(heisenberg$V2,heisenberg$V1,type="o",col="red",main="Memory Usage Over Time",xlab="Time (seconds)",ylab="Memory (gigabytes)")
> text(max(heisenberg$V2),max(heisenberg$V1),max(heisenberg$V1)) #Displays max value

But the part I am stuck on is saving the graph as a jpg or png. Or how I could execute this command within my bash script. Would I absolutely need to have another script written in R language and run it? Would this be possible to do all in one?

---

Edit

Here is the code for my script.r

png("mem_usage_2965.png",height=800,width=800)
heisenberg <- read.csv(file="2965.log",head=FALSE,sep=" ")
plot(heisenberg$V2,heisenberg$V1,type="o",col="red",main="oases_k85",xlab="Time (seconds)",ylab="Memory (gigabytes)")
text(max(heisenberg),max(heisenberg),max(heisenberg))
dev.off()

Can anyone help as to why the text doesn’t print the maximum value in the outputted png? I am calling it in a bash script like R CMD BATCH script.r script.out

Answer 1

Wrap your plot calls in:

jpeg("myplot.jpg")
....plot code here....
dev.off()

or

png("myplot.png")
....plot code here....
dev.off()

See their respective help pages: ?png for details of other arguments.

For a PNG this would be:

png("my_plot.png", height = 800, width = 600)
plot(heisenberg$V2,heisenberg$V1,type="o",col="red",main="Memory Usage Over Time",xlab="Time (seconds)",ylab="Memory (gigabytes)")
text(max(heisenberg$V2),max(heisenberg$V1),max(heisenberg$V1)) #Displays max value
dev.off()

As for running this in a bash script, you need to invoke R to run your script containing the R code to load the data and draw the plots. For this there are several options, two are:

R CMD BATCH --no-save --no-restore my_script.R

or use Rscript

Rscript my_script.R

where my_script.R is a text file containing syntactically-valid R code required to produce the plots.