[R] rbind wastes memory

lutz.thieme@amd.com
Mon, 30 May 2005 13:51:50 -0000

Hello everybody,

if I try to (r)bind a number of large dataframes I run out of memory because R
wastes memory and seems to "forget" to release memory.

For example I have 10 files. Each file contains a large dataframe "ds"
(3500 cols
by 800 rows) which needs ~20 MB RAM if it is loaded as the only object.
Now I try to bind all data frames to a large one and need more than 1165MB (!)
RAM (To simplify the R code, I use the same file ten times):

________ start example 1 __________
load(myFile)
ds.tmp	<- ds
for (Cycle in 1:10) {
	ds.tmp	<- rbind(ds.tmp, ds)
}
________ end example 1 __________



Stepping into details I found the following (comment shows RAM usage after this
line
was executed):
load(myFile)			# 40MB (19MB for R itself)
ds.tmp	<- ds			# 40MB; => only a pointer seems to be copied
x<-rbind(ds.tmp, ds)		# 198MB
x<-rbind(ds.tmp, ds)		# 233MB; the same instruction a second time leads to
				# 35MB more RAM usage - why?


Now I played around, but I couldn't find a solution. For example I bound
each dataframe
step by step and removed the variables and cleared memory, but I still need
1140MB(!)
RAM:

________ start example 2 __________
tmpFile<- paste(myFile,'.tmp',sep="")
load(myFile)
ds.tmp	 <- ds
save(ds.tmp, file=tmpFile, compress=T)

for (Cycle in 1:10) {
	ds	<- NULL
	ds.tmp <- NULL
	rm(ds, ds.tmp)
	gc()
	load(tmpFile)
	load(myFile)
	ds.tmp	<- rbind(ds.tmp, ds)
	save(ds.tmp,file=tmpFile, compress=T)
	cat(Cycle,': ',object.size(ds),object.size(ds.tmp),'\n')
}
________ end example 1 __________


platform i386-pc-solaris2.8
arch     i386
os       solaris2.8
system   i386, solaris2.8
status
major    1
minor    9.1
year     2004
month    06
day      21
language R




How can I avoid to run in that memory problem? Any ideas are very appreciated.
Thank you in advance & kind regards,



Lutz Thieme
AMD Saxony/ Product Engineering	AMD Saxony Limited Liability Company & Co.
KG
phone:	+ 49-351-277-4269		M/S E22-PE, Wilschdorfer Landstr. 101
fax:	+ 49-351-277-9-4269		D-01109 Dresden, Germany