[R] rbind wastes memory

lutz.thieme@amd.com lutz.thieme at amd.com
Mon May 30 15:51:50 CEST 2005

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 __________
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(!) 

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

for (Cycle in 1:10) {
	ds	<- NULL
	ds.tmp <- NULL
	rm(ds, ds.tmp)
	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  
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

More information about the R-help mailing list