[R] rbind wastes memory

Roger D. Peng
Mon, 30 May 2005 15:00:12 -0000

Rather than 'rbind' in a loop, try putting your dataframes in a list and
then doing something like 'do.call("rbind",
list.of.data.frames")'.

-roger

lutz.thieme at amd.com wrote:
> 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
>
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>

--
Roger D. Peng