Hello again, Thanks, that explanation helps me understand the issue more. My platform is Platform: x86_64-unknown-linux-gnu (64-bit) (Ubuntu 10.04 to be more precise).
- Dario. ---- Original message ---- >Date: Tue, 1 Feb 2011 21:29:38 -0500 >From: Simon Urbanek <simon.urba...@r-project.org> >Subject: Re: [Rd] Memory Leak >To: d.strbe...@garvan.org.au >Cc: r-devel@r-project.org > > >On Feb 1, 2011, at 9:00 PM, Dario Strbenac wrote: > >> Hello, >> >> I'm trying to track down the cause of some extreme memory usage and I've >> been using Dirk Eddelbuettel's lsos() function he posted on stack overflow. >> There is a large difference between R's RAM usage : >> >> PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND >> 6637 darstr 20 0 30.0g 29g 4712 S 0 63.2 10:34.43 R >> >> and what objects I have loaded in memory : >> >>> lsos() >> Type Size PrettySize Rows Columns >> A list 552387720 526.8 Mb 2 NA >> B GRangesList 552376408 526.8 Mb 4 NA >> C SimpleRleList 353421896 337 Mb 24 NA >> D GRanges 236410608 225.5 Mb 15272853 NA >> E data.frame 6981952 6.7 Mb 24966 14 >> F data.frame 6782136 6.5 Mb 24966 13 >> G list 4393704 4.2 Mb 24964 NA >> H matrix 3195760 3 Mb 24964 16 >> I list 1798752 1.7 Mb 24964 NA >> J GRanges 312656 305.3 Kb 24964 NA >> >> (The total looks like about 1.5 GB) >> >> I haven't got any calls to external C code in my R script, although the >> Bioconductor packages I am using do. How can I regain those missing >> Gigabytes ? >> > >There is no reason why the two numbers should have anything in common. The OS >(assuming the above is supposed to be ps output) reports memory that the OS >reserved (it is not necessarily what the application is currently using) and >lsos (assuming you meant to point to this: >http://stackoverflow.com/questions/1358003/tricks-to-manage-the-available-memory-in-an-r-session > ) simply shows approximate size estimates of objects in your workspace. So >you can expect the former to be larger than the latter (often but not >necessarily always) but that's about all you can say. > >If you want to know what R objects are allocated, just look at gc() - it has >the actual numbers. However, that only includes transient allocations using >the R GC, any memory reserved directly from the OS will not be included. >Furthermore, many OSes don't release memory from processes for performance >reasons so even if you had exact allocation numbers they would not match what >you see in ps. > >I you want to lean more, you'll have to grab the tools available for your >platform to find out who's allocating what. Since you didn't even mention your >platform I can't really help you with the specifics, though. > >Cheers, >Simon ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
