我有一个程序将一个大的SpatialPolygonsDataFrame
对象(1.4Gb)加载到内存中执行一些分析,然后尝试删除该对象。但是,使用系统命令free
查看系统内存会显示该对象保持不变,直到R会话重置为止。
我可以使用rworldmap
和rworlxtra
包重现内存泄漏,制作一个大型世界地图列表,每个地图都为SpatialPolygonsDataFrame
,然后尝试删除它们:
install.packages("sp")
install.packages("rworldmap")
install.packages("rworldxtra")
library(sp)
library(rworldmap)
library(rworldxtra)
these.maps.large <- lapply(1:100, function(x) assign(paste0("a_", x), getMap(resolution = "high")))
these.maps.smaller <- lapply(1:20, function(x) assign(paste0("a_", x), getMap(resolution = "high")))
# This frees the memory
rm(list="these.maps.smaller")
gc(reset=T)
# This fails to free the memory
rm(list="these.maps.large")
gc(reset=T)
修改 以下是在每个阶段之后调用system2(&#34; free&#34;)的输出。
Restarting R session...
> library(sp)
> library(rworldmap)
### Welcome to rworldmap ###
For a short introduction type : vignette('rworldmap')
> library(rworldxtra)
> system2("free")
total used free shared buff/cache available
Mem: 131987656 1386468 118712292 540008 11888896 129731040
Swap: 4194300 3505464 688836
> these.maps.large <- lapply(1:100, function(x) assign(paste0("a_", x), getMap(resolution = "high")))
> system2("free")
total used free shared buff/cache available
Mem: 131987656 2708040 117390660 540008 11888956 128409404
Swap: 4194300 3505464 688836
> rm(list="these.maps.large")
> gc(reset=T)
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 585803 31.3 9601876 512.8 585803 31.3
Vcells 711198 5.5 96623732 737.2 711198 5.5
> system2("free")
total used free shared buff/cache available
Mem: 131987656 2708428 117390424 540008 11888804 128409168
Swap: 4194300 3505464 688836
Restarting R session...
> library(sp)
> library(rworldmap)
### Welcome to rworldmap ###
For a short introduction type : vignette('rworldmap')
> library(rworldxtra)
> system2("free")
total used free shared buff/cache available
Mem: 131987656 1386696 118711988 540008 11888972 129730744
Swap: 4194300 3505464 688836
> these.maps.smaller <- lapply(1:20, function(x) assign(paste0("a_", x), getMap(resolution = "high")))
> system2("free")
total used free shared buff/cache available
Mem: 131987656 1699628 118399100 540008 11888928 129417836
Swap: 4194300 3505464 688836
> rm(list="these.maps.smaller")
> gc(reset=T)
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 702817 37.6 2564361 137.0 702817 37.6
Vcells 966452 7.4 21638748 165.1 966452 7.4
> system2("free")
total used free shared buff/cache available
Mem: 131987656 1699612 118399116 540008 11888928 129417852
Swap: 4194300 3505464 688836
有没有人知道为什么会这样,并且可以在不重置会话的情况下删除其中一个大型sp对象?
R版本3.2.3(2015-12-10) 平台:x86_64-redhat-linux-gnu(64位) 运行于:Scientific Linux 7.2(氮气)
答案 0 :(得分:2)
您不显示输出。我明白了:
> rm(list="these.maps.smaller")
> gc(reset=T)
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 7782803 415.7 14442815 771.4 7782803 415.7
Vcells 113371012 865.0 184235296 1405.7 113371012 865.0
> # This fails to free the memory
> rm(list="these.maps.large")
> gc(reset=T)
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 524121 28 11554252 617.1 524121 28
Vcells 649283 5 147388236 1124.5 649283 5
表明删除这些大型地图会释放大部分内存;该值几乎等于加载包后在新会话中获得的值。