人们使用什么技巧来管理交互式R会话的可用内存?我使用下面的函数[基于Petr Pikal和David Hinds在2004年发布的r-help列表]来列出(和/或排序)最大的对象,并偶尔rm()其中一些对象。但到目前为止最有效的解决办法是……在64位Linux下运行,有充足的内存。

大家还有什么想分享的妙招吗?请每人寄一份。

# improved list of objects
.ls.objects <- function (pos = 1, pattern, order.by,
                        decreasing=FALSE, head=FALSE, n=5) {
    napply <- function(names, fn) sapply(names, function(x)
                                         fn(get(x, pos = pos)))
    names <- ls(pos = pos, pattern = pattern)
    obj.class <- napply(names, function(x) as.character(class(x))[1])
    obj.mode <- napply(names, mode)
    obj.type <- ifelse(is.na(obj.class), obj.mode, obj.class)
    obj.size <- napply(names, object.size)
    obj.dim <- t(napply(names, function(x)
                        as.numeric(dim(x))[1:2]))
    vec <- is.na(obj.dim)[, 1] & (obj.type != "function")
    obj.dim[vec, 1] <- napply(names, length)[vec]
    out <- data.frame(obj.type, obj.size, obj.dim)
    names(out) <- c("Type", "Size", "Rows", "Columns")
    if (!missing(order.by))
        out <- out[order(out[[order.by]], decreasing=decreasing), ]
    if (head)
        out <- head(out, n)
    out
}
# shorthand
lsos <- function(..., n=10) {
    .ls.objects(..., order.by="Size", decreasing=TRUE, head=TRUE, n=n)
}

当前回答

这是个好把戏。

另一个建议是尽可能使用内存效率高的对象:例如,使用矩阵而不是data.frame。

这并没有真正解决内存管理问题,但是一个不为人所知的重要函数是memory.limit()。可以使用memory.limit(size=2500)命令增加默认值,这里的大小以MB为单位。正如Dirk提到的,为了真正利用这一点,您需要使用64位。

其他回答

请注意这些数据。table包的tables()似乎是Dirk的.ls.objects()自定义函数的一个很好的替代品(在前面的回答中有详细说明),尽管只是针对data.frames/tables,而不是矩阵,数组,列表。

I'm fortunate and my large data sets are saved by the instrument in "chunks" (subsets) of roughly 100 MB (32bit binary). Thus I can do pre-processing steps (deleting uninformative parts, downsampling) sequentially before fusing the data set. Calling gc () "by hand" can help if the size of the data get close to available memory. Sometimes a different algorithm needs much less memory. Sometimes there's a trade off between vectorization and memory use. compare: split & lapply vs. a for loop. For the sake of fast & easy data analysis, I often work first with a small random subset (sample ()) of the data. Once the data analysis script/.Rnw is finished data analysis code and the complete data go to the calculation server for over night / over weekend / ... calculation.

Rm (list=ls())是一种让你保持诚实和保持事物可重复性的好方法。

为了进一步说明频繁重启的常见策略,我们可以使用littler,它允许我们直接从命令行运行简单的表达式。这里有一个例子,我有时会用不同的BLAS为一个简单的交叉刺计时。

 r -e'N<-3*10^3; M<-matrix(rnorm(N*N),ncol=N); print(system.time(crossprod(M)))'

同样的,

 r -lMatrix -e'example(spMatrix)'

加载Matrix包(通过——packages | -l开关)并运行spMatrix函数的示例。由于总是“新鲜”开始,这个方法在包开发过程中也是一个很好的测试。

最后但并非最不重要的是,r在脚本中使用'#!/usr/bin/r shebang-header。Rscript是little不可用的替代方案(例如在Windows上)。

For both speed and memory purposes, when building a large data frame via some complex series of steps, I'll periodically flush it (the in-progress data set being built) to disk, appending to anything that came before, and then restart it. This way the intermediate steps are only working on smallish data frames (which is good as, e.g., rbind slows down considerably with larger objects). The entire data set can be read back in at the end of the process, when all the intermediate objects have been removed.

dfinal <- NULL
first <- TRUE
tempfile <- "dfinal_temp.csv"
for( i in bigloop ) {
    if( !i %% 10000 ) { 
        print( i, "; flushing to disk..." )
        write.table( dfinal, file=tempfile, append=!first, col.names=first )
        first <- FALSE
        dfinal <- NULL   # nuke it
    }

    # ... complex operations here that add data to 'dfinal' data frame  
}
print( "Loop done; flushing to disk and re-reading entire data set..." )
write.table( dfinal, file=tempfile, append=TRUE, col.names=FALSE )
dfinal <- read.table( tempfile )