How to delete temporary files in parallel task in R - r

Is it possible to delete temporary files from within a parallelized R task?
I rely on parallelization with doParallel and foreach in R to perform various calculations on small subsets of a huge raster file. This involves cropping a subset of the large raster many times. My basic syntax looks similar to this:
grid <- raster::raster("grid.tif")
data <- raster::raster("data.tif")
cl <- parallel::makeCluster(32)
doParallel::registerDoParallel(cl)
m <- foreach(col=ncol(grid)) %:% foreach(row=nrow(grid)) %dopar% {
# get extent of subset
cell <- raster::cellFromRowCol(grid, row, col)
ext <- raster::extentFromCells(grid, cell)
# crop main raster to subset extent
subset <- raster::crop(data, ext)
# ...
# perform some processing steps on the raster subset
# ...
# save results to a separate file
saveRDS(subset, paste0("output_folder/", row, "_", col)
}
The algorithm works perfectly fine and achieves what I want it to. However, raster::crop(data, ext) creates a small temporary file everytime it is called. This seems to be standard behavior of the raster package, but it becomes a problem, because these temp files are only deleted after the whole code has been executed, and take up way too much disk space in the meantime (hundreds of GB).
In a serial execution of the task I can simply delete the temporary file with file.remove(subset#file#name). However, this does not work anymore when running the task in parallel. Instead, the command is simply ignored and the temp file stays where it is until the whole task is done.
Any ideas as to why this is the case and how I could solve this problem?

There is a function for this removeTmpFiles.
You should be able to use f <- filename(subset), avoid reading from slots (#). I do not see why you would not be able to remove it. But perhaps it needs some fiddling with the path?
temp files are only created when the raster package deems it necessary, based on RAM available and required. See canProcessInMemory( , verbose=TRUE). The default settings are somewhat conservative, and you can change them with rasterOptions() (memfrac and maxmemory)
Another approach is to provide a filename argument to crop. Then you know what the filename is, and you can delete it. Of course you need to take care of not overwriting data from different tasks, so you may need to use some unique id associated with it.
saveRDS( ) won't work if the raster is backed up by a tempfile (as it will disappear).

Related

Importing very large dataset into h2o from sqlite

I have a database of about 500G. It comprises of 16 tables, each containing 2 or 3 column (first column can be discarded) and 1,375,328,760 rows. I need all the tables to be joined as one dataframe in h2o as they are needed for running a prediction in an XGB model. I have tried to convert the individual sql tables into the h2o environment using as.h2o, and h2o.cbind them 2 or 3 tables at a time, until they are one dataset. However, I get this "GC overhead limit exceeded: java.lang.OutOfMemoryError", after converting 4 tables.
Is there a way around this?
My machine specs are 124G RAM, OS (Rhel 7.8), Root(1tb), Home(600G) and 2TB external HDD.
The model is run on this local machine and the max_mem_size is set at 100G. The details of the code are below.
library(data.table)
library(h2o)
h2o.init(
nthreads=14,
max_mem_size = "100G")
h2o.removeAll()
setwd("/home/stan/Documents/LUR/era_aq")
l1.hex <- as.h2o(d2)
l2.hex <- as.h2o(lai)
test_l1.hex <-h2o.cbind(l1.hex,l2.hex[,-1])
h2o.rm (l1.hex,l2.hex)
l3.hex <- as.h2o(lu100)
l4.hex <- as.h2o(lu1000)
test_l2.hex <-h2o.cbind(l3.hex,l4.hex[,-1])
h2o.rm(l3.hex,l4.hex)
l5.hex <- as.h2o(lu1250)
l6.hex <- as.h2o(lu250)
test_l3.hex <-h2o.cbind(l5.hex,l6.hex[,-1])
h2o.rm(l5.hex,l6.hex)
l7.hex <- as.h2o(pbl)
l8.hex <- as.h2o(msl)
test_l4.hex <-h2o.cbind(l7.hex,l8.hex[,-1])
h2o.rm(ll7.hex,l8.hex)
test.hex <-h2o.cbind(test_l1.hex,test_l2.hex[,-1],test_l3.hex[,-1],test_l4.hex[,-1])
test <- test.hex[,-1]
test[1:3,]```
First, as Tom says in the comments, you're gonna need a bigger boat. H2O holds all data in memory, and generally you need 3 to 4x the data size to be able to do anything useful with it. A dataset of 500GB means you need the total memory of your cluster to be 1.5-2TB.
(H2O stores the data compressed, and I don't think sqlite does, in which case you might get away with only needing 1TB.)
Second, as.h2o() is an inefficient way to load big datasets. What will happen is your dataset is loaded into R's memory space, then it is saved to a csv file, then that csv file is streamed over TCP/IP to the H2O process.
So, the better way is to export directly from sqlite to a csv file. And then use h2o.importFile() to load that csv file into H2O.
h2o.cbind() is also going to involve a lot of copying. If you can find a tool or script to column-bind the csv files in advance of import, it might be more efficient. A quick search found csvkit, but I'm not sure if it needs to load the files into memory, or can do work with the files completely on disk.
Since memory is a premium and all R runs in RAM, avoid storing large helper data.table andh20 objects in your global environment. Consider setting up a function to build a list for compilation that temporary objects are removed when function is out of scope. Ideally, you build your h2o objects directly from file source:
# BUILD LIST OF H20 OBJECTS WITHOUT HELPER COPIES
h2o_list <- lapply(list_of_files, function(f) as.h2o(data.table::fread(f))[-1])
# h2o_list <- lapply(list_of_files, function(f) h2o.importFile(f)[-1])
# CBIND ALL H20 OBJECTS
test.h2o <- do.call(h2o.cbind, h2o_list)
Or even combine both lines with named function as opposed to anonymous function. Then, only final object remains after processing.
build_h2o <- function(f) as.h2o(data.table::fread(f))[-1])
# build_h2o <- function(f) h2o.importFile(f)[-1]
test.h2o <- do.call(h2o.cbind, lapply(list_of_files, build_h2o))
Extend function with if for some datasets that need to retain first column or not.
build_h2o <- function(f) {
if (grepl("lai|lu1000|lu250|msl", f)) { tmp <- fread(f)[-1] }
else { tmp <- fread(f) }
return(as.h2o(tmp))
}
Finally, if possible, leverage data.table methods like cbindlist:
final_dt <- cbindlist(lapply(list_of_files, function(f) fread(f)[-1]))
test.h2o <- as.h2o(final_dt)
rm(final_dt)
gc()

How to restart R and continue a benchmark script from previous line (on Windows)?

I want to benchmark the time and profile memory used by several functions (regression with random effects and other analysis) applied to different dataset sizes.
My computer has 16GB RAM and I want to see how R behaves with large datasets and what is the limit.
In order to do it I was using a loop and the package bench.
After each iteration I clean the memory with gc(reset=TRUE).
But when the dataset is very large the garbage collector doesn't work properly, it just frees part of the memory.
At the end all the memory stays filled, and I need to restar my R session.
My full dataset is called allDT and I do something like this:
for (NN in (1:10)*100000) {
gc(reset=TRUE)
myDT <- allDT[sample(.N,NN)]
assign(paste0("time",NN), mark(
model1 = glmer(Out~var1+var2+var3+(1|City/ID),data=myDT),
model2 = glmer(Out~var1+var2+var3+(1|ID),data=myDT),
iterations = 1, check=F))
}
That way I can get the results for each size.
The method is not fair because at the end the memory doesn't get properly cleaned.
I've thought an alternative is to restart the whole R program after every iteration (exit R and start it again, this is the only way I've found you can have the memory cleaned), loading again the data and continuing from the last step.
Is there any simple way to do it or any alternative?
Maybe I need to save the results on disk every time but it will be difficult to keep track of the last executed line, specially if R hangs.
I may need to create an external batch file and run a loop calling R at every iteration. Though I prefer to do it everything from R without any external scripting/batch.
One thing I do for benchmarks like this is to launch another instance of R and have that other R instance return the results to stdout (or simpler, just save it as a file).
Example:
times <- c()
for( i in 1:length(param) ) {
system(sprintf("Rscript functions/mytest.r %s", param[i]))
times[i] <- readRDS("/tmp/temp.rds")
}
In the mytest.r file read in parameters and save results to a file.
args <- commandArgs(trailingOnly=TRUE)
NN <- args[1]
allDT <- readRDS("mydata.rds")
...
# save results
saveRDS(myresult, file="/tmp/temp.rds")

Using a for loop to write in multiple .grd files

I am working with very large data layers for a SDM class and because of this I ended up breaking some of my layers into a bunch of blocks to avoid memory restraint. These blocks were written out as .grd files, and now I need to get them read back into R and merged together. I am extremely new to R an programming in general so any help would be appreciated. What I have been trying so far looks like this:
merge.coarse=raster("coarseBlock1.grd")
for ("" in 2:nBlocks){
merge.coarse=merge(merge.coarse,raster(paste("coarseBlock", ".grd", sep="")))
}
where my files are in coarseBlock.grd and are sequentially numbered from 1 to nBlocks (259)
Any feed back would be greatly appreciated.
Using for loops is generally slow in R. Also, using functions like merge and rbind in a for loop eat up a lot of memory because of the way R passes values to these functions.
A more efficient way to do this task would be to call lapply (see this tutorial on apply functions for details) to load the files into R. This will result in a list which can then be collapsed using the rbind function:
rasters <- lapply(list.files(GRDFolder), FUN = raster)
merge.coarse <- do.call(rbind, rasters)
I'm not too familiar with .grd files, but this overall process should at least get you going in the right direction. Assuming all your .grd files (1 through 259) are stored in the same folder (which I will refer to as GRDFolder), then you can try this:
merge.coarse <- raster("coarseBlock1.grd")
for(filename in list.files(GRDFolder))
{
temp <- raster(filename)
merge.coarse <- rbind(merge.coarse, temp)
}

R: Improving workflow and keeping track of output

I have what I think is a common enough issue, on optimising workflow in R. Specifically, how can I avoid the common issue of having a folder full of output (plots, RData files, csv, etc.), without, after some time, having a clue where they came from or how they were produced? In part, it surely involves trying to be intelligent about folder structure. I have been looking around, but I'm unsure of what the best strategy is. So far, I have tackled it in a rather unsophisticated (overkill) way: I created a function metainfo (see below) that writes a text file with metadata, with a given file name. The idea is that if a plot is produced, this command is issued to produce a text file with exactly the same file name as the plot (except, of course, the extension), with information on the system, session, packages loaded, R version, function and file the metadata function was called from, etc. The questions are:
(i) How do people approach this general problem? Are there obvious ways to avoid the issue I mentioned?
(ii) If not, does anyone have any tips on improving this function? At the moment it's perhaps clunky and not ideal. Particularly, getting the file name from which the plot is produced doesn't necessarily work (the solution I use is one provided by #hadley in 1). Any ideas would be welcome!
The function assumes git, so please ignore the probable warning produced. This is the main function, stored in a file metainfo.R:
MetaInfo <- function(message=NULL, filename)
{
# message - character string - Any message to be written into the information
# file (e.g., data used).
# filename - character string - the name of the txt file (including relative
# path). Should be the same as the output file it describes (RData,
# csv, pdf).
#
if (is.null(filename))
{
stop('Provide an output filename - parameter filename.')
}
filename <- paste(filename, '.txt', sep='')
# Try to get as close as possible to getting the file name from which the
# function is called.
source.file <- lapply(sys.frames(), function(x) x$ofile)
source.file <- Filter(Negate(is.null), source.file)
t.sf <- try(source.file <- basename(source.file[[length(source.file)]]),
silent=TRUE)
if (class(t.sf) == 'try-error')
{
source.file <- NULL
}
func <- deparse(sys.call(-1))
# MetaInfo isn't always called from within another function, so func could
# return as NULL or as general environment.
if (any(grepl('eval', func, ignore.case=TRUE)))
{
func <- NULL
}
time <- strftime(Sys.time(), "%Y/%m/%d %H:%M:%S")
git.h <- system('git log --pretty=format:"%h" -n 1', intern=TRUE)
meta <- list(Message=message,
Source=paste(source.file, ' on ', time, sep=''),
Functions=func,
System=Sys.info(),
Session=sessionInfo(),
Git.hash=git.h)
sink(file=filename)
print(meta)
sink(file=NULL)
}
which can then be called in another function, stored in another file, e.g.:
source('metainfo.R')
RandomPlot <- function(x, y)
{
fn <- 'random_plot'
pdf(file=paste(fn, '.pdf', sep=''))
plot(x, y)
MetaInfo(message=NULL, filename=fn)
dev.off()
}
x <- 1:10
y <- runif(10)
RandomPlot(x, y)
This way, a text file with the same file name as the plot is produced, with information that could hopefully help figure out how and where the plot was produced.
In terms of general R organization: I like to have a single script that recreates all work done for a project. Any project should be reproducible with a single click, including all plots or papers associated with that project.
So, to stay organized: keep a different directory for each project, each project has its own functions.R script to store non-package functions associated with that project, and each project has a master script that starts like
## myproject
source("functions.R")
source("read-data.R")
source("clean-data.R")
etc... all the way through. This should help keep everything organized, and if you get new data you just go to early scripts to fix up headers or whatever and rerun the entire project with a single click.
There is a package called Project Template that helps organize and automate the typical workflow with R scripts, data files, charts, etc. There is also a number of helpful documents like this one Workflow of statistical data analysis by Oliver Kirchkamp.
If you use Emacs and ESS for your analyses, learning Org-Mode is a must. I use it to organize all my work. Here is how it integrates with R: R Source Code Blocks in Org Mode.
There is also this new free tool called Drake which is advertised as "make for data".
I think my question belies a certain level of confusion. Having looked around, as well as explored the suggestions provided so far, I have reached the conclusion that it is probably not important to know where and how a file is produced. You should in fact be able to wipe out any output, and reproduce it by rerunning code. So while I might still use the above function for extra information, it really is a question of being ruthless and indeed cleaning up folders every now and then. These ideas are more eloquently explained here. This of course does not preclude the use of Make/Drake or Project Template, which I will try to pick up on. Thanks again for the suggestions #noah and #alex!
There is also now an R package called drake (Data Frames in R for Make), independent from Factual's Drake. The R package is also a Make-like build system that links code/dependencies with output.
install.packages("drake") # It is on CRAN.
library(drake)
load_basic_example()
plot_graph(my_plan)
make(my_plan)
Like it's predecessor remake, it has the added bonus that you do not have to keep track of a cumbersome pile of files. Objects generated in R are cached during make() and can be reloaded easily.
readd(summ_regression1_small) # Read objects from the cache.
loadd(small, large) # Load objects into your R session.
print(small)
But you can still work with files as single-quoted targets. (See 'report.Rmd' and 'report.md' in my_plan from the basic example.)
There is package developed by RStudio called pins that might address this problem.

freeing up memory in R

In R, I am trying to combine and convert several sets of timeseries data as an xts from http://www.truefx.com/?page=downloads however, the files are large and there many files so this is causing me issues on my laptop. They are stored as a csv file which have been compressed as a zip file.
Downloading them and unzipping them is easy enough (although takes up a lot of space on a hard drive).
Loading the 350MB+ files for one month's worth of data into the R is reasonably straight forward with the new fread() function in the data.table package.
Some datatable transformations are done (inside a function) so that the timestamps can be read easily and a mid column is produced. Then the datatable is saved as an RData file on the hard drive, and all references are to the datatable object are removed from the workspace, and a gc() is run after removal...however when looking at the R session in my Activity Monitor (run from a Mac)...it still looks like it is taking up almost 1GB of RAM...and things seem a bit laggy...I was intending to load several years worth of the csv files at the same time, convert them to useable datatables, combine them and then create a single xts object, which seems infeasible if just one month uses 1GB of RAM.
I know I can sequentially download each file, convert it, save it shut down R and repeat until i have a bunch of RData files that i can just load and bind, but was hopeing there might be a more efficient manner to do this so that after removing all references to a datatable you get back not "normal" or at startup levels of RAM usage. Are there better ways of clearing memory than gc()? Any suggestions would be greatly appreciated.
In my project I had to deal with many large files. I organized the routine on the following principles:
Isolate memory-hungry operations in separate R scripts.
Run each script in new process which is destroyed after execution. Thus system gives used memory back.
Pass parameters to the scripts via text file.
Consider the toy example below.
Data generation:
setwd("/path/to")
write.table(matrix(1:5e7, ncol=10), "temp.csv") # 465.2 Mb file
slave.R - memory consuming part
setwd("/path/to")
library(data.table)
# simple processing
f <- function(dt){
dt <- dt[1:nrow(dt),]
dt[,new.row:=1]
return (dt)
}
# reads parameters from file
csv <- read.table("io.csv")
infile <- as.character(csv[1,1])
outfile <- as.character(csv[2,1])
# memory-hungry operations
dt <- as.data.table(read.csv(infile))
dt <- f(dt)
write.table(dt, outfile)
master.R - executes slaves in separate processes
setwd("/path/to")
# 3 files processing
for(i in 1:3){
# sets iteration-specific parameters
csv <- c("temp.csv", paste("temp", i, ".csv", sep=""))
write.table(csv, "io.csv")
# executes slave process
system("R -f slave.R")
}

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