Hello,
I've written a function to try to answer to your op request, but I've
run into a problem. See in the end.
In the mean time, inline.
Em 28-09-2012 17:44, Jonathan Greenberg escreveu:
Rui:
Quick follow-up -- it looks like seek does do what I want (I see Simon
suggested it some time ago) -- what do mean by "trash your disk"?
Nothing special, just that sometimes there are good ways of doing so.
mmap seems to be safe.
What I'm
trying to accomplish is getting parallel, asynchronous writes to a large
binary image (just a binary file) working. Each node writes to a different
sector of the file via mmap, "filling in" the values as the process runs,
but the file needs to be pre-created before I can mmap it. Running a
writeBin with a bunch of 0s would mean I'd basically have to write the file
twice, but the seek/ff trick seems to be much faster.
Do I risk doing some damage to my filesystem if I use seek? I see there is
a strongly worded warning in the help for ?seek:
"Use of seek on Windows is discouraged. We have found so many errors in the
Windows implementation of file positioning that users are advised to use it
only at their own risk, and asked not to waste the *R* developers' time
with bug reports on Windows' deficiencies." --> there's no detail here on
which errors people have experienced, so I'm not sure if doing something as
simple as just "creating" a file using seek falls under the "discouraging"
category.
I'm not a great system programmer but in 20+ years of using seek on
Windows has shown nothing of the sort. In fact, I've just found a
problem with ubuntu 12.04, where seek gives the expected result on
Windows, it goes up to a certain point on ubuntu and then "stops
seeking", or whatever is happening. I installed ubuntu very recently so
I really don't know why the behavior that you can see in the example run
below. But I do that Windows 7 is causing no problem, as expected.
As a note, we are trying to work this up on both Windows and *nix systems,
hence our wanting to have a single approach that works on both OSs.
--j
#
# Function: creates a file of ascii nulls using seek/writeBin. File size
can be big.
#
createBig <- function(filename, size){
if(size == 0) return(0)
chunk <- .Machine$integer.max
nchunks <- as.integer(size / chunk)
rest <- size - as.double(nchunks)*as.double(chunk)
fl <- file(filename, open = "wb")
for(i in seq_len(nchunks)){
seek(fl, where = chunk - 1, origin = "current", rw = "write")
writeBin(raw(1), fl)
# ---------- debug ----------
print(seek(fl, where = NA))
}
if(rest > 0){
seek(fl, where = rest - 1, origin = "current", rw = "write")
writeBin(raw(1), fl)
}
close(fl)
}
As you can see from the debug prints, on Windows 7, everything works as
planned while on ubuntu 12.04 when it reaches 17Gb seek stops seeking.
The increments in file size become 1 byte at a time, explained by the
writeBin instruction. (The different, slightly larger, size is
irrelevant, the code was ran several times all with the same result: at
17179869176 bytes it no longer works.)
#----------------------------------------------------------------------------
#
# System: Windows 7 / R 2.15.1
size <- 10*.Machine$integer.max + sample(.Machine$integer.max, 1)
size
[1] 22195364413
createBig("Test.txt", size)
[1] 2147483647
[1] 4294967294
[1] 6442450941
[1] 8589934588
[1] 10737418235
[1] 12884901882
[1] 15032385529
[1] 17179869176
[1] 19327352823
[1] 21474836470
file.info("Test.txt")$size
[1] 22195364413
file.info("Test.txt")$size %/% .Machine$integer.max
[1] 10
file.info("Test.txt")$size %% .Machine$integer.max
[1] 720527943
sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=Portuguese_Portugal.1252 LC_CTYPE=Portuguese_Portugal.1252
[3] LC_MONETARY=Portuguese_Portugal.1252 LC_NUMERIC=C
[5] LC_TIME=Portuguese_Portugal.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] fortunes_1.5-0
#----------------------------------------------------------------------------
#
# System: ubuntu 12.04 precise pangolim / R 2.15.1
size <- 10*.Machine$integer.max + sample(.Machine$integer.max, 1)
size
[1] 23091487381
createBig("Test.txt", size)
[1] 2147483647
[1] 4294967294
[1] 6442450941
[1] 8589934588
[1] 10737418235
[1] 12884901882
[1] 15032385529
[1] 17179869176
[1] 17179869177
[1] 17179869178
file.info("Test.txt")$size
[1] 17179869179
file.info("Test.txt")$size %/% .Machine$integer.max
[1] 8
file.info("Test.txt")$size %% .Machine$integer.max
[1] 3
sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=pt_PT.UTF-8 LC_NUMERIC=C
[3] LC_TIME=pt_PT.UTF-8 LC_COLLATE=pt_PT.UTF-8
[5] LC_MONETARY=pt_PT.UTF-8 LC_MESSAGES=pt_PT.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=pt_PT.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
loaded via a namespace (and not attached):
[1] tools_2.15.1
On Thu, Sep 27, 2012 at 3:49 PM, Rui Barradas <ruipbarra...@sapo.pt> wrote:
Hello,
If you really need to trash your disk, why not use seek()?
fl <- file("Test.txt", open = "wb")
seek(fl, where = 1024, origin = "start", rw = "write")
[1] 0
writeChar(character(1), fl, nchars = 1, useBytes = TRUE)
Warning message:
In writeChar(character(1), fl, nchars = 1, useBytes = TRUE) :
writeChar: more characters requested than are in the string - will
zero-pad
close(fl)
File "Test.txt" is now 1Kb in size.
Hope this helps,
Rui Barradas
Em 27-09-2012 20:17, Jonathan Greenberg escreveu:
Folks:
Asked this question some time ago, and found what appeared (at first) to be
the best solution, but I'm now finding a new problem. First off, it seemed
like ff as Jens suggested worked:
# outdata_ncells = the number of rows * number of columns * number of bands
in an image:
out<-ff(vmode="double",length=outdata_ncells,filename=filename)
finalizer(out) <- close
close(out)
This was working fine until I attempted to set length to a VERY large
number: outdata_ncells = 17711913600. This would create a file that is
131.964GB. Big, but not obscenely so (and certainly not larger than the
filesystem can handle). However, length appears to be restricted
by .Machine$integer.max (I'm on a 64-bit windows box):
.Machine$integer.max
[1] 2147483647
Any suggestions on how to solve this problem for much larger file sizes?
--j
On Thu, May 3, 2012 at 10:44 AM, Jonathan Greenberg <j...@illinois.edu>
<j...@illinois.edu>wrote:
Thanks, all! I'll try these out. I'm trying to work up something that is
platform independent (if possible) for use with mmap. I'll do some tests
on these suggestions and see which works best. I'll try to report back in a
few days. Cheers!
--j
2012/5/3 "Jens Oehlschlägel" <jens.oehlschlae...@truecluster.com>
<jens.oehlschlae...@truecluster.com>
Jonathan,
On some filesystems (e.g. NTFS, see below) it is possible to create
'sparse' memory-mapped files, i.e. reserving the space without the cost of
actually writing initial values.
Package 'ff' does this automatically and also allows to access the file
in parallel. Check the example below and see how big file creation is
immediate.
Jens Oehlschlägel
library(ff)
library(snowfall)
ncpus <- 2
n <- 1e8
system.time(
+ x <- ff(vmode="double", length=n, filename="c:/Temp/x.ff")
+ )
User System verstrichen
0.01 0.00 0.02
# check finalizer, with an explicit filename we should have a 'close'
finalizer
finalizer(x)
[1] "close"
# if not, set it to 'close' inorder to not let slaves delete x on slave
shutdown
finalizer(x) <- "close"
sfInit(parallel=TRUE, cpus=ncpus, type="SOCK")
R Version: R version 2.15.0 (2012-03-30)
snowfall 1.84 initialized (using snow 0.3-9): parallel execution on 2
CPUs.
sfLibrary(ff)
Library ff loaded.
Library ff loaded in cluster.
Warnmeldung:
In library(package = "ff", character.only = TRUE, pos = 2, warn.conflicts
= TRUE, :
'keep.source' is deprecated and will be ignored
sfExport("x") # note: do not export the same ff multiple times
# explicitely opening avoids a gc problem
sfClusterEval(open(x, caching="mmeachflush")) # opening with
'mmeachflush' inststead of 'mmnoflush' is a bit slower but prevents OS
write storms when the file is larger than RAM
[[1]]
[1] TRUE
[[2]]
[1] TRUE
system.time(
+ sfLapply( chunk(x, length=ncpus), function(i){
+ x[i] <- runif(sum(i))
+ invisible()
+ })
+ )
User System verstrichen
0.00 0.00 30.78
system.time(
+ s <- sfLapply( chunk(x, length=ncpus), function(i) quantile(x[i],
c(0.05, 0.95)) )
+ )
User System verstrichen
0.00 0.00 4.38
# for completeness
sfClusterEval(close(x))
[[1]]
[1] TRUE
[[2]]
[1] TRUE
csummary(s)
5% 95%
Min. 0.04998 0.95
1st Qu. 0.04999 0.95
Median 0.05001 0.95
Mean 0.05001 0.95
3rd Qu. 0.05002 0.95
Max. 0.05003 0.95
# stop slaves
sfStop()
Stopping cluster
# with the close finalizer we are responsible for deleting the file
explicitely (unless we want to keep it)
delete(x)
[1] TRUE
# remove r-side metadata
rm(x)
# truly free memory
gc()
*Gesendet:* Donnerstag, 03. Mai 2012 um 00:23 Uhr
*Von:* "Jonathan Greenberg" <j...@illinois.edu> <j...@illinois.edu>
*An:* r-help <r-help@r-project.org> <r-help@r-project.org>,
r-sig-...@r-project.org
*Betreff:* [R-sig-hpc] Quickest way to make a large "empty" file on
disk?
R-helpers:
What would be the absolute fastest way to make a large "empty" file (e.g.
filled with all zeroes) on disk, given a byte size and a given number
number of empty values. I know I can use writeBin, but the "object" in
this case may be far too large to store in main memory. I'm asking because
I'm going to use this file in conjunction with mmap to do parallel writes
to this file. Say, I want to create a blank file of 10,000 floating point
numbers.
Thanks!
--j
--
Jonathan A. Greenberg, PhD
Assistant Professor
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
607 South Mathews Avenue, MC 150
Urbana, IL 61801
Phone: 415-763-5476
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype:
jgrn3007http://www.geog.illinois.edu/people/JonathanGreenberg.html
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--
Jonathan A. Greenberg, PhD
Assistant Professor
Department of Geography and Geographic Information Science
University of Illinois at Urbana-Champaign
607 South Mathews Avenue, MC 150
Urbana, IL 61801
Phone: 415-763-5476
AIM: jgrn307, MSN: jgrn...@hotmail.com, Gchat: jgrn307, Skype:
jgrn3007http://www.geog.illinois.edu/people/JonathanGreenberg.html
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