[R-sig-Geo] rgdal: problem reading a bigger raster dataset (R 4.0.0/3.6.3, Ubuntu 20.04)
Michael Sumner
md@umner @end|ng |rom gm@||@com
Mon Apr 27 15:58:40 CEST 2020
Try stars it worked for me on a test
On Mon., 27 Apr. 2020, 23:54 Thorsten Behrens, <thorsten.m.behrens using gmail.com>
wrote:
> Roger,
>
> thanks a lot for your reply!
>
> I have 256GB RAM installed (mentioned it somewhere). And there, all is
> fine when I run:
>
> rDemTest = raster(nrow = 48000, ncol = 72000, ext = extent(c(0, 72000,
>
> values(rDemTest) = 1
>
> When limiting the memory to about 8GB with ulimit::memory_limit(8000),
> the max size which can be allocated seems to be around 10000 x 10000px.
> In this case all tests run fine. Unfortunately it seems to be related to
> the size of the grid (48000 x 72000) and therefore the problem can't be
> reproduced on machines with 8GB RAM. For some processing steps I need
> grids of that size in the memory, which is why I have 256 GB installed.
>
> Normally, I use the raster package and not rgdal::readGDAL(). This was
> just a desperate attempt to find the source of the problem.
>
> This is what I use in my code:
>
> rDem = raster(sFileNameTiff)
> mDem = raster::as.matrix(rDem)
>
> But maybe this is the same...
>
> Any further suggestions are much appreciated!
>
> Thanks again!
>
> Best,
>
> Thorsten
>
>
>
>
> Am 27.04.2020 um 14:50 schrieb Roger Bivand:
> > On Mon, 27 Apr 2020, Thorsten Behrens wrote:
> >
> >> Dear all,
> >>
> >> my problem is that I want to read a big geotiff raster dataset into R
> >> and convert it to a matrix, which does not work.
> >> The file is big but there is sufficient memory. I need all the data
> >> in the memory at the same time.
> >>
> >> The error occurs under R 3.6.3 as well as 4.0.0 using Ubuntu 20.04
> >> LTS with the latest version of the packages (see session info below)
> >> and 256GB RAM installed.
> >>
> >> When loading the raster dataset using rgdal (via readGDAL or
> >> raster::readAll) I get the follwoing error in R 4.0.0:
> >>
> >> ```
> >> Error in rgdal::getRasterData(con, offset = offs, region.dim = reg,
> >> band = object using data@band) :
> >> long vectors not supported yet: memory.c:3782
> >> ```
> >
> > On a 16GB Fedora platform:
> >
> >> library(raster) # 3.1-5
> >> rDemTest = raster(nrow = 48000, ncol = 72000, ext = extent(c(0, 72000,
> > 0,
> > + 48000))) # all fine
> >> rDemTest
> > class : RasterLayer
> > dimensions : 48000, 72000, 3.456e+09 (nrow, ncol, ncell)
> > resolution : 1, 1 (x, y)
> > extent : 0, 72000, 0, 48000 (xmin, xmax, ymin, ymax)
> > crs : NA
> >
> >> values(rDemTest) = 1
> > Error: cannot allocate vector of size 25.7 Gb
> >
> > So you are deceiving yourself into thinking that all is fine at this
> > point. Please try to instantiate an example that can be reproduced on
> > a machine with 8GB RAM.
> >
> > Further note that rgdal::readGDAL() is not how you handle very large
> > objects in files, and never has been. raster can handle blocks of data
> > from bands in file; stars and gdalcubes can use proxy=TRUE for the
> > same purpose. Why did you choose rgdal::readGDAL() when this is not
> > its purpose?
> >
> > You did not say how much RAM is on your platform.
> >
> > Roger
> >
> >>
> >> In R 3.6.3 is is "... memory.c:3717"
> >>
> >> However, I can load the same file with the tiff package and a file of
> >> the same size in the native raster package format (*.grd) with the
> >> raster package but again not with the rgdal package.
> >>
> >> gdalinfo (gdalUtils) does not complain (see below). Hence, Even
> >> Rouault assumes the problem is related to rgdal and not gdal
> >> (https://github.com/OSGeo/gdal/issues/2442).
> >>
> >> Below you find reproducible code, which generates a raster file,
> >> saves the two formats (.tiff and .grd) and tries to read them with
> >> the different packages.
> >>
> >> Is this a known limitation? Any help is greatly appreciated!
> >>
> >> Thanks a lot in advance!
> >>
> >> Best wishes and stay healthy,
> >> Thorsten
> >>
> >>
> >>
> >> ### Steps to reproduce the problem.
> >>
> >> R code:
> >>
> >> ```
> >> library(rgdal) # 1.4-8
> >> library(raster) # 3.1-5
> >> library(tiff) # 0.1-5
> >>
> >> ## generate and manipulate a big raster dataset
> >> # - generate
> >> rDemTest = raster(nrow = 48000, ncol = 72000, ext = extent(c(0,
> >> 72000, 0, 48000))) # all fine
> >>
> >> # - manipulate
> >> values(rDemTest) = 1 # all fine
> >>
> >> # - convert
> >> mDemTest = raster::as.matrix(rDemTest) # all fine
> >> str(mDemTest)
> >>
> >> ## save a big dataset
> >>
> >> # - as raster/gdal
> >> sFileNameTiff = "BigData.tif"
> >> writeRaster(rDemTest, sFileNameTiff, "GTiff", overwrite = TRUE,
> >> NAflag = -9999) # all fine
> >>
> >> # - as raster native
> >> sFileNameNative = "BigData.grd"
> >> writeRaster(rDemTest, sFileNameNative, "raster", overwrite = TRUE,
> >> NAflag = -9999) # all fine
> >>
> >>
> >> ## load the big raster datasets with different packages and options
> >> # - load the tiff data with the gdal package via the raster package
> >> rDem = raster(sFileNameTiff) # all fine
> >> extent(rDem) # all fine
> >> mDem = raster::as.matrix(rDem) # error
> >> rDem = readAll(rDem) # error
> >>
> >> # - load the native raster data with the raster package
> >> rDem = raster(sFileNameNative) # all fine
> >> extent(rDem) # all fine
> >> mDem = raster::as.matrix(rDem) # all fine
> >> str(mDem)
> >>
> >> # - load the tiff data with the tiff package
> >> mDem = readTIFF(sFileNameTiff) # all fine
> >> str(mDem)
> >>
> >> # - load the tiff data with the gdal package
> >> sfDem = readGDAL(sFileNameTiff) # error
> >>
> >> # - load the native raster data with the gdal package
> >> sfDem = readGDAL(sFileNameNative) # error
> >>
> >> ```
> >>
> >>
> >> ### Startup messages when rgdal is attached (requested by Roger Bivand)
> >>> library(rgdal)
> >> rgdal: version: 1.4-8, (SVN revision 845)
> >> Geospatial Data Abstraction Library extensions to R successfully loaded
> >> Loaded GDAL runtime: GDAL 3.0.4, released 2020/01/28
> >> Path to GDAL shared files:
> >> GDAL binary built with GEOS: TRUE
> >> Loaded PROJ.4 runtime: Rel. 6.3.1, February 10th, 2020, [PJ_VERSION:
> >> 631]
> >> Path to PROJ.4 shared files: (autodetected)
> >> Linking to sp version: 1.4-1
> >>
> >>
> >> ### Session info
> >>> sessionInfo()
> >> R version 4.0.0 (2020-04-24)
> >> Platform: x86_64-pc-linux-gnu (64-bit)
> >> Running under: Ubuntu 20.04 LTS
> >>
> >> Matrix products: default
> >> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
> >> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
> >>
> >> locale:
> >> [1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C LC_TIME=de_DE.UTF-8
> >> [4] LC_COLLATE=de_DE.UTF-8 LC_MONETARY=de_DE.UTF-8
> >> LC_MESSAGES=de_DE.UTF-8
> >> [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C
> >> [10] LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8
> >> LC_IDENTIFICATION=C
> >>
> >> attached base packages:
> >> [1] stats graphics grDevices utils datasets methods base
> >>
> >> other attached packages:
> >> [1] gdalUtils_2.0.3.2 rgdal_1.4-8 tiff_0.1-5 raster_3.1-5
> >> sp_1.4-1
> >>
> >> loaded via a namespace (and not attached):
> >> [1] compiler_4.0.0 tools_4.0.0 Rcpp_1.0.4.6
> >> R.methodsS3_1.8.0 codetools_0.2-16
> >> [6] grid_4.0.0 iterators_1.0.12 foreach_1.5.0
> >> R.utils_2.9.2 R.oo_1.23.0
> >> [11] lattice_0.20-41
> >>
> >>
> >> ### gdalInfo
> >>> gdalinfo(sFileNameTiff)
> >> [1] "Driver: GTiff/GeoTIFF"
> >> [2] "Files: BigData.tif"
> >> [3] "Size is 72000, 48000"
> >> [4] "Origin = (0.000000000000000,48000.000000000000000)"
> >> [5] "Pixel Size = (1.000000000000000,-1.000000000000000)"
> >> [6] "Image Structure Metadata:"
> >> [7] " COMPRESSION=LZW"
> >> [8] " INTERLEAVE=BAND"
> >> [9] "Corner Coordinates:"
> >> [10] "Upper Left ( 0.000, 48000.000) "
> >> [11] "Lower Left ( 0.0000000, 0.0000000) "
> >> [12] "Upper Right ( 72000.000, 48000.000) "
> >> [13] "Lower Right ( 72000.000, 0.000) "
> >> [14] "Center ( 36000.000, 24000.000) "
> >> [15] "Band 1 Block=72000x1 Type=Float32, ColorInterp=Gray"
> >> [16] " Min=1.000 Max=1.000 "
> >> [17] " Minimum=1.000, Maximum=1.000, Mean=nan, StdDev=nan"
> >> [18] " NoData Value=-9999"
> >> [19] " Metadata:"
> >> [20] " STATISTICS_MAXIMUM=1"
> >> [21] " STATISTICS_MEAN=nan"
> >> [22] " STATISTICS_MINIMUM=1"
> >> [23] " STATISTICS_STDDEV=nan"
> >>
> >> _______________________________________________
> >> R-sig-Geo mailing list
> >> R-sig-Geo using r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
> >>
> >>
> >
>
> _______________________________________________
> R-sig-Geo mailing list
> R-sig-Geo using r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
[[alternative HTML version deleted]]
More information about the R-sig-Geo
mailing list