[gdal-dev] Using ogr2ogr with limited memory

Thu Sep 28 11:36:35 PDT 2023

I believe that you could try to increase your swap RAM,
for linux it is pretty straightforward, and having a SSD or NVME it will
perform good.
Free disk space is a must have to this to work,
as you are going to need about 10 - 20 Gb disk space as swap, according to
Even calcs + 8Gb that you have.
Not as fast as true RAM, but may be able to get the job done,

On Thu, Sep 28, 2023 at 3:18 PM Scott via gdal-dev <gdal-dev at lists.osgeo.org>
wrote:

> Thanks for digging into that Even!
>
> Can I create my new .fgb in sections?
>
> If I limit the number of source rows with -sql, doing that multiple
> times with -update, will it still build the entire R-tree when writing
> to the destination?
>
> I'm looking for a way to get the desired results.
>
> On 9/28/23 11:04, Even Rouault wrote:
> > ok, that now makes sense. Writing a .fgb files comes into those
> > exceptions where RAM consumption might be important, as it involves
> > building a packed Hilbert R-Tree in memory. With the current
> > implementation, you need at least the number of features times some
> > constant amount of RAM, at least to store the list of each feature
> > bounding box + their offset in a temporary file. From what I can see
> > this constant is at least 40 bytes. So in your particular case this
> > requires at least 145459485 * 40 = 5.5 GB of RAM. And probably (not
> > totally sure) twice that to store this initial list and the tree itself.
> > I guess the implementation could be made smarter and use on-disk
> > temporary memory, but that would likely involve serious implementation
> > complications. I let Björn comment more on this if he follows this
> > discussion.
> >
> > I've submitted a doc enhancement to mention this requirement:
> > https://github.com/OSGeo/gdal/pull/8490
> >
> > Le 28/09/2023 à 19:17, Scott a écrit :
> >> USA.fgb is 36 GB. I've renamed it from its original source which can
> >> be found here:
> >> https://beta.source.coop/vida/google-microsoft-open-buildings
> >>
> >> ogr2ogr -sql "select area_in_meters from bfp_USA" -nln footprints
> >> footprints.fgb ~/Downloads/USA.fgb
> >>
> >> GDAL 3.7.1
> >> OS Debian Buster
> >>
> >> Output from ogrinfo -ro -al USA.fgb
> >>
> >> Layer name: bfp_USA
> >> Geometry: Unknown (any)
> >> Feature Count: 145459485
> >> Extent: (-160.221701, 17.677691) - (-64.583428, 71.360579)
> >> Layer SRS WKT:
> >> GEOGCRS["WGS 84",
> >>     DATUM["World Geodetic System 1984",
> >>         ELLIPSOID["WGS 84",6378137,298.257223563,
> >>             LENGTHUNIT["metre",1]]],
> >>     PRIMEM["Greenwich",0,
> >>         ANGLEUNIT["degree",0.0174532925199433]],
> >>     CS[ellipsoidal,2],
> >>         AXIS["geodetic latitude (Lat)",north,
> >>             ORDER[1],
> >>             ANGLEUNIT["degree",0.0174532925199433]],
> >>         AXIS["geodetic longitude (Lon)",east,
> >>             ORDER[2],
> >>             ANGLEUNIT["degree",0.0174532925199433]],
> >>     USAGE[
> >>         SCOPE["unknown"],
> >>         AREA["World"],
> >>         BBOX[-90,-180,90,180]],
> >>     ID["EPSG",4326]]
> >> Data axis to CRS axis mapping: 2,1
> >> boundary_id: Integer64 (0.0)
> >> bf_source: String (0.0)
> >> confidence: Real (0.0)
> >> area_in_meters: Real (0.0)
> >> OGRFeature(bfp_USA):0
> >>   boundary_id (Integer64) = 116
> >>   bf_source (String) = google
> >>   confidence (Real) = 0.906
> >>   area_in_meters (Real) = 187.4652
> >>   POLYGON ((-64.6399621676723 17.7225504518464,-64.6400377660957
> >> 17.722583049763,-64.6400238635835 17.7226126625647,-64.6400901719124
> >> 17.7226412545727,-64.640104074415
> >>  17.722611641767,-64.6401239848718 17.7226202271066,-64.6401528522526
> >> 17.7225587385527,-64.6400955687758 17.7225340380511,-64.6401051288881
> >> 17.7225136746756,-64.640040
> >> 1136221 17.7224856402151,-64.640030553504
> >> 17.7225060035881,-64.6399910351014 17.7224889633119,-64.6399621676723
> >> 17.7225504518464))
> >>
> >> OGRFeature(bfp_USA):1
> >>   boundary_id (Integer64) = 116
> >>   bf_source (String) = microsoft
> >>   area_in_meters (Real) = 51.0777955237376
> >>   POLYGON ((-64.6398677811851 17.7219759840792,-64.6397939789141
> >> 17.7219853127982,-64.6398020235506 17.7220430591893,-64.6398758258215
> >> 17.7220337304732,-64.63986778118
> >> 51 17.7219759840792))
> >>
> >> OGRFeature(bfp_USA):2
> >>   boundary_id (Integer64) = 116
> >>   bf_source (String) = google
> >>   confidence (Real) = 0.8323
> >>   area_in_meters (Real) = 178.5448
> >>   POLYGON ((-64.6397672401299 17.7220665249078,-64.6397654280552
> >> 17.722041016034,-64.6395789582891 17.7220531822569,-64.6395832735872
> >> 17.7221139302758,-64.639696737462
> >> 3 17.7221065273415,-64.639698399651 17.7221299263498,-64.6398064310524
> >> 17.7221228777942,-64.6398022655579 17.7220642396531,-64.6397672401299
> >> 17.7220665249078))
> >>
> >>
> >> On 9/28/23 10:03, Even Rouault wrote:
> >>>
> >>> Le 28/09/2023 à 18:47, Scott via gdal-dev a écrit :
> >>>>
> >>>> I should have been more specific.
> >>>>
> >>>> One particular machine has 8GB of memory. When I try to do the most
> >>>> simple ogr2ogr command on large files, the host runs out of memory
> >>>> (vmstat shows this) and ogr2ogr terminates with 'Killed', nothing
> more.
> >>>>
> >>>> The data formats I have experienced this with are .fgb, .parquet and
> >>>> .gpkg. The data files are 10's of GB.
> >>>
> >>> As input ? as output? Which operating system ? Which GDAL version ?
> >>> The output of "ogrinfo -al -so the_input" might also be helpful. An
> >>> exact ogr2ogr command line invocation that triggers the issue would
> >>> certainly be useful.  In general, most GDAL drivers and ogr2ogr
> >>> itself operate in streaming mode with low RAM requirements, but there
> >>> might be exceptions (some configurations of GeoJSON file may require
> >>> full ingestion on reading for example).  I'm also aware of issues
> >>> with RAM fragmentation due to how some memory allocators work, but
> >>> they seem to be restricted to multithreaded uses
> >>> (
> https://gdal.org/user/multithreading.html#ram-fragmentation-and-multi-threading),
> which current ogr2ogr shouldn't trigger
> >>>
> >>> Even
> >>>
> >>>>
> >>>> Thanks for the responses!
> >>>> _______________________________________________
> >>>> gdal-dev mailing list
> >>>> gdal-dev at lists.osgeo.org
> >>>> https://lists.osgeo.org/mailman/listinfo/gdal-dev
> >>>
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