Issue with rgrass7 and readRAST

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Issue with rgrass7 and readRAST

Thomas Adams-2
Hi,

I'm using R in combination with GRASS GIS 7.8.3, attempting to read a GRASS
raster file into R with the rgrass7 interface. I have done this kind of
thing countless times previously without problems. It's quite possible I am
running into memory issues, but my Ubuntu 18.04 Linux computer has 32 GB of
RAM.

My GRASS raster file:

Type of Map:  raster               Number of Categories: 0
Data Type:    CELL
Rows:         22663
Columns:      28794
Total Cells:  652558422
~90m resolution

Using...

srtm <- readRAST("mozambique_srtm_patch",cat=FALSE)

After quite some time, I get...

Error in execGRASS("r.out.bin", flags = rOutBinFlags, input = vname[i],  :
  The command:
r.out.bin -b -i input=mozambique_srtm_patch
output=/media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/teaiii-Leopard-WS/mozambique_srtm_patch
bytes=4 null=-81
produced an error (1) during execution:
Creating BIL support files...
Exporting raster as integer values (bytes=4)
ERROR: Error writing data
In addition: Warning messages:
1: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
  Discarded ellps unknown in CRS definition: +proj=merc +lat_ts=0 +lon_0=0
+x_0=0 +y_0=0 +R=6378137 +units=m +no_defs
2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
  Discarded datum unknown in CRS definition

Libraries loaded include: sp, rgrass7, rgdal, raster...

Any thoughts?

Best,
Tom

--
Thomas E Adams, III
1724 Sage Lane
Blacksburg, VA 24060
[hidden email] (personal)
[hidden email] (work)

1 (513) 739-9512 (cell)

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Re: Issue with rgrass7 and readRAST

Roger Bivand
Administrator
Tom

On Fri, 10 Jul 2020, Thomas Adams wrote:

> Hi,
>
> I'm using R in combination with GRASS GIS 7.8.3, attempting to read a GRASS
> raster file into R with the rgrass7 interface. I have done this kind of
> thing countless times previously without problems. It's quite possible I am
> running into memory issues, but my Ubuntu 18.04 Linux computer has 32 GB of
> RAM.
>

I have not succeeded in reproducing this, I'm afraid. I created a location
with cell counts to match, and ran r.out.bin first to check whether there
were any issues writing the data to a temporary file. Then I ran the
equivalent of your command (readRAST()), again without problems. I'm on a
16 GB PC, so the problem is puzzling. I'm curious about the free space on
your

/media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/
teaiii-Leopard-WS

directory. Did you check whether any output arrived there, since the error
message is coming from r.out.bin?

The error is on line 53 in raster/r.out.bin/main.c, when the system
function fwrite() returns an error.

Thanks for your patience.

Roger


> My GRASS raster file:
>
> Type of Map:  raster               Number of Categories: 0
> Data Type:    CELL
> Rows:         22663
> Columns:      28794
> Total Cells:  652558422
> ~90m resolution
>
> Using...
>
> srtm <- readRAST("mozambique_srtm_patch",cat=FALSE)
>
> After quite some time, I get...
>
> Error in execGRASS("r.out.bin", flags = rOutBinFlags, input = vname[i],  :
>  The command:
> r.out.bin -b -i input=mozambique_srtm_patch
> output=/media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/teaiii-Leopard-WS/mozambique_srtm_patch
> bytes=4 null=-81
> produced an error (1) during execution:
> Creating BIL support files...
> Exporting raster as integer values (bytes=4)
> ERROR: Error writing data
> In addition: Warning messages:
> 1: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
>  Discarded ellps unknown in CRS definition: +proj=merc +lat_ts=0 +lon_0=0
> +x_0=0 +y_0=0 +R=6378137 +units=m +no_defs
> 2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
>  Discarded datum unknown in CRS definition
>
> Libraries loaded include: sp, rgrass7, rgdal, raster...
>
> Any thoughts?
>
> Best,
> Tom
>
>

--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: [hidden email]
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en

_______________________________________________
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Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
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Re: Issue with rgrass7 and readRAST

Thomas Adams-2
Hi Roger!

Here is what was written in
/media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/teaiii-Leopard-WS:

drwxr-xr-x 3 teaiii teaiii   4096 Sep 23  2019 ..
-rw-r--r-- 1 teaiii teaiii 131072 Jul  9 10:02 801.0.gpkg
-rw-r--r-- 1 teaiii teaiii 131072 Jul  9 10:04 466.0.gpkg
-rw-r--r-- 1 teaiii teaiii      0 Jul  9 20:32 801.0
-rw-r--r-- 1 teaiii teaiii      0 Jul  9 22:40 188.0
-rw-r--r-- 1 teaiii teaiii      0 Jul  9 22:51 222.0

And there is plenty of space on the disk drive...

Tom

On Sat, Jul 11, 2020 at 9:26 AM Roger Bivand <[hidden email]> wrote:

> Tom
>
> On Fri, 10 Jul 2020, Thomas Adams wrote:
>
> > Hi,
> >
> > I'm using R in combination with GRASS GIS 7.8.3, attempting to read a
> GRASS
> > raster file into R with the rgrass7 interface. I have done this kind of
> > thing countless times previously without problems. It's quite possible I
> am
> > running into memory issues, but my Ubuntu 18.04 Linux computer has 32 GB
> of
> > RAM.
> >
>
> I have not succeeded in reproducing this, I'm afraid. I created a location
> with cell counts to match, and ran r.out.bin first to check whether there
> were any issues writing the data to a temporary file. Then I ran the
> equivalent of your command (readRAST()), again without problems. I'm on a
> 16 GB PC, so the problem is puzzling. I'm curious about the free space on
> your
>
> /media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/
> teaiii-Leopard-WS
>
> directory. Did you check whether any output arrived there, since the error
> message is coming from r.out.bin?
>
> The error is on line 53 in raster/r.out.bin/main.c, when the system
> function fwrite() returns an error.
>
> Thanks for your patience.
>
> Roger
>
>
> > My GRASS raster file:
> >
> > Type of Map:  raster               Number of Categories: 0
> > Data Type:    CELL
> > Rows:         22663
> > Columns:      28794
> > Total Cells:  652558422
> > ~90m resolution
> >
> > Using...
> >
> > srtm <- readRAST("mozambique_srtm_patch",cat=FALSE)
> >
> > After quite some time, I get...
> >
> > Error in execGRASS("r.out.bin", flags = rOutBinFlags, input = vname[i],
> :
> >  The command:
> > r.out.bin -b -i input=mozambique_srtm_patch
> >
> output=/media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/teaiii-Leopard-WS/mozambique_srtm_patch
> > bytes=4 null=-81
> > produced an error (1) during execution:
> > Creating BIL support files...
> > Exporting raster as integer values (bytes=4)
> > ERROR: Error writing data
> > In addition: Warning messages:
> > 1: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
> >  Discarded ellps unknown in CRS definition: +proj=merc +lat_ts=0 +lon_0=0
> > +x_0=0 +y_0=0 +R=6378137 +units=m +no_defs
> > 2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
> >  Discarded datum unknown in CRS definition
> >
> > Libraries loaded include: sp, rgrass7, rgdal, raster...
> >
> > Any thoughts?
> >
> > Best,
> > Tom
> >
> >
>
> --
> Roger Bivand
> Department of Economics, Norwegian School of Economics,
> Helleveien 30, N-5045 Bergen, Norway.
> voice: +47 55 95 93 55; e-mail: [hidden email]
> https://orcid.org/0000-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>


--
Thomas E Adams, III
1724 Sage Lane
Blacksburg, VA 24060
[hidden email] (personal)
[hidden email] (work)

1 (513) 739-9512 (cell)

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Re: Issue with rgrass7 and readRAST

Roger Bivand
Administrator
In reply to this post by Thomas Adams-2
Briefly, please try to run r.out.bin manually, to the same output or another. This is what is failing on theGRASS side.

Roger

-------
Roger Bivand
Norwegian School of Economics, Bergen, Norway
[hidden email]

________________________________
Fra: Thomas Adams <[hidden email]>
Sendt: l�rdag 11. juli 2020, 17:59
Til: Roger Bivand
Kopi: [hidden email]
Emne: Re: [R-sig-Geo] Issue with rgrass7 and readRAST

Hi Roger!

Here is what was written in /media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/teaiii-Leopard-WS:

drwxr-xr-x 3 teaiii teaiii   4096 Sep 23  2019 ..
-rw-r--r-- 1 teaiii teaiii 131072 Jul  9 10:02 801.0.gpkg
-rw-r--r-- 1 teaiii teaiii 131072 Jul  9 10:04 466.0.gpkg
-rw-r--r-- 1 teaiii teaiii      0 Jul  9 20:32 801.0
-rw-r--r-- 1 teaiii teaiii      0 Jul  9 22:40 188.0
-rw-r--r-- 1 teaiii teaiii      0 Jul  9 22:51 222.0

And there is plenty of space on the disk drive...

Tom

On Sat, Jul 11, 2020 at 9:26 AM Roger Bivand <[hidden email]<mailto:[hidden email]>> wrote:
Tom

On Fri, 10 Jul 2020, Thomas Adams wrote:

> Hi,
>
> I'm using R in combination with GRASS GIS 7.8.3, attempting to read a GRASS
> raster file into R with the rgrass7 interface. I have done this kind of
> thing countless times previously without problems. It's quite possible I am
> running into memory issues, but my Ubuntu 18.04 Linux computer has 32 GB of
> RAM.
>

I have not succeeded in reproducing this, I'm afraid. I created a location
with cell counts to match, and ran r.out.bin first to check whether there
were any issues writing the data to a temporary file. Then I ran the
equivalent of your command (readRAST()), again without problems. I'm on a
16 GB PC, so the problem is puzzling. I'm curious about the free space on
your

/media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/
teaiii-Leopard-WS

directory. Did you check whether any output arrived there, since the error
message is coming from r.out.bin?

The error is on line 53 in raster/r.out.bin/main.c, when the system
function fwrite() returns an error.

Thanks for your patience.

Roger


> My GRASS raster file:
>
> Type of Map:  raster               Number of Categories: 0
> Data Type:    CELL
> Rows:         22663
> Columns:      28794
> Total Cells:  652558422
> ~90m resolution
>
> Using...
>
> srtm <- readRAST("mozambique_srtm_patch",cat=FALSE)
>
> After quite some time, I get...
>
> Error in execGRASS("r.out.bin", flags = rOutBinFlags, input = vname[i],  :
>  The command:
> r.out.bin -b -i input=mozambique_srtm_patch
> output=/media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/teaiii-Leopard-WS/mozambique_srtm_patch
> bytes=4 null=-81
> produced an error (1) during execution:
> Creating BIL support files...
> Exporting raster as integer values (bytes=4)
> ERROR: Error writing data
> In addition: Warning messages:
> 1: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
>  Discarded ellps unknown in CRS definition: +proj=merc +lat_ts=0 +lon_0=0
> +x_0=0 +y_0=0 +R=6378137 +units=m +no_defs
> 2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
>  Discarded datum unknown in CRS definition
>
> Libraries loaded include: sp, rgrass7, rgdal, raster...
>
> Any thoughts?
>
> Best,
> Tom
>
>
--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: [hidden email]<mailto:[hidden email]>
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en


--
Thomas E Adams, III
1724 Sage Lane
Blacksburg, VA 24060
[hidden email]<mailto:[hidden email]> (personal)
[hidden email]<mailto:[hidden email]> (work)

1 (513) 739-9512 (cell)



        [[alternative HTML version deleted]]


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Helleveien 30
N-5045 Bergen, Norway
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Re: Issue with rgrass7 and readRAST

Thomas Adams-2
Hi Roger,

r.out.bin from GRASS did succeed... r.out.bin
input=mozambique_srtm_patch@teaiii output=mozambique_srtm_patch null=-999
Exporting raster as integer values (bytes=2)

A very large file!!
-rw-r--r--   1 teaiii teaiii 1045368225220 Jul 11 13:26
mozambique_srtm_patch

Tom


On Sat, Jul 11, 2020 at 12:12 PM Roger Bivand <[hidden email]> wrote:

> Briefly, please try to run r.out.bin manually, to the same output or
> another. This is what is failing on theGRASS side.
>
> Roger
>
> -------
> Roger Bivand
> Norwegian School of Economics, Bergen, Norway
> [hidden email]
>
> ------------------------------
> *Fra:* Thomas Adams <[hidden email]>
> *Sendt:* lørdag 11. juli 2020, 17:59
> *Til:* Roger Bivand
> *Kopi:* [hidden email]
> *Emne:* Re: [R-sig-Geo] Issue with rgrass7 and readRAST
>
> Hi Roger!
>
> Here is what was written in
> /media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/teaiii-Leopard-WS:
>
> drwxr-xr-x 3 teaiii teaiii   4096 Sep 23  2019 ..
> -rw-r--r-- 1 teaiii teaiii 131072 Jul  9 10:02 801.0.gpkg
> -rw-r--r-- 1 teaiii teaiii 131072 Jul  9 10:04 466.0.gpkg
> -rw-r--r-- 1 teaiii teaiii      0 Jul  9 20:32 801.0
> -rw-r--r-- 1 teaiii teaiii      0 Jul  9 22:40 188.0
> -rw-r--r-- 1 teaiii teaiii      0 Jul  9 22:51 222.0
>
> And there is plenty of space on the disk drive...
>
> Tom
>
> On Sat, Jul 11, 2020 at 9:26 AM Roger Bivand <[hidden email]> wrote:
>
>> Tom
>>
>> On Fri, 10 Jul 2020, Thomas Adams wrote:
>>
>> > Hi,
>> >
>> > I'm using R in combination with GRASS GIS 7.8.3, attempting to read a
>> GRASS
>> > raster file into R with the rgrass7 interface. I have done this kind of
>> > thing countless times previously without problems. It's quite possible
>> I am
>> > running into memory issues, but my Ubuntu 18.04 Linux computer has 32
>> GB of
>> > RAM.
>> >
>>
>> I have not succeeded in reproducing this, I'm afraid. I created a
>> location
>> with cell counts to match, and ran r.out.bin first to check whether there
>> were any issues writing the data to a temporary file. Then I ran the
>> equivalent of your command (readRAST()), again without problems. I'm on a
>> 16 GB PC, so the problem is puzzling. I'm curious about the free space on
>> your
>>
>> /media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/
>> teaiii-Leopard-WS
>>
>> directory. Did you check whether any output arrived there, since the
>> error
>> message is coming from r.out.bin?
>>
>> The error is on line 53 in raster/r.out.bin/main.c, when the system
>> function fwrite() returns an error.
>>
>> Thanks for your patience.
>>
>> Roger
>>
>>
>> > My GRASS raster file:
>> >
>> > Type of Map:  raster               Number of Categories: 0
>> > Data Type:    CELL
>> > Rows:         22663
>> > Columns:      28794
>> > Total Cells:  652558422
>> > ~90m resolution
>> >
>> > Using...
>> >
>> > srtm <- readRAST("mozambique_srtm_patch",cat=FALSE)
>> >
>> > After quite some time, I get...
>> >
>> > Error in execGRASS("r.out.bin", flags = rOutBinFlags, input =
>> vname[i],  :
>> >  The command:
>> > r.out.bin -b -i input=mozambique_srtm_patch
>> >
>> output=/media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/teaiii-Leopard-WS/mozambique_srtm_patch
>> > bytes=4 null=-81
>> > produced an error (1) during execution:
>> > Creating BIL support files...
>> > Exporting raster as integer values (bytes=4)
>> > ERROR: Error writing data
>> > In addition: Warning messages:
>> > 1: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
>> >  Discarded ellps unknown in CRS definition: +proj=merc +lat_ts=0
>> +lon_0=0
>> > +x_0=0 +y_0=0 +R=6378137 +units=m +no_defs
>> > 2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
>> >  Discarded datum unknown in CRS definition
>> >
>> > Libraries loaded include: sp, rgrass7, rgdal, raster...
>> >
>> > Any thoughts?
>> >
>> > Best,
>> > Tom
>> >
>> >
>>
>> --
>> Roger Bivand
>> Department of Economics, Norwegian School of Economics,
>> Helleveien 30, N-5045 Bergen, Norway.
>> voice: +47 55 95 93 55; e-mail: [hidden email]
>> https://orcid.org/0000-0003-2392-6140
>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>
>
>
> --
> Thomas E Adams, III
> 1724 Sage Lane
> Blacksburg, VA 24060
> [hidden email] (personal)
> [hidden email] (work)
>
> 1 (513) 739-9512 (cell)
>
>
>

--
Thomas E Adams, III
1724 Sage Lane
Blacksburg, VA 24060
[hidden email] (personal)
[hidden email] (work)

1 (513) 739-9512 (cell)

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Re: Issue with rgrass7 and readRAST

Thomas Adams-2
Hi Roger,

I believe I may have been correct about the memory issue... it's possible,
in GRASS, that I did not restrict my REGION sufficiently, using g.region.
Additionally, I applied a MASK for my country of interest, Mozambique,
before starting R, which yielded:

srtm <- readRAST("mozambique_srtm_patch",cat=FALSE)
Creating BIL support files...
Exporting raster as integer values (bytes=4)
 100%
Warning messages:
1: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
  Discarded ellps unknown in CRS definition: +proj=merc +lat_ts=0 +lon_0=0
+x_0=0 +y_0=0 +R=6378137 +units=m +no_defs
2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
  Discarded datum unknown in CRS definition
> image(srtm)
Error in rasterImage(m, bb[1, 1], bb[2, 1], bb[1, 2], bb[2, 2], interpolate
= interpolate,  :
  cannot allocate memory block of size 16777216 Tb

Still, a huge amount of memory needed (is 16777216 Tb correct??)

My thought was to resample the SRTM data in GRASS to 1km resolution, then
start R, and proceed, which quite honestly, for my purposes, really is
sufficient. By doing this, everything worked perfectly! I was able to read
the srtm data quickly and generate an image. I am puzzled by the "cannot
allocate memory block of size 16777216 Tb" message with my GRASS Region
settings in place.

Thank you for all your help!

Best,
Tom



On Sat, Jul 11, 2020 at 11:02 PM Thomas Adams <[hidden email]> wrote:

> Hi Roger,
>
> r.out.bin from GRASS did succeed... r.out.bin
> input=mozambique_srtm_patch@teaiii output=mozambique_srtm_patch null=-999
> Exporting raster as integer values (bytes=2)
>
> A very large file!!
> -rw-r--r--   1 teaiii teaiii 1045368225220 Jul 11 13:26
> mozambique_srtm_patch
>
> Tom
>
>
> On Sat, Jul 11, 2020 at 12:12 PM Roger Bivand <[hidden email]> wrote:
>
>> Briefly, please try to run r.out.bin manually, to the same output or
>> another. This is what is failing on theGRASS side.
>>
>> Roger
>>
>> -------
>> Roger Bivand
>> Norwegian School of Economics, Bergen, Norway
>> [hidden email]
>>
>> ------------------------------
>> *Fra:* Thomas Adams <[hidden email]>
>> *Sendt:* lørdag 11. juli 2020, 17:59
>> *Til:* Roger Bivand
>> *Kopi:* [hidden email]
>> *Emne:* Re: [R-sig-Geo] Issue with rgrass7 and readRAST
>>
>> Hi Roger!
>>
>> Here is what was written in
>> /media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/teaiii-Leopard-WS:
>>
>> drwxr-xr-x 3 teaiii teaiii   4096 Sep 23  2019 ..
>> -rw-r--r-- 1 teaiii teaiii 131072 Jul  9 10:02 801.0.gpkg
>> -rw-r--r-- 1 teaiii teaiii 131072 Jul  9 10:04 466.0.gpkg
>> -rw-r--r-- 1 teaiii teaiii      0 Jul  9 20:32 801.0
>> -rw-r--r-- 1 teaiii teaiii      0 Jul  9 22:40 188.0
>> -rw-r--r-- 1 teaiii teaiii      0 Jul  9 22:51 222.0
>>
>> And there is plenty of space on the disk drive...
>>
>> Tom
>>
>> On Sat, Jul 11, 2020 at 9:26 AM Roger Bivand <[hidden email]> wrote:
>>
>>> Tom
>>>
>>> On Fri, 10 Jul 2020, Thomas Adams wrote:
>>>
>>> > Hi,
>>> >
>>> > I'm using R in combination with GRASS GIS 7.8.3, attempting to read a
>>> GRASS
>>> > raster file into R with the rgrass7 interface. I have done this kind of
>>> > thing countless times previously without problems. It's quite possible
>>> I am
>>> > running into memory issues, but my Ubuntu 18.04 Linux computer has 32
>>> GB of
>>> > RAM.
>>> >
>>>
>>> I have not succeeded in reproducing this, I'm afraid. I created a
>>> location
>>> with cell counts to match, and ran r.out.bin first to check whether
>>> there
>>> were any issues writing the data to a temporary file. Then I ran the
>>> equivalent of your command (readRAST()), again without problems. I'm on
>>> a
>>> 16 GB PC, so the problem is puzzling. I'm curious about the free space
>>> on
>>> your
>>>
>>> /media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/
>>> teaiii-Leopard-WS
>>>
>>> directory. Did you check whether any output arrived there, since the
>>> error
>>> message is coming from r.out.bin?
>>>
>>> The error is on line 53 in raster/r.out.bin/main.c, when the system
>>> function fwrite() returns an error.
>>>
>>> Thanks for your patience.
>>>
>>> Roger
>>>
>>>
>>> > My GRASS raster file:
>>> >
>>> > Type of Map:  raster               Number of Categories: 0
>>> > Data Type:    CELL
>>> > Rows:         22663
>>> > Columns:      28794
>>> > Total Cells:  652558422
>>> > ~90m resolution
>>> >
>>> > Using...
>>> >
>>> > srtm <- readRAST("mozambique_srtm_patch",cat=FALSE)
>>> >
>>> > After quite some time, I get...
>>> >
>>> > Error in execGRASS("r.out.bin", flags = rOutBinFlags, input =
>>> vname[i],  :
>>> >  The command:
>>> > r.out.bin -b -i input=mozambique_srtm_patch
>>> >
>>> output=/media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/teaiii-Leopard-WS/mozambique_srtm_patch
>>> > bytes=4 null=-81
>>> > produced an error (1) during execution:
>>> > Creating BIL support files...
>>> > Exporting raster as integer values (bytes=4)
>>> > ERROR: Error writing data
>>> > In addition: Warning messages:
>>> > 1: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
>>> >  Discarded ellps unknown in CRS definition: +proj=merc +lat_ts=0
>>> +lon_0=0
>>> > +x_0=0 +y_0=0 +R=6378137 +units=m +no_defs
>>> > 2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
>>> >  Discarded datum unknown in CRS definition
>>> >
>>> > Libraries loaded include: sp, rgrass7, rgdal, raster...
>>> >
>>> > Any thoughts?
>>> >
>>> > Best,
>>> > Tom
>>> >
>>> >
>>>
>>> --
>>> Roger Bivand
>>> Department of Economics, Norwegian School of Economics,
>>> Helleveien 30, N-5045 Bergen, Norway.
>>> voice: +47 55 95 93 55; e-mail: [hidden email]
>>> https://orcid.org/0000-0003-2392-6140
>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>
>>
>>
>> --
>> Thomas E Adams, III
>> 1724 Sage Lane
>> Blacksburg, VA 24060
>> [hidden email] (personal)
>> [hidden email] (work)
>>
>> 1 (513) 739-9512 (cell)
>>
>>
>>
>
> --
> Thomas E Adams, III
> 1724 Sage Lane
> Blacksburg, VA 24060
> [hidden email] (personal)
> [hidden email] (work)
>
> 1 (513) 739-9512 (cell)
>
>

--
Thomas E Adams, III
1724 Sage Lane
Blacksburg, VA 24060
[hidden email] (personal)
[hidden email] (work)

1 (513) 739-9512 (cell)

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Re: Issue with rgrass7 and readRAST

Roger Bivand
Administrator
On Sun, 12 Jul 2020, Thomas Adams wrote:

> Hi Roger,
>
> I believe I may have been correct about the memory issue... it's possible,
> in GRASS, that I did not restrict my REGION sufficiently, using g.region.
> Additionally, I applied a MASK for my country of interest, Mozambique,
> before starting R, which yielded:
>
> srtm <- readRAST("mozambique_srtm_patch",cat=FALSE)
> Creating BIL support files...
> Exporting raster as integer values (bytes=4)
> 100%
> Warning messages:
> 1: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
>  Discarded ellps unknown in CRS definition: +proj=merc +lat_ts=0 +lon_0=0
> +x_0=0 +y_0=0 +R=6378137 +units=m +no_defs
> 2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
>  Discarded datum unknown in CRS definition
>> image(srtm)
> Error in rasterImage(m, bb[1, 1], bb[2, 1], bb[1, 2], bb[2, 2], interpolate
> = interpolate,  :
>  cannot allocate memory block of size 16777216 Tb
I'd got to an errant g.region before r.out.bin too.

graphics::rasterImage() is reporting the error. The metric is wrong, but
the problem is real. The object is about 650M x 4 bytes, which image()
needs to manipulate too, creating several copies (in the imported object
it is a vector, but is cast to a matrix and transposed).

>
> Still, a huge amount of memory needed (is 16777216 Tb correct??)
>
> My thought was to resample the SRTM data in GRASS to 1km resolution, then
> start R, and proceed, which quite honestly, for my purposes, really is
> sufficient. By doing this, everything worked perfectly! I was able to read
> the srtm data quickly and generate an image. I am puzzled by the "cannot
> allocate memory block of size 16777216 Tb" message with my GRASS Region
> settings in place.

Please try r.out.gdal in 90m, then stars::read_stars(..., proxy=TRUE)
(outside rgrass7). We need to try to get stars to work in rgrass7, but we
had not gone into that yet. In stars and gdalcubes, the idea is to do work
on the back end, and only bring data to (say) display in the feasible
resolution. So I think something like:

library(stars)
big <- read_stars("big.tif", proxy=TRUE)
plot(big)

automates the downsampling. The default arguments to readRAST() assume
that uncompressed binary is the optimal transfer strategy, and that all
the data should be in R's workspace.

I can speculate that if GDAL used the GRASS plugin, it might be possibble
to proxy the actual GRASS CELL or DCELL. However, someone else would need
to take responsibility for implementing prototypes for that. The same
applies to support for stars, alternatively for terra in addition (raster
is used by many, but with limited resources, stars and terra should be
preferred).

Roger

>
> Thank you for all your help!
>
> Best,
> Tom
>
>
>
> On Sat, Jul 11, 2020 at 11:02 PM Thomas Adams <[hidden email]> wrote:
>
>> Hi Roger,
>>
>> r.out.bin from GRASS did succeed... r.out.bin
>> input=mozambique_srtm_patch@teaiii output=mozambique_srtm_patch null=-999
>> Exporting raster as integer values (bytes=2)
>>
>> A very large file!!
>> -rw-r--r--   1 teaiii teaiii 1045368225220 Jul 11 13:26
>> mozambique_srtm_patch
>>
>> Tom
>>
>>
>> On Sat, Jul 11, 2020 at 12:12 PM Roger Bivand <[hidden email]> wrote:
>>
>>> Briefly, please try to run r.out.bin manually, to the same output or
>>> another. This is what is failing on theGRASS side.
>>>
>>> Roger
>>>
>>> -------
>>> Roger Bivand
>>> Norwegian School of Economics, Bergen, Norway
>>> [hidden email]
>>>
>>> ------------------------------
>>> *Fra:* Thomas Adams <[hidden email]>
>>> *Sendt:* lørdag 11. juli 2020, 17:59
>>> *Til:* Roger Bivand
>>> *Kopi:* [hidden email]
>>> *Emne:* Re: [R-sig-Geo] Issue with rgrass7 and readRAST
>>>
>>> Hi Roger!
>>>
>>> Here is what was written in
>>> /media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/teaiii-Leopard-WS:
>>>
>>> drwxr-xr-x 3 teaiii teaiii   4096 Sep 23  2019 ..
>>> -rw-r--r-- 1 teaiii teaiii 131072 Jul  9 10:02 801.0.gpkg
>>> -rw-r--r-- 1 teaiii teaiii 131072 Jul  9 10:04 466.0.gpkg
>>> -rw-r--r-- 1 teaiii teaiii      0 Jul  9 20:32 801.0
>>> -rw-r--r-- 1 teaiii teaiii      0 Jul  9 22:40 188.0
>>> -rw-r--r-- 1 teaiii teaiii      0 Jul  9 22:51 222.0
>>>
>>> And there is plenty of space on the disk drive...
>>>
>>> Tom
>>>
>>> On Sat, Jul 11, 2020 at 9:26 AM Roger Bivand <[hidden email]> wrote:
>>>
>>>> Tom
>>>>
>>>> On Fri, 10 Jul 2020, Thomas Adams wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> I'm using R in combination with GRASS GIS 7.8.3, attempting to read a
>>>> GRASS
>>>>> raster file into R with the rgrass7 interface. I have done this kind of
>>>>> thing countless times previously without problems. It's quite possible
>>>> I am
>>>>> running into memory issues, but my Ubuntu 18.04 Linux computer has 32
>>>> GB of
>>>>> RAM.
>>>>>
>>>>
>>>> I have not succeeded in reproducing this, I'm afraid. I created a
>>>> location
>>>> with cell counts to match, and ran r.out.bin first to check whether
>>>> there
>>>> were any issues writing the data to a temporary file. Then I ran the
>>>> equivalent of your command (readRAST()), again without problems. I'm on
>>>> a
>>>> 16 GB PC, so the problem is puzzling. I'm curious about the free space
>>>> on
>>>> your
>>>>
>>>> /media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/
>>>> teaiii-Leopard-WS
>>>>
>>>> directory. Did you check whether any output arrived there, since the
>>>> error
>>>> message is coming from r.out.bin?
>>>>
>>>> The error is on line 53 in raster/r.out.bin/main.c, when the system
>>>> function fwrite() returns an error.
>>>>
>>>> Thanks for your patience.
>>>>
>>>> Roger
>>>>
>>>>
>>>>> My GRASS raster file:
>>>>>
>>>>> Type of Map:  raster               Number of Categories: 0
>>>>> Data Type:    CELL
>>>>> Rows:         22663
>>>>> Columns:      28794
>>>>> Total Cells:  652558422
>>>>> ~90m resolution
>>>>>
>>>>> Using...
>>>>>
>>>>> srtm <- readRAST("mozambique_srtm_patch",cat=FALSE)
>>>>>
>>>>> After quite some time, I get...
>>>>>
>>>>> Error in execGRASS("r.out.bin", flags = rOutBinFlags, input =
>>>> vname[i],  :
>>>>>  The command:
>>>>> r.out.bin -b -i input=mozambique_srtm_patch
>>>>>
>>>> output=/media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/teaiii-Leopard-WS/mozambique_srtm_patch
>>>>> bytes=4 null=-81
>>>>> produced an error (1) during execution:
>>>>> Creating BIL support files...
>>>>> Exporting raster as integer values (bytes=4)
>>>>> ERROR: Error writing data
>>>>> In addition: Warning messages:
>>>>> 1: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
>>>>>  Discarded ellps unknown in CRS definition: +proj=merc +lat_ts=0
>>>> +lon_0=0
>>>>> +x_0=0 +y_0=0 +R=6378137 +units=m +no_defs
>>>>> 2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
>>>>>  Discarded datum unknown in CRS definition
>>>>>
>>>>> Libraries loaded include: sp, rgrass7, rgdal, raster...
>>>>>
>>>>> Any thoughts?
>>>>>
>>>>> Best,
>>>>> Tom
>>>>>
>>>>>
>>>>
>>>> --
>>>> Roger Bivand
>>>> Department of Economics, Norwegian School of Economics,
>>>> Helleveien 30, N-5045 Bergen, Norway.
>>>> voice: +47 55 95 93 55; e-mail: [hidden email]
>>>> https://orcid.org/0000-0003-2392-6140
>>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
>>>>
>>>
>>>
>>> --
>>> Thomas E Adams, III
>>> 1724 Sage Lane
>>> Blacksburg, VA 24060
>>> [hidden email] (personal)
>>> [hidden email] (work)
>>>
>>> 1 (513) 739-9512 (cell)
>>>
>>>
>>>
>>
>> --
>> Thomas E Adams, III
>> 1724 Sage Lane
>> Blacksburg, VA 24060
>> [hidden email] (personal)
>> [hidden email] (work)
>>
>> 1 (513) 739-9512 (cell)
>>
>>
>
>
--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; e-mail: [hidden email]
https://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
_______________________________________________
R-sig-Geo mailing list
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Roger Bivand
Department of Economics
Norwegian School of Economics
Helleveien 30
N-5045 Bergen, Norway
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Re: Issue with rgrass7 and readRAST

Thomas Adams-2
Hi Roger,

I did run with a 90m resolution, with the same error:
> srtm <- readRAST("mozambique_srtm_90m",cat=FALSE)
Creating BIL support files...
Exporting raster as integer values (bytes=4)
 100%
Warning messages:
1: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
  Discarded ellps unknown in CRS definition: +proj=merc +lat_ts=0 +lon_0=0
+x_0=0 +y_0=0 +R=6378137 +units=m +no_defs
2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
  Discarded datum unknown in CRS definition
> image(srtm)
Error in rasterImage(m, bb[1, 1], bb[2, 1], bb[1, 2], bb[2, 2], interpolate
= interpolate,  :
  cannot allocate memory block of size 16777216 Tb

However, with a 250m resolution the import and visualization worked fine:

> srtm <- readRAST("mozambique_srtm_250m",cat=FALSE)
Creating BIL support files...
Exporting raster as integer values (bytes=4)
 100%
Warning messages:
1: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
  Discarded ellps unknown in CRS definition: +proj=merc +lat_ts=0 +lon_0=0
+x_0=0 +y_0=0 +R=6378137 +units=m +no_defs
2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
  Discarded datum unknown in CRS definition
> image(srtm,col = terrain.colors(20))

Thank you for your help!

Best regards,
Tom


On Sun, Jul 12, 2020 at 9:19 AM Roger Bivand <[hidden email]> wrote:

> On Sun, 12 Jul 2020, Thomas Adams wrote:
>
> > Hi Roger,
> >
> > I believe I may have been correct about the memory issue... it's
> possible,
> > in GRASS, that I did not restrict my REGION sufficiently, using g.region.
> > Additionally, I applied a MASK for my country of interest, Mozambique,
> > before starting R, which yielded:
> >
> > srtm <- readRAST("mozambique_srtm_patch",cat=FALSE)
> > Creating BIL support files...
> > Exporting raster as integer values (bytes=4)
> > 100%
> > Warning messages:
> > 1: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
> >  Discarded ellps unknown in CRS definition: +proj=merc +lat_ts=0 +lon_0=0
> > +x_0=0 +y_0=0 +R=6378137 +units=m +no_defs
> > 2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
> >  Discarded datum unknown in CRS definition
> >> image(srtm)
> > Error in rasterImage(m, bb[1, 1], bb[2, 1], bb[1, 2], bb[2, 2],
> interpolate
> > = interpolate,  :
> >  cannot allocate memory block of size 16777216 Tb
>
> I'd got to an errant g.region before r.out.bin too.
>
> graphics::rasterImage() is reporting the error. The metric is wrong, but
> the problem is real. The object is about 650M x 4 bytes, which image()
> needs to manipulate too, creating several copies (in the imported object
> it is a vector, but is cast to a matrix and transposed).
>
> >
> > Still, a huge amount of memory needed (is 16777216 Tb correct??)
> >
> > My thought was to resample the SRTM data in GRASS to 1km resolution, then
> > start R, and proceed, which quite honestly, for my purposes, really is
> > sufficient. By doing this, everything worked perfectly! I was able to
> read
> > the srtm data quickly and generate an image. I am puzzled by the "cannot
> > allocate memory block of size 16777216 Tb" message with my GRASS Region
> > settings in place.
>
> Please try r.out.gdal in 90m, then stars::read_stars(..., proxy=TRUE)
> (outside rgrass7). We need to try to get stars to work in rgrass7, but we
> had not gone into that yet. In stars and gdalcubes, the idea is to do work
> on the back end, and only bring data to (say) display in the feasible
> resolution. So I think something like:
>
> library(stars)
> big <- read_stars("big.tif", proxy=TRUE)
> plot(big)
>
> automates the downsampling. The default arguments to readRAST() assume
> that uncompressed binary is the optimal transfer strategy, and that all
> the data should be in R's workspace.
>
> I can speculate that if GDAL used the GRASS plugin, it might be possibble
> to proxy the actual GRASS CELL or DCELL. However, someone else would need
> to take responsibility for implementing prototypes for that. The same
> applies to support for stars, alternatively for terra in addition (raster
> is used by many, but with limited resources, stars and terra should be
> preferred).
>
> Roger
>
> >
> > Thank you for all your help!
> >
> > Best,
> > Tom
> >
> >
> >
> > On Sat, Jul 11, 2020 at 11:02 PM Thomas Adams <[hidden email]> wrote:
> >
> >> Hi Roger,
> >>
> >> r.out.bin from GRASS did succeed... r.out.bin
> >> input=mozambique_srtm_patch@teaiii output=mozambique_srtm_patch
> null=-999
> >> Exporting raster as integer values (bytes=2)
> >>
> >> A very large file!!
> >> -rw-r--r--   1 teaiii teaiii 1045368225220 Jul 11 13:26
> >> mozambique_srtm_patch
> >>
> >> Tom
> >>
> >>
> >> On Sat, Jul 11, 2020 at 12:12 PM Roger Bivand <[hidden email]>
> wrote:
> >>
> >>> Briefly, please try to run r.out.bin manually, to the same output or
> >>> another. This is what is failing on theGRASS side.
> >>>
> >>> Roger
> >>>
> >>> -------
> >>> Roger Bivand
> >>> Norwegian School of Economics, Bergen, Norway
> >>> [hidden email]
> >>>
> >>> ------------------------------
> >>> *Fra:* Thomas Adams <[hidden email]>
> >>> *Sendt:* lørdag 11. juli 2020, 17:59
> >>> *Til:* Roger Bivand
> >>> *Kopi:* [hidden email]
> >>> *Emne:* Re: [R-sig-Geo] Issue with rgrass7 and readRAST
> >>>
> >>> Hi Roger!
> >>>
> >>> Here is what was written in
> >>>
> /media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/teaiii-Leopard-WS:
> >>>
> >>> drwxr-xr-x 3 teaiii teaiii   4096 Sep 23  2019 ..
> >>> -rw-r--r-- 1 teaiii teaiii 131072 Jul  9 10:02 801.0.gpkg
> >>> -rw-r--r-- 1 teaiii teaiii 131072 Jul  9 10:04 466.0.gpkg
> >>> -rw-r--r-- 1 teaiii teaiii      0 Jul  9 20:32 801.0
> >>> -rw-r--r-- 1 teaiii teaiii      0 Jul  9 22:40 188.0
> >>> -rw-r--r-- 1 teaiii teaiii      0 Jul  9 22:51 222.0
> >>>
> >>> And there is plenty of space on the disk drive...
> >>>
> >>> Tom
> >>>
> >>> On Sat, Jul 11, 2020 at 9:26 AM Roger Bivand <[hidden email]>
> wrote:
> >>>
> >>>> Tom
> >>>>
> >>>> On Fri, 10 Jul 2020, Thomas Adams wrote:
> >>>>
> >>>>> Hi,
> >>>>>
> >>>>> I'm using R in combination with GRASS GIS 7.8.3, attempting to read a
> >>>> GRASS
> >>>>> raster file into R with the rgrass7 interface. I have done this kind
> of
> >>>>> thing countless times previously without problems. It's quite
> possible
> >>>> I am
> >>>>> running into memory issues, but my Ubuntu 18.04 Linux computer has 32
> >>>> GB of
> >>>>> RAM.
> >>>>>
> >>>>
> >>>> I have not succeeded in reproducing this, I'm afraid. I created a
> >>>> location
> >>>> with cell counts to match, and ran r.out.bin first to check whether
> >>>> there
> >>>> were any issues writing the data to a temporary file. Then I ran the
> >>>> equivalent of your command (readRAST()), again without problems. I'm
> on
> >>>> a
> >>>> 16 GB PC, so the problem is puzzling. I'm curious about the free space
> >>>> on
> >>>> your
> >>>>
> >>>> /media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/
> >>>> teaiii-Leopard-WS
> >>>>
> >>>> directory. Did you check whether any output arrived there, since the
> >>>> error
> >>>> message is coming from r.out.bin?
> >>>>
> >>>> The error is on line 53 in raster/r.out.bin/main.c, when the system
> >>>> function fwrite() returns an error.
> >>>>
> >>>> Thanks for your patience.
> >>>>
> >>>> Roger
> >>>>
> >>>>
> >>>>> My GRASS raster file:
> >>>>>
> >>>>> Type of Map:  raster               Number of Categories: 0
> >>>>> Data Type:    CELL
> >>>>> Rows:         22663
> >>>>> Columns:      28794
> >>>>> Total Cells:  652558422
> >>>>> ~90m resolution
> >>>>>
> >>>>> Using...
> >>>>>
> >>>>> srtm <- readRAST("mozambique_srtm_patch",cat=FALSE)
> >>>>>
> >>>>> After quite some time, I get...
> >>>>>
> >>>>> Error in execGRASS("r.out.bin", flags = rOutBinFlags, input =
> >>>> vname[i],  :
> >>>>>  The command:
> >>>>> r.out.bin -b -i input=mozambique_srtm_patch
> >>>>>
> >>>>
> output=/media/teaiii/development/grass/greensboro_mercator/teaiii/.tmp/teaiii-Leopard-WS/mozambique_srtm_patch
> >>>>> bytes=4 null=-81
> >>>>> produced an error (1) during execution:
> >>>>> Creating BIL support files...
> >>>>> Exporting raster as integer values (bytes=4)
> >>>>> ERROR: Error writing data
> >>>>> In addition: Warning messages:
> >>>>> 1: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
> >>>>>  Discarded ellps unknown in CRS definition: +proj=merc +lat_ts=0
> >>>> +lon_0=0
> >>>>> +x_0=0 +y_0=0 +R=6378137 +units=m +no_defs
> >>>>> 2: In showSRID(uprojargs, format = "PROJ", multiline = "NO") :
> >>>>>  Discarded datum unknown in CRS definition
> >>>>>
> >>>>> Libraries loaded include: sp, rgrass7, rgdal, raster...
> >>>>>
> >>>>> Any thoughts?
> >>>>>
> >>>>> Best,
> >>>>> Tom
> >>>>>
> >>>>>
> >>>>
> >>>> --
> >>>> Roger Bivand
> >>>> Department of Economics, Norwegian School of Economics,
> >>>> Helleveien 30, N-5045 Bergen, Norway.
> >>>> voice: +47 55 95 93 55; e-mail: [hidden email]
> >>>> https://orcid.org/0000-0003-2392-6140
> >>>> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en
> >>>>
> >>>
> >>>
> >>> --
> >>> Thomas E Adams, III
> >>> 1724 Sage Lane
> >>> Blacksburg, VA 24060
> >>> [hidden email] (personal)
> >>> [hidden email] (work)
> >>>
> >>> 1 (513) 739-9512 (cell)
> >>>
> >>>
> >>>
> >>
> >> --
> >> Thomas E Adams, III
> >> 1724 Sage Lane
> >> Blacksburg, VA 24060
> >> [hidden email] (personal)
> >> [hidden email] (work)
> >>
> >> 1 (513) 739-9512 (cell)
> >>
> >>
> >
> >
>
> --
> Roger Bivand
> Department of Economics, Norwegian School of Economics,
> Helleveien 30, N-5045 Bergen, Norway.
> voice: +47 55 95 93 55; e-mail: [hidden email]
> https://orcid.org/0000-0003-2392-6140
> https://scholar.google.no/citations?user=AWeghB0AAAAJ&hl=en



--
Thomas E Adams, III
1724 Sage Lane
Blacksburg, VA 24060
[hidden email] (personal)
[hidden email] (work)

1 (513) 739-9512 (cell)

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