[GRASSLIST:9361] More v.in.ascii problems

[Patton, Eric]

I have a 945MB text file that contains x,y,z, and cats. I run the following:

 
v.in.ascii -zt input=SiteB_0.5m_backscatter.txt output=TEST_backscatter x=3
y=2 z=4 cat=1 fs=' '

And receive the following error:

Maximum input row length: 34
Maximum number of columns: 4
Minimum number of columns: 4
Building topology ...
Registering lines:       6 [main] v.in.ascii 3388 fixup_mmaps_after_fork:
WARNING: VirtualProtectEx to return to previous state in parent failed for
MAP_PRIVATE address 
0x5BF0000, Win32 error 87
 113738 [main] v.in.ascii 3388 fixup_mmaps_after_fork: WARNING:
VirtualProtect to copy protection to child failed forMAP_PRIVATE address
0x5BF0000, Win32 error 487
 212186 [main] v.in.ascii 3388 fixup_mmaps_after_fork: ReadProcessMemory
(2nd try) failed for MAP_PRIVATE address 0x5BF0000, Win32 error 487
C:\cygwin\usr\local\grass6.1.cvs\bin\v.in.ascii (3388): ***
recreate_mmaps_after_fork_failed
     76 [main] v.in.ascii 2884 fork_parent: child 3388 died waiting for dll
loading
45286676 [main] v.in.ascii 1364 fixup_mmaps_after_fork: WARNING:
VirtualProtect to copy protection to child failed forMAP_PRIVATE address
0x5BF0000, Win32 error 487
45347289 [main] v.in.ascii 1364 fixup_mmaps_after_fork: ReadProcessMemory
(2nd try) failed for MAP_PRIVATE address 0x5BF0000, Win32 error 487
C:\cygwin\usr\local\grass6.1.cvs\bin\v.in.ascii (1364): ***
recreate_mmaps_after_fork_failed
47040634 [main] v.in.ascii 2884 fork_parent: child 1364 died waiting for dll
loading
ERROR: G_realloc: out of memory

Would the -b flag mentioned by Roger  alleviate this problem? I'm working on
Cygwin/XP with 6.1cvs (Sept2). I do have a Ubuntu Breezy installation up and
running, but I can't use the latest 6.1 cvs on it until I get my tk and tcl
links sorted out.

~ Eric.

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
Eric Patton
 
Technologist, Geo-Spatial Data Services
Geological Survey of Canada (Atlantic)
Natural Resources Canada
Bedford Institute of Oceanography
Dartmouth, Nova Scotia, Canada B2Y 4A2
 
Postal address: P.O. Box 1006
Courier address: 1 Challenger Drive
 
Telephone: (902)426-7732
Facsimile:  (902)426-4104
E-mail:       epatton at NRCan.gc.ca
 

-----Original Message-----
From: owner-GRASSLIST at baylor.edu [mailto:owner-GRASSLIST at baylor.edu] On
Behalf Of Roger Bivand
Sent: Wednesday, December 07, 2005 10:04 AM
To: Hamish
Cc: jgomezdans at gmail.com; GRASSLIST at baylor.edu; grass5 at grass.itc.it
Subject: [GRASSLIST:9358] Re: v.in.ascii problems

On Thu, 8 Dec 2005, Hamish wrote:

> > There is an on-going discussion about this on the GRASS development 
> > list. >>From a simple test I ran last night, v.in.ascii -b (the -b 
> > flag is new in GRASS 6.1 CVS) does not build topology, and this 
> > removes one of the two humps in memory consumption. The other hump 
> > (> 200MB for a 1M point file with a single attribute) was associated 
> > with writing the dbf file (the file is 60MB), and is where things 
> > stick now. In addition, the -b flag leaves the vector data set at 
> > level 1 topology (absent), and almost all vector commands need level 2.
> > 
> > I do now know whether the use of a different database driver than 
> > the default would help. The dbf writing stage preceeds the topology 
> > building, so the two memory-intensive humps are separate, with 
> > topology being a little larger. Reading 1M points on a 1.5GHz P4 
> > with topology took about 7 minutes, without about half that time.
> 
> 
> Use the -z and -t flags to avoid making the table. (and the z= option) 
> If the input is just x,y,z data there is no need for a table.

For me in an x-y location my data with 1M points and -zbt now read in just
under a minute; lidaratm2.txt in effectively the same time (64 rather than
57 seconds, z here is double not int) and v.in.ascii stays at a respectable
3.3MB size. d.vect works, but as you say prints a warning.

> 
> At minimum, we need v.info, v.surf.rst, v.univar, v.out.ascii (points) 
> and some sort of subsampling module (ie s.cellstats port) working with 
> this data. d.vect works already (with a warning). maybe v.surf.idw too.
> 
> Probably not many more modules though? -- I think if Radim doesn't 
> want this to be common-place use of the vector model then it probably 
> shouldn't be. He knows it better than anyone.. So for now massive 
> point datasets need to be treated as a special case to the vector 
> model & only a work-around solution.
> 
> 
> e.g. with the sample LIDAR data (GRASS downloads page)
> 
> G61> v.in.ascii -zbt in=lidaratm2.txt out=lidaratm2 x=1 y=2 z=3 fs=,
> 
> The first 250k points take about 20 seconds to load.
> 
> 
> If I use the full million it gets stuck on the scanning step:
> 
> D3/3: row 374430 : 28 chars
> 
> Interesting, that line is the second value with elevation > 100.
> 
> changing the first z value to 500.054 it segfaults pretty quick:
> 
> D5/5: Vect_hist_write()
> D4/5: G_getl2: ->-75.622346,35.949693,500.054<-
> D3/5: row 1 : 28 chars
> D4/5: token: -75.622346
> D4/5: is_latlong north: -75.622346
> D4/5: row 1 col 0: '-75.622346' is_int = 0 is_double = 1
> D4/5: token: 35.949693
> D4/5: is_latlong north: 35.949693
> D4/5: row 1 col 1: '35.949693' is_int = 0 is_double = 1
> D4/5: row 1 col 2: '500.054' is_int = 0 is_double = 1
> D4/5: G_getl2: ->-75.629469,35.949693,11.962<-
> D3/5: row 2 : 27 chars
> D4/5: token: -75.629469
> D4/5: is_latlong north: -75.629469
> D4/5: row 2 col 0: 'H629469' is_int = 0 is_double = 0 Segmentation 
> fault
> 
> where is 'H629469' coming from?

I was also seeing seg-faults with my data in a long-lat location, so
switched to x-y (current CVS 6.1).

Roger

> 
> v.in.ascii/points.c
>  tmp_token is getting corrupted, cascades from there
> 
> int points_analyse (){
> ...
>     char **tokens;
> ...
>     tmp_token=(char *) G_malloc(256);
> ...
>     while (1) {
> ...
>         tokens = G_tokenize (buf, fs); ...
>         for ( i = 0; i < ntokens; i++ ) { ...
> [*]                 sprintf(tmp_token, "%f", northing);
> ...
> 		    /* replace current DMS token by decimal degree */
>                     tokens[i]=tmp_token;
> 
> BOOM. pointer abuse. (bug is new lat/lon scanning code, only in 
> 6.1CVS)
> 
> [*] and if northing column is longer than 256 without hitting the fs, 
>    buffer overflow??  add ,int maxlength, parameter to G_tokenize()?
>    or can %f never be more than 256 bytes long?
>     same %f effectively cutting down precision of lat/lon coords to 6 
>    spots after the decimal place? (be that pretty small on the ground)
> 
> 
> improvements come one bug at a time...
> 
> Hamish
> 

--
Roger Bivand
Economic Geography Section, Department of Economics, Norwegian School of
Economics and Business Administration, Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 95 43
e-mail: Roger.Bivand at nhh.no