Details Ticket 4244


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Serial Number 4244
Subject segmentation library short read()s
Area grass6
Queue grass
Requestors hamish_nospam@yahoo.com,neteler@itc.it,werchowyna@epf.pl
Owner none
Status resolved
Last User Contact Mon Apr 17 18:48:42 2006 (2 yr ago)
Current Priority 30
Final Priority 70
Due No date assigned
Last Action Tue Apr 18 02:06:25 2006 (2 yr ago)
Created Fri Aug 12 13:13:59 2005 (3 yr ago)

Transaction History Ticket 4244


Fri, Aug 12 2005 13:13:59    Request created by guest (as #3514)  
Subject: r.surf.contour - dozens of warnings

Platform: GNU/Linux/i386
grass obtained from: CVS
grass binary for platform: Compiled from Sources
GRASS Version: 61 cvs 09.08.05

example:

GRASS 6.1.cvs (caves_utm33):~ > r.surf.contour input=melio_poz_clear_rast output=melio_poz_clear_ras
t_10_dem2
WARNING: segment_pagein: No such file or directory
WARNING: bseg_put(): could not read segment file at r:64 c:0
WARNING: segment_pagein: No such file or directory
WARNING: bseg_get(): could not read segment file at r:64 c:23
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
WARNING: segment_pagein: No such file or directory
WARNING: cseg_get(): could not read segment file
 100%

Although it completes, looks scarry. What is it?

Maciek
Fri, Aug 12 2005 15:52:17    Mail sent by glynn@gclements.plus.com (as #3514)  
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Date Fri, 12 Aug 2005 16:37:16 +0100
To Request Tracker <grass-bugs@intevation.de>
Cc grass5@grass.itc.it
Subject Re: [GRASS5] [bug #3514] (grass) r.surf.contour - dozens of warnings
In-Reply-To <20050812111359.6A05C101F1E@lists.intevation.de>
References <20050812111359.6A05C101F1E@lists.intevation.de>
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Request Tracker wrote:

> this bug's URL: http://intevation.de/rt/webrt?serial_num=3514

> Subject: r.surf.contour - dozens of warnings

> GRASS 6.1.cvs (caves_utm33):~ > r.surf.contour input=melio_poz_clear_rast output=melio_poz_clear_r
ast_10_dem2
> 
> WARNING: segment_pagein: No such file or directory

> Although it completes, looks scarry. What is it?

    if (read (SEG->fd, SEG->scb[cur].buf, SEG->size) != SEG->size)
    {
	G_warning ("segment_pagein: %s\n", strerror(errno));
	return -1;
    }

The warning occurs if read() returns a short count, i.e. if you try to
read beyond the end of the file, or an error.

The actual error message is bogus; read() only sets errno if it
returns a negative result, not if it returns a short count.

-- 
Glynn Clements <glynn@gclements.plus.com>


Sat, Aug 13 2005 11:43:31    Area changed to grass6.1 by msieczka (as #3514)  
Wed, Aug 31 2005 20:54:16    Area changed to grass6 by mneteler (as #3514)  
Fri, Oct 14 2005 15:34:43    Request created by guest (as #3741)  
Subject: r.cost WARNING: segment_pagein: No such file or directory

Platform: GNU/Linux/i386
grass obtained from: CVS
grass binary for platform: Compiled from Sources
GRASS Version: CVS

Hi,

the following problem appears when using r.cost:

r.cost in=allarea.one out=distance2water start_rast=streams percent_memory=100
WARNING: segment_pagein: No such file or directory
WARNING: segment_pagein: No such file or directory
Peak cost value: 64.485281

Interestingly, the result map is generated.
But the message is confusing.

Thanks

 Daniela
Wed, Dec 21 2005 11:15:20    Request 3741 merged into 3514 by hbowman (as #3741)  
Wed, Dec 21 2005 11:18:58    Comments added by hbowman (as #3514)  
This is in  lib/segment/pagein.c  for those playing along at home.


Hamish
Wed, Dec 21 2005 17:48:48    User changed to neteler@itc.it,werchowyna@epf.pl by mneteler (as #3514)  
Wed, Dec 21 2005 17:49:25    Comments added by mneteler (as #3514)  
the same happens in the new r.walk since it is a r.cost
derivate

Markus
Wed, Mar 1 2006 08:20:31    Mail sent by hamish_nospam@yahoo.com (as #3514)  
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From Hamish <hamish_nospam@yahoo.com>
To Glynn Clements <glynn@gclements.plus.com>
Cc grass-bugs@intevation.de, grass5@grass.itc.it
Subject Re: [GRASS5] [bug #3514] (grass) r.surf.contour - dozens of warnings
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> > this bug's URL: http://intevation.de/rt/webrt?serial_num=3514
> 
> > Subject: r.surf.contour - dozens of warnings
> 
> > GRASS 6.1.cvs (caves_utm33):~ > r.surf.contour
> > input=melio_poz_clear_rast output=melio_poz_clear_rast_10_dem2
> > 
> > WARNING: segment_pagein: No such file or directory
> 
> > Although it completes, looks scarry. What is it?
> 
>     if (read (SEG->fd, SEG->scb[cur].buf, SEG->size) != SEG->size)
>     {
> 	G_warning ("segment_pagein: %s\n", strerror(errno));
> 	return -1;
>     }
> 
> The warning occurs if read() returns a short count, i.e. if you try to
> read beyond the end of the file, or an error.
> 
> The actual error message is bogus; read() only sets errno if it
> returns a negative result, not if it returns a short count.


I've updated the warning in lib/segment/pagein.c, and added a level 2 
debug message stating how much was read & how much was asked for.

This shows that the error that pops up in r.cost (at least for me) is a 
short count:


G61> r.cost -vk in= out= start_points=`v.to.points -v coastline` \
       percent_memory=50

Null cells excluded from cost evaluation.
Source map is: Integer cell type
20800 rows, 12100 cols.
Creating some temporary files ...
Reading southland_regional_bound ...
D2/2: segment_pagein: read_result=524268  SEG->size=524288
WARNING: segment_pagein: short count during read()
 100%
Initializing output
D2/2: segment_pagein: read_result=524268  SEG->size=524288
WARNING: segment_pagein: short count during read()
 100%
WARNING: Adapted sites library used for vector points (module should be
         updated to GRASS 6 vector library).
[...]
Finding cost path
   7%
[...?]


Hamish


ps - r.cost can make lots of big temp files. We should catch ^C etc &
remove them. In about 10 minutes I just made 12gig worth....

"top" reports r.cost is using 1948mb ram for a region this big, with
seg=50% and 90k start points.  :/ going into swap makes me sad.
If I try seg=100% then G_malloc() gives an out of memory error right 
at the start, which is nice.


Wed, Apr 5 2006 05:26:55    Request created by hbowman  
Subject: segmentation library short read()s

Hi,

as many have noticed, sometime after 6.0 was released modules using the
segmentation library started to see read errors. After fixing the reported
error message in pagein.c we see that a short read is happening:
WARNING: segment_pagein: short count during read(), got 4076, expected 4096
WARNING: segment_pagein: short count during read(), got 1004, expected 1024
...

seems to be consistently short 20 bytes.

spearfish60 example:
================
GRASS 6.1-cvs
G6.1> r.cost in=elevation.10m out=cost_test.61 coordinate=599732,4920952
WARNING: segment_pagein: short count during read(), got 524268, expected
         524288
WARNING: segment_pagein: short count during read(), got 524268, expected
         524288
[done]

================
GRASS 6.0.2
G6.0.2> r.cost in=elevation.10m out=cost_test.602 coordinate=599732,4920952
Peak cost value: 645941.903859
[done]


Resultant maps differ slightly!!

G61> r.univar -g cost_test61 | grep sum
sum=86555328769.3534545898
G61> r.univar -g cost_test602 | grep sum
sum=86555572145.8440551758


also seen in r.surf.contour, r.watershed, r.walk, ...


two relevant changes to the segment lib since 6.0:
"Roberto Flor (ITC-irst): use lseek"
http://freegis.org/cgi-bin/viewcvs.cgi/grass6/lib/segment/format.c.diff?r1=2.0&r2=2.1
"added missing config.h for off_t (as suggested by Glynn; bug #3974)"
http://freegis.org/cgi-bin/viewcvs.cgi/grass6/lib/segment/seek.c.diff?r1=2.0&r2=2.1
could it be some site_t change somewhere else...?


Hamish
Wed, Apr 5 2006 05:39:40    Request 3514 merged into 4244 by hbowman (as #3514)  
Wed, Apr 5 2006 06:49:43    Mail sent by glynn@gclements.plus.com  
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Date Wed, 5 Apr 2006 05:49:36 +0100
To Request Tracker <grass-bugs@intevation.de>
Cc grass5@grass.itc.it
Subject Re: [GRASS5] [bug #4244] (grass) segmentation library short read()s
In-Reply-To <20060405032655.EA4341005AE@lists.intevation.de>
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Request Tracker wrote:

> this bug's URL: http://intevation.de/rt/webrt?serial_num=4244
> -------------------------------------------------------------------------
> 
> Subject: segmentation library short read()s
> 
> Hi,
> 
> as many have noticed, sometime after 6.0 was released modules using the
> segmentation library started to see read errors. After fixing the reported
> error message in pagein.c we see that a short read is happening:
> WARNING: segment_pagein: short count during read(), got 4076, expected 4096
> WARNING: segment_pagein: short count during read(), got 1004, expected 1024
> ...
> 
> seems to be consistently short 20 bytes.

It is caused by this change to zero_fill():

	RCS file: /grassrepository/grass6/lib/segment/format.c,v
	Working file: format.c

	----------------------------
	revision 2.1
	date: 2005/06/30 15:48:40;  author: markus;  state: Exp;  lines: +28 -4
	Roberto Flor (ITC-irst): use lseek
	----------------------------

Specifically, the line:

    if ( lseek(fd,nbytes-1,SEEK_SET) < 0 ) { 

should use SEEK_CUR rather than SEEK_SET, as it is supposed to be
writing nbytes from the current position, not from the start of the
file.

Note that there is a 20-byte header (5 "int"s) at the start of the
file, which would explain why the read() is always 20 bytes short
(zero_fill() is always called just after the header has been written).

I'm not sure why that header is there in the first place; segment
files aren't supposed to be shared across different processes, are
they?

-- 
Glynn Clements <glynn@gclements.plus.com>


Wed, Apr 5 2006 12:55:15    Mail sent by hamish_nospam@yahoo.com  
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Date Wed, 5 Apr 2006 22:54:46 +1200
From Hamish <hamish_nospam@yahoo.com>
To Glynn Clements <glynn@gclements.plus.com>
Cc grass-bugs@intevation.de, grass5@grass.itc.it
Subject Re: [GRASS5] [bug #4244] (grass) segmentation library short read()s
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> > this bug's URL: http://intevation.de/rt/webrt?serial_num=4244
> > -------------------------------------------------------------------
> > 
> > Subject: segmentation library short read()s
..
> > as many have noticed, sometime after 6.0 was released modules using
> > the segmentation library started to see read errors. After fixing
> > the reported error message in pagein.c we see that a short read is
> > happening: WARNING: segment_pagein: short count during read(), got
> > 4076, expected 4096 WARNING: segment_pagein: short count during
> > read(), got 1004, expected 1024 ...
> > 
> > seems to be consistently short 20 bytes.
> 
> It is caused by this change to zero_fill():
> 
> 	RCS file: /grassrepository/grass6/lib/segment/format.c,v
..
> 	revision 2.1
..
> Specifically, the line:
> 
>     if ( lseek(fd,nbytes-1,SEEK_SET) < 0 ) { 
> 
> should use SEEK_CUR rather than SEEK_SET, as it is supposed to be
> writing nbytes from the current position, not from the start of the
> file.

I can confirm that change gets rid of the warnings and the r.univar 
sum of values now matches the 6.0.2 value.


> Note that there is a 20-byte header (5 "int"s) at the start of the
> file, which would explain why the read() is always 20 bytes short
> (zero_fill() is always called just after the header has been written).
> 
> I'm not sure why that header is there in the first place; segment
> files aren't supposed to be shared across different processes, are
> they?

Don't know. I wouldn't have thought so.


Hamish


Mon, Apr 17 2006 09:34:49    Comments added by hbowman  
[reposted from the grass5 mailing list...]

From: Roberto Flor <flor itc it>
CC: Markus Neteler <neteler itc it>
Subject: Re: [GRASS5] [bug #4244] (grass) segmentation library short read()s
Date: Wed, 05 Apr 2006 16:45:33 +0200
To: grass5 grass itc it

Glynn Clements wrote:

>Request Tracker wrote:
>
>  
>
>Specifically, the line:
>
>    if ( lseek(fd,nbytes-1,SEEK_SET) < 0 ) { 
>
>should use SEEK_CUR rather than SEEK_SET, as it is supposed to be
>writing nbytes from the current position, not from the start of the
>file.
>
>Note that there is a 20-byte header (5 "int"s) at the start of the
>file, which would explain why the read() is always 20 bytes short
>(zero_fill() is always called just after the header has been written).
>
>I'm not sure why that header is there in the first place; segment
>files aren't supposed to be shared across different processes, are
>they?
>
>  
>
The patch is quite correct; the segment file was shorter of 20 bytes
when using the lseek zero_fill.
The header is required because the segment_format just create the file,
while the segment_init initialize it.
The typical segment library usage was:
    fd=open_for_writing
    segment_format(fd,..)
    close(fd)
    fd=open_for_reading_writing
    segment_init(fd,...)
 
and the parameters are shared through the header.
The lseek zero_fill  does not really allocate the file, it just  extend
the file size, so it's  possible  a write error  later, but it's a lot
faster than writing zero bytes to a file. The write error are handled
inside segment_pageout and segment_put_row with a G_warning and a -1
return code.


_______________________________________________
grass5 mailing list
grass5@grass.itc.it
http://grass.itc.it/mailman/listinfo/grass5

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To Roberto Flor <flor@itc.it>, glynn@gclements.plus.com
Cc grass5@grass.itc.it, grass-bugs@intevation.de
Subject Re: [GRASS5] [bug #4244] (grass) segmentation library short read()s
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> Request Tracker wrote:
> this bug's URL: http://intevation.de/rt/webrt?serial_num=4244
> ----------------------------------------------------------------
> 
> Subject: segmentation library short read()s
...

> >Specifically, the line:
> >
> >    if ( lseek(fd,nbytes-1,SEEK_SET) < 0 ) { 
> >
> >should use SEEK_CUR rather than SEEK_SET, as it is supposed to be
> >writing nbytes from the current position, not from the start of the
> >file.
> >
> >Note that there is a 20-byte header (5 "int"s) at the start of the
> >file, which would explain why the read() is always 20 bytes short
> >(zero_fill() is always called just after the header has been
> >written).
> >
> >I'm not sure why that header is there in the first place; segment
> >files aren't supposed to be shared across different processes, are
> >they?
>
> The patch is quite correct; the segment file was shorter of 20 bytes
> when using the lseek zero_fill.
> The header is required because the segment_format just create the
> file, while the segment_init initialize it.
> The typical segment library usage was:
>     fd=open_for_writing
>     segment_format(fd,..)
>     close(fd)
>     fd=open_for_reading_writing
>     segment_init(fd,...)
>  
> and the parameters are shared through the header.
> The lseek zero_fill  does not really allocate the file, it just 
> extend the file size, so it's  possible  a write error  later, but
> it's a lot faster than writing zero bytes to a file. The write error
> are handled inside segment_pageout and segment_put_row with a
> G_warning and a -1 return code.



.... so, should this change be committed to CVS or not?

> >    if ( lseek(fd,nbytes-1,SEEK_SET) < 0 ) { 
> >
> >should use SEEK_CUR rather than SEEK_SET

If not, I find it worring that r.cost output is not the same from GRASS
6.0 to GRASS 6.1.


thanks,
Hamish


Mon, Apr 17 2006 18:48:42    Mail sent by glynn@gclements.plus.com  
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To Hamish <hamish_nospam@yahoo.com>
Cc Roberto Flor <flor@itc.it>, grass5@grass.itc.it, grass-bugs@intevation.de
Subject Re: [GRASS5] [bug #4244] (grass) segmentation library short read()s
In-Reply-To <20060417194133.074af5f8.hamish_nospam@yahoo.com>
References <20060405032655.EA4341005AE@lists.intevation.de> <17459.19552.789687.746068@cerise.gclements.plus.com> <4433D80D.1020503@itc.it> <20060417194133.074af5f8.hamish_nospam@yahoo.com>
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Hamish wrote:

> > Request Tracker wrote:
> > this bug's URL: http://intevation.de/rt/webrt?serial_num=4244
> > ----------------------------------------------------------------
> > 
> > Subject: segmentation library short read()s
> ...
> 
> > >Specifically, the line:
> > >
> > >    if ( lseek(fd,nbytes-1,SEEK_SET) < 0 ) { 
> > >
> > >should use SEEK_CUR rather than SEEK_SET, as it is supposed to be
> > >writing nbytes from the current position, not from the start of the
> > >file.

[snip]

> .... so, should this change be committed to CVS or not?

Yes.

-- 
Glynn Clements <glynn@gclements.plus.com>


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Return-Path <hamish_nospam@yahoo.com>
Delivered-To grass-bugs@lists.intevation.de
Date Tue, 18 Apr 2006 11:52:16 +1200
From Hamish <hamish_nospam@yahoo.com>
To Glynn Clements via RT <grass-bugs@intevation.de>
Cc neteler@itc.it, werchowyna@epf.pl
Subject Re: [bug #4244] (grass) segmentation library short read()s
Message-Id <20060418115216.5fcf6f05.hamish_nospam@yahoo.com>
In-Reply-To <20060417164842.552961005B7@lists.intevation.de>
References <20060417164842.552961005B7@lists.intevation.de>
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> > > Request Tracker wrote:
> > > this bug's URL: http://intevation.de/rt/webrt?serial_num=4244
> > > ----------------------------------------------------------------
> > > 
> > > Subject: segmentation library short read()s
> > ...
> > 
> > > >Specifically, the line:
> > > >
> > > >    if ( lseek(fd,nbytes-1,SEEK_SET) < 0 ) { 
> > > >
> > > >should use SEEK_CUR rather than SEEK_SET, as it is supposed to be
> > > >writing nbytes from the current position, not from the start of the
> > > >file.
> 
> [snip]
> 
> > .... so, should this change be committed to CVS or not?
> 
> Yes.


thanks.

fix applied in CVS, closing bug.



Hamish


Tue, Apr 18 2006 02:06:25    Status changed to resolved by hbowman  
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