[GRASS-dev] [GRASS GIS] #1214: r.li.edgedensity: segmentation fault

GRASS GRASS developer
1

#1214: r.li.edgedensity: segmentation fault
---------------------+------------------------------------------------------
Reporter: neteler | Owner: grass-dev@…
     Type: defect | Status: new
Priority: normal | Milestone: 6.4.1
Component: Raster | Version: svn-releasebranch64
Keywords: | Platform: Linux
      Cpu: x86-64 |
---------------------+------------------------------------------------------
Running r.li.edgedensity in 6.4.svn, we obtain a segmentation fault.
The input map corine_1_2000_nonull contains a ring-like area surrounded by
-1 cells and -1 in the center (if that matters):

{{{
(gdb) r map=corine_1_2000_nonull conf=corine_1_2000
output=corine_1_2000_edge
Starting program: /usr/local/grass-6.4.1svn/bin/r.li.edgedensity
map=corine_1_2000_nonull conf=corine_1_2000 output=corine_1_2000_edge
Detaching after fork from child process 30690.
Detaching after fork from child process 30691.
Detaching after fork from child process 30692.
Detaching after fork from child process 30693.
Detaching after fork from child process 30694.
Detaching after fork from child process 30695.
Detaching after fork from child process 30696.
Detaching after fork from child process 30697.
Detaching after fork from child process 30698.
Detaching after fork from child process 30699.

Program received signal SIGSEGV, Segmentation fault.
0x00002aaaaaf42655 in next_Area (parsed=1, l=0x604690, g=0x6046b0,
m=0x7fffffffadc0) at daemon.c:651
651 memcpy(&tmp, l->head->m, sizeof(msg));

(gdb) bt full
#0 0x00002aaaaaf42655 in next_Area (parsed=1, l=0x604690, g=0x6046b0,
m=0x7fffffffadc0) at daemon.c:651
         tmp = {type = 2, f = {f_a = {aid = 2, x = 0, y = 0, rl = 147, cl =
295}, f_ma = {aid = 2, x = 0,
               y = 0, rl = 147, cl = 295,
               mask = "corine_1_2000", '\000' <repeats 191 times>"\324,
.\364\252\252*", '\000' <repeats 14 times>,
"\001\000\000\000\300\255\377\377\377\177\000\000\000\000\000\000\006",
'\000' <repeats 14 times>}, f_d = {aid = 2, pid = 0, res =
3.1193338127189503e-312}, f_e = {aid = 2, pid = 0}, f_t = {pid = 2}}}
#1 0x00002aaaaaf40845 in calculateIndex (file=0x604250 "corine_1_2000",
f=0x401238 <edgedensity>,
     parameters=0x0, raster=0x604230 "corine_1_2000_nonull",
output=0x604270 "corine_1_2000_edge")
     at daemon.c:156
         pathSetup =
"/home/lucadelu/.r.li/history/corine_1_2000\000\000\000\000\000\000/grassdata/eu_laea/slovenia",
'\000' <repeats 77 times>, "Xڀh<", '\000' <repeats 11 times>"\250,
\331\363\252\252*\000\000h8\300i<\000\000\000'|\200h<", '\000' <repeats 67
times>, "\001", '\000' <repeats 23 times>, "\037a\200h<", '\000' <repeats
70 times>, "j<\000\000\000\000
\000j<\000\000\000\224\037\000j<\000\000\000\224\037\000j<", '\000'
<repeats 11 times>, "Xڀh<\000\000\000\000
j<\000\000\000\250\331\363\252\252*\000\000\363"...
         out =
"/home/lucadelu/.r.li/output/corine_1_2000_edge\000\000\033", '\000'
<repeats 11 times>"\377, \377\377\377\034\036\260\252\252*", '\000'
<repeats 946 times>"\300,
\314\377\377\377\177\000\000\266\070\260\252\252*\000\000\266\070\260\252\252*\000\000\a\000\000\000\000\000\000\000?5\204i<\000\000\000\020\000\000\000\060\000\000\000@\311\377\377\377\177\000\000\200\310\377\377\377\177\000\000\266\070\260\252\252*\000\000\a\000\000\000\000\000\000\000?5\204i<\000\000\000\b\000\000\000\000\000\000\000\260\314\377\377\377\177\000\000\020\000\000\000\060\000\000\000\200\311\377\377\377\177\000\000\300\310\377\377\377\177\000\000\035\036\260\252\252*\000\000\b\000\000\000\000\000\000\000?5\204i<\000\000\000\261\070\260\252\252*\000\000'\214\200h<\000\000\000\030\036\260\252\252*\000\000\330v\024\253\252*\000\000\006\000\000\000\000\000\000\000"...
         parsed = 1 '\001'
         reportChannelName = 0x604710
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.0"
         random_access_name = 0x3c68a1bbc0 ""
         history = {mapid = '\000' <repeats 79 times>, title = '\000'
<repeats 79 times>,
           mapset = '\000' <repeats 79 times>, creator = '\000' <repeats 79
times>,
           maptype = '\000' <repeats 79 times>, datsrc_1 = '\000' <repeats
79 times>,
           datsrc_2 = '\000' <repeats 79 times>, keywrd = '\000' <repeats
79 times>, edlinecnt = 0,
           edhist = {'\000' <repeats 79 times> <repeats 45 times>,
"\000\000\000\000\060\307\377\377\377\177\000\000\266\070\260\252\252*\000\000\266\070\260\252\252*\000\000\a\000\000\000\000\000\000\000?5\204i<",
'\000' <repeats 11 times>"\360,
\306\377\377\377\177\000\000\000\000\000\000\000\000\000\000p\307\377\377\377\177\000\000\035\036\260\252",
"\252*\000\000\035\036\260\252\252*\000\000\b\000\000\000\000\000\000\000?5\204i<\000\000\000\261\070\260\252\252*\000\000\060\307\377\377\377\177\000\000\000\000\000\000\000\000\000\000P\302\377\377\377\177",
'\000' <repeats 18 times>"\377, \377\377\377",
"\377\377\377\377\240\310\377\377\377\177\000\000\030\036\260\252\252*\000\000\200\307\377\377\377\177\000\000\000\000\000\000\001",
'\000' <repeats 27 times>"\377,
\377\377\377\377\377\377\377\030\036\260\252\252*\000\000\000\000\000",
             "\000\000\000\000\070\306\377\377\377\177\000\000
\000\000\000\001", '\000' <repeats 59 times>, " \000\000", '\000' <repeats
15 times>, "s", '\000' <repeats 60 times>, "\022\000\000"}}
         g = 0x6046b0
         receiveChannel = 15
         res = 16
         child = {{pid = 30690, pipe = 0x604750
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.1",
             channel = 5}, {pid = 30691,
             pipe = 0x604790
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.2", channel = 6}, {
             pid = 30692, pipe = 0x6047d0
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.3",
             channel = 7}, {pid = 30693,
             pipe = 0x604810
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.4", channel = 8}, {
             pid = 30694, pipe = 0x604850
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.5",
             channel = 9}, {pid = 30695,
             pipe = 0x604890
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.6", channel = 10}, {
             pid = 30696, pipe = 0x6048d0
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.7",
             channel = 11}, {pid = 30697,
             pipe = 0x604910
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.8", channel = 12}, {
             pid = 30698, pipe = 0x604950
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.9",
             channel = 13}, {pid = 30699,
             pipe = 0x604990
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.10", channel = 14}}
         i = 2
         mypid = 30687
         doneDir = -1
         withoutJob = 32767
         mv_fd = 1753295058
         random_access = 60
         l = 0x604690
         m = {type = 2, f = {f_a = {aid = 2, x = 0, y = 0, rl = 147, cl =
295}, f_ma = {aid = 2, x = 0,
               y = 0, rl = 147, cl = 295, mask = "corine_1_2000", '\000'
<repeats 242 times>}, f_d = {
               aid = 2, pid = 0, res = 3.1193338127189503e-312}, f_e = {aid
= 2, pid = 0}, f_t = {
               pid = 2}}}
         doneJob = {type = 0, f = {f_a = {aid = 0, x = 0, y = 0, rl = 0, cl
= 0}, f_ma = {aid = 0, x = 0,
               y = 0, rl = 0, cl = 0, mask = '\000' <repeats 255 times>},
f_d = {aid = 0, pid = 0,
               res = 0}, f_e = {aid = 0, pid = 0}, f_t = {pid = 0}}}
         testpath = "/home/lucadelu/.r.li/history/", '\000' <repeats 4066
times>
#2 0x0000000000401236 in main (argc=4, argv=0x7fffffffe3c8) at
edgedensity.c:72
         raster = 0x2aaaaad14ee0
         conf = 0x604090
         output = 0x604150
         class = 0x604470
         module = 0x2aaaaad14f80
         par = 0x0
(gdb)
}}}

Any ideas what's wrong in raster/r.li/r.li.daemon/daemon.c ?

Markus

--
Ticket URL: <http://trac.osgeo.org/grass/ticket/1214&gt;
GRASS GIS <http://grass.osgeo.org>

2

Hi,

does anyone have an idea why memcpy() fails below?

thanks
Markus

On Thu, Nov 11, 2010 at 9:21 AM, GRASS GIS <trac@osgeo.org> wrote:

#1214: r.li.edgedensity: segmentation fault
---------------------+------------------------------------------------------
Reporter: neteler | Owner: grass-dev@…
Type: defect | Status: new
Priority: normal | Milestone: 6.4.1
Component: Raster | Version: svn-releasebranch64
Keywords: | Platform: Linux
Cpu: x86-64 |
---------------------+------------------------------------------------------
Running r.li.edgedensity in 6.4.svn, we obtain a segmentation fault.
The input map corine_1_2000_nonull contains a ring-like area surrounded by
-1 cells and -1 in the center (if that matters):

{{{
(gdb) r map=corine_1_2000_nonull conf=corine_1_2000
output=corine_1_2000_edge
Starting program: /usr/local/grass-6.4.1svn/bin/r.li.edgedensity
map=corine_1_2000_nonull conf=corine_1_2000 output=corine_1_2000_edge
Detaching after fork from child process 30690.
Detaching after fork from child process 30691.
Detaching after fork from child process 30692.
Detaching after fork from child process 30693.
Detaching after fork from child process 30694.
Detaching after fork from child process 30695.
Detaching after fork from child process 30696.
Detaching after fork from child process 30697.
Detaching after fork from child process 30698.
Detaching after fork from child process 30699.

Program received signal SIGSEGV, Segmentation fault.
0x00002aaaaaf42655 in next_Area (parsed=1, l=0x604690, g=0x6046b0,
m=0x7fffffffadc0) at daemon.c:651
651 memcpy(&tmp, l->head->m, sizeof(msg));

(gdb) bt full
#0 0x00002aaaaaf42655 in next_Area (parsed=1, l=0x604690, g=0x6046b0,
m=0x7fffffffadc0) at daemon.c:651
tmp = {type = 2, f = {f_a = {aid = 2, x = 0, y = 0, rl = 147, cl =
295}, f_ma = {aid = 2, x = 0,
y = 0, rl = 147, cl = 295,
mask = "corine_1_2000", '\000' <repeats 191 times>"\324,
.\364\252\252*", '\000' <repeats 14 times>,
"\001\000\000\000\300\255\377\377\377\177\000\000\000\000\000\000\006",
'\000' <repeats 14 times>}, f_d = {aid = 2, pid = 0, res =
3.1193338127189503e-312}, f_e = {aid = 2, pid = 0}, f_t = {pid = 2}}}
#1 0x00002aaaaaf40845 in calculateIndex (file=0x604250 "corine_1_2000",
f=0x401238 <edgedensity>,
parameters=0x0, raster=0x604230 "corine_1_2000_nonull",
output=0x604270 "corine_1_2000_edge")
at daemon.c:156
pathSetup =
"/home/lucadelu/.r.li/history/corine_1_2000\000\000\000\000\000\000/grassdata/eu_laea/slovenia",
'\000' <repeats 77 times>, "Xڀh<", '\000' <repeats 11 times>"\250,
\331\363\252\252*\000\000h8\300i<\000\000\000'|\200h<", '\000' <repeats 67
times>, "\001", '\000' <repeats 23 times>, "\037a\200h<", '\000' <repeats
70 times>, "j<\000\000\000\000
\000j<\000\000\000\224\037\000j<\000\000\000\224\037\000j<", '\000'
<repeats 11 times>, "Xڀh<\000\000\000\000
j<\000\000\000\250\331\363\252\252*\000\000\363"...
out =
"/home/lucadelu/.r.li/output/corine_1_2000_edge\000\000\033", '\000'
<repeats 11 times>"\377, \377\377\377\034\036\260\252\252*", '\000'
<repeats 946 times>"\300,
\314\377\377\377\177\000\000\266\070\260\252\252*\000\000\266\070\260\252\252*\000\000\a\000\000\000\000\000\000\000?5\204i<\000\000\000\020\000\000\000\060\000\000\000@\311\377\377\377\177\000\000\200\310\377\377\377\177\000\000\266\070\260\252\252*\000\000\a\000\000\000\000\000\000\000?5\204i<\000\000\000\b\000\000\000\000\000\000\000\260\314\377\377\377\177\000\000\020\000\000\000\060\000\000\000\200\311\377\377\377\177\000\000\300\310\377\377\377\177\000\000\035\036\260\252\252*\000\000\b\000\000\000\000\000\000\000?5\204i<\000\000\000\261\070\260\252\252*\000\000'\214\200h<\000\000\000\030\036\260\252\252*\000\000\330v\024\253\252*\000\000\006\000\000\000\000\000\000\000"...
parsed = 1 '\001'
reportChannelName = 0x604710
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.0"
random_access_name = 0x3c68a1bbc0 ""
history = {mapid = '\000' <repeats 79 times>, title = '\000'
<repeats 79 times>,
mapset = '\000' <repeats 79 times>, creator = '\000' <repeats 79
times>,
maptype = '\000' <repeats 79 times>, datsrc_1 = '\000' <repeats
79 times>,
datsrc_2 = '\000' <repeats 79 times>, keywrd = '\000' <repeats
79 times>, edlinecnt = 0,
edhist = {'\000' <repeats 79 times> <repeats 45 times>,
"\000\000\000\000\060\307\377\377\377\177\000\000\266\070\260\252\252*\000\000\266\070\260\252\252*\000\000\a\000\000\000\000\000\000\000?5\204i<",
'\000' <repeats 11 times>"\360,
\306\377\377\377\177\000\000\000\000\000\000\000\000\000\000p\307\377\377\377\177\000\000\035\036\260\252",
"\252*\000\000\035\036\260\252\252*\000\000\b\000\000\000\000\000\000\000?5\204i<\000\000\000\261\070\260\252\252*\000\000\060\307\377\377\377\177\000\000\000\000\000\000\000\000\000\000P\302\377\377\377\177",
'\000' <repeats 18 times>"\377, \377\377\377",
"\377\377\377\377\240\310\377\377\377\177\000\000\030\036\260\252\252*\000\000\200\307\377\377\377\177\000\000\000\000\000\000\001",
'\000' <repeats 27 times>"\377,
\377\377\377\377\377\377\377\030\036\260\252\252*\000\000\000\000\000",
"\000\000\000\000\070\306\377\377\377\177\000\000
\000\000\000\001", '\000' <repeats 59 times>, " \000\000", '\000' <repeats
15 times>, "s", '\000' <repeats 60 times>, "\022\000\000"}}
g = 0x6046b0
receiveChannel = 15
res = 16
child = {{pid = 30690, pipe = 0x604750
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.1",
channel = 5}, {pid = 30691,
pipe = 0x604790
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.2", channel = 6}, {
pid = 30692, pipe = 0x6047d0
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.3",
channel = 7}, {pid = 30693,
pipe = 0x604810
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.4", channel = 8}, {
pid = 30694, pipe = 0x604850
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.5",
channel = 9}, {pid = 30695,
pipe = 0x604890
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.6", channel = 10}, {
pid = 30696, pipe = 0x6048d0
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.7",
channel = 11}, {pid = 30697,
pipe = 0x604910
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.8", channel = 12}, {
pid = 30698, pipe = 0x604950
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.9",
channel = 13}, {pid = 30699,
pipe = 0x604990
"/grassdata/eu_laea/slovenia/.tmp/blade06/30687.10", channel = 14}}
i = 2
mypid = 30687
doneDir = -1
withoutJob = 32767
mv_fd = 1753295058
random_access = 60
l = 0x604690
m = {type = 2, f = {f_a = {aid = 2, x = 0, y = 0, rl = 147, cl =
295}, f_ma = {aid = 2, x = 0,
y = 0, rl = 147, cl = 295, mask = "corine_1_2000", '\000'
<repeats 242 times>}, f_d = {
aid = 2, pid = 0, res = 3.1193338127189503e-312}, f_e = {aid
= 2, pid = 0}, f_t = {
pid = 2}}}
doneJob = {type = 0, f = {f_a = {aid = 0, x = 0, y = 0, rl = 0, cl
= 0}, f_ma = {aid = 0, x = 0,
y = 0, rl = 0, cl = 0, mask = '\000' <repeats 255 times>},
f_d = {aid = 0, pid = 0,
res = 0}, f_e = {aid = 0, pid = 0}, f_t = {pid = 0}}}
testpath = "/home/lucadelu/.r.li/history/", '\000' <repeats 4066
times>
#2 0x0000000000401236 in main (argc=4, argv=0x7fffffffe3c8) at
edgedensity.c:72
raster = 0x2aaaaad14ee0
conf = 0x604090
output = 0x604150
class = 0x604470
module = 0x2aaaaad14f80
par = 0x0
(gdb)
}}}

Any ideas what's wrong in raster/r.li/r.li.daemon/daemon.c ?

Markus

--
Ticket URL: <http://trac.osgeo.org/grass/ticket/1214&gt;
GRASS GIS <http://grass.osgeo.org>

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3

Markus Neteler wrote:

does anyone have an idea why memcpy() fails below?

> Program received signal SIGSEGV, Segmentation fault.
> 0x00002aaaaaf42655 in next_Area (parsed=1, l=0x604690, g=0x6046b0,
> m=0x7fffffffadc0) at daemon.c:651
> 651 memcpy(&tmp, l->head->m, sizeof(msg));

tmp is a local variable of type msg, so either l, l->head or
l->head->m are bogus. No idea which, although l itself appears sane.

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

4

#1214: r.li.edgedensity: segmentation fault
---------------------+------------------------------------------------------
Reporter: neteler | Owner: grass-dev@…
     Type: defect | Status: new
Priority: normal | Milestone: 6.4.1
Component: Raster | Version: svn-releasebranch64
Keywords: | Platform: Linux
      Cpu: x86-64 |
---------------------+------------------------------------------------------

Comment(by rashadkm):

related * Tickets: #2024.
Markus, Could you try the patch attached in the related ticket

--
Ticket URL: <http://trac.osgeo.org/grass/ticket/1214#comment:1&gt;
GRASS GIS <http://grass.osgeo.org>

5

#1214: r.li.edgedensity: segmentation fault
------------------------------+---------------------------------------------
Reporter: neteler | Owner: grass-dev@…
     Type: defect | Status: new
Priority: normal | Milestone: 6.4.4
Component: Raster | Version: svn-releasebranch64
Keywords: r.li.edgedensity | Platform: Linux
      Cpu: x86-64 |
------------------------------+---------------------------------------------
Changes (by neteler):

  * keywords: => r.li.edgedensity
  * milestone: 6.4.1 => 6.4.4

--
Ticket URL: <http://trac.osgeo.org/grass/ticket/1214#comment:2&gt;
GRASS GIS <http://grass.osgeo.org>

6

#1214: r.li.edgedensity: segmentation fault
------------------------------+---------------------------------------------
Reporter: neteler | Owner: grass-dev@…
     Type: defect | Status: new
Priority: normal | Milestone: 6.4.4
Component: Raster | Version: svn-releasebranch64
Keywords: r.li.edgedensity | Platform: Linux
      Cpu: x86-64 |
------------------------------+---------------------------------------------

Comment(by hamish):

Hi,

you might test in grass7 where the server/client stuff has been removed so
r.li.daemon is simpler. If that works and 6.x doesn't, it narrows down
where to look.

Also, to help with reproducibility it would be good if we could all test
with the same data and commands- see the r.li module help page examples or
the r.li/TODO which has a number of usage examples using the standard
sample datasets.

Hamish

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/1214#comment:3&gt;
GRASS GIS <http://grass.osgeo.org>

7

#1214: r.li.edgedensity: segmentation fault
------------------------------+---------------------------------------------
Reporter: neteler | Owner: grass-dev@…
     Type: defect | Status: new
Priority: normal | Milestone: 6.4.4
Component: Raster | Version: svn-releasebranch64
Keywords: r.li.edgedensity | Platform: Linux
      Cpu: x86-64 |
------------------------------+---------------------------------------------

Comment(by rashadkm):

Replying to [comment:3 hamish]:
> Hi,
>
> you might test in grass7 where the server/client stuff has been removed
so r.li.daemon is simpler. If that works and 6.x doesn't, it narrows down
where to look.
>
edegedensity and patchdensity fails for me in grass70 and works in grass65
and grass64
svn revision: 58968
location: nc_spm_08
mapset: PERMANENT

{{{
r.li.patchdensity map=geology conf=geology_mov output=pdens_out
r.li.edgedensity map=geology conf=geology_mov output=edens_out
}}}

geology_mov:
{{{
SAMPLINGFRAME 0|0|1|1
SAMPLEAREA -1|-1|0.03571428571428571|0.02631578947368421
MOVINGWINDOW
}}}

r.li.patchdensity map=lc96ras conf=lc96_overlay output=pdens_out_overlay
r.li.edgedensity map=lc96ras conf=lc96_overlay output=edens_out_overlay

lc96_overlay:
{{{
SAMPLINGFRAME 0|0|1|1
MASKEDOVERLAYAREA
rli_samp_btest_480|205983.75|205812.75|929030.5031|928916.5031
MASKEDOVERLAYAREA
rli_samp_btest_874|61716.75|61403.25|728333.5031|727963.0031
RASTERMAP lc96ras@PERMANENT
VECTORMAP btest@PERMANENT
}}}

btest created from:
{{{
v.extract input=boundary_county@PERMANENT output=btest random=3
}}}

> Also, to help with reproducibility it would be good if we could all test
with the same data and commands- see the r.li module help page examples or
the r.li/TODO which has a number of usage examples using the standard
sample datasets.
>
I am using geology map from spearfish60 dataset for moving window
configuration.
For vector overlay option i use the data lc96ras.img mentioned in bug
#2024 comment #4.

>
> Hamish

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/1214#comment:4&gt;
GRASS GIS <http://grass.osgeo.org>

8

#1214: r.li.edgedensity: segmentation fault
------------------------------+---------------------------------------------
Reporter: neteler | Owner: grass-dev@…
     Type: defect | Status: new
Priority: normal | Milestone: 6.4.4
Component: Raster | Version: svn-releasebranch64
Keywords: r.li.edgedensity | Platform: Linux
      Cpu: x86-64 |
------------------------------+---------------------------------------------

Comment(by hamish):

Replying to [comment:4 rashadkm]:
> edegedensity and patchdensity fails for me in grass70 and
> works in grass65 and grass64
> svn revision: 58968
> location: nc_spm_08
> mapset: PERMANENT
>
> {{{
> r.li.patchdensity map=geology conf=geology_mov output=pdens_out
> r.li.edgedensity map=geology conf=geology_mov output=edens_out
> }}}
>
> geology_mov:
> {{{
> SAMPLINGFRAME 0|0|1|1
> SAMPLEAREA -1|-1|0.03571428571428571|0.02631578947368421
> MOVINGWINDOW
> }}}

I'll start with this one, both fail for me in grass7 too.

r.li.edgedensity segfaults in Rast_get_cellhd():

{{{
(gdb) list
78 {
79 struct Cell_head hd;
80 int ris = -1;
81 double indice = 0;
82
83 Rast_get_cellhd(ad->raster, "", &hd);
84
85 switch (ad->data_type) {
86 case CELL_TYPE:
87 {
}}}

on the fifth pass into the function, although I'm not sure why, 'hd' is
defined only a few lines earlier and `ad->raster` seems ok and the same
setup as r.li.patchdensity. (weirdness generally makes me suspect the
stack getting smashed sometime earlier)

----
I can get r.li.patchdensity to work in grass7 if I comment out the
`G_free(sup);` at the very end of main.c, but then of course it leaks
memory for every row of raster data. I notice in `top` that while it's
running 5-10% of the CPU time is spent for the system: there's something
horribly inefficient going on internally.

I'd also note while visually similar the r.li.patchdensity raster output
is numerically different from G6.5's r.li.patchdensity run with the same
input files, so beware in trusting the results.

Again, the valgrind errors are probably a good place to start:

{{{
==15739==
==15739== Conditional jump or move depends on uninitialised value(s)
==15739== at 0x4E2FA8D: RLI_get_cell_raster_row (worker.c:256)
==15739== by 0x4010B0: patch_density (main.c:101)
==15739== by 0x4E2F763: worker_process (worker.c:179)
==15739== by 0x4E2CF2A: calculateIndex (daemon.c:133)
==15739== by 0x400EB4: main (main.c:54)
==15739==
==15739== Invalid read of size 4
==15739== at 0x401316: patch_density (main.c:153)
==15739== by 0x4E2F763: worker_process (worker.c:179)
==15739== by 0x4E2CF2A: calculateIndex (daemon.c:133)
==15739== by 0x400EB4: main (main.c:54)
==15739== Address 0x62e7464 is 4 bytes inside a block of size 2,004
free'd
==15739== at 0x4C240FD: free (vg_replace_malloc.c:366)
==15739== by 0x526F1A6: G_free (alloc.c:151)
==15739== by 0x4015E8: patch_density (main.c:205)
==15739== by 0x4E2F763: worker_process (worker.c:179)
==15739== by 0x4E2CF2A: calculateIndex (daemon.c:133)
==15739== by 0x400EB4: main (main.c:54)
==15739==
(many more)
...

Program received signal SIGABRT, Aborted.

(gdb) bt
#0 0x00007ffff71af1b5 in *__GI_raise (sig=<value optimized out>)
     at ../nptl/sysdeps/unix/sysv/linux/raise.c:64
#1 0x00007ffff71b1fc0 in *__GI_abort () at abort.c:92
#2 0x00007ffff71e55bb in __libc_message (do_abort=<value optimized out>,
     fmt=<value optimized out>) at
../sysdeps/unix/sysv/linux/libc_fatal.c:189
#3 0x00007ffff71eee16 in malloc_printerr (action=3,
     str=0x7ffff72a66f8 "free(): invalid next size (fast)", ptr=<value
optimized out>)
     at malloc.c:6267
#4 0x00007ffff71f3b8c in *__GI___libc_free (mem=<value optimized out>) at
malloc.c:3739
#5 0x00007ffff776e1a7 in G_free (buf=0x6167f0) at alloc.c:151
#6 0x00000000004015e9 in patch_density (fd=0, par=0x0, ad=0x602990,
result=0x7ffff7dde540)
     at main.c:205
#7 0x00007ffff7bdc764 in worker_process (ret=0x7fffffffb970,
m=0x7fffffffba90)
     at worker.c:179
#8 0x00007ffff7bd9f2b in calculateIndex (file=0x6026e0 "geology_mov",
     f=0x400eb7 <patch_density>, parameters=0x0, raster=0x6026c0
"geology_30m",
     output=0x602700 "pdens_out7") at daemon.c:133
#9 0x0000000000400eb5 in main (argc=4, argv=0x7fffffffdd78) at main.c:54

...

(gdb) frame 6
#6 0x00000000004015e9 in patch_density (fd=0, par=0x0, ad=0x602990,
result=0x7ffff7dde540)
     at main.c:205
205 G_free(sup);
(gdb) list
200 if (area != 0)
201 *result = (count / area) * 1000000;
202 else
203 *result = -1;
204
205 G_free(sup);
206
207 return RLI_OK;
208 }
}}}

?

Hamish

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/1214#comment:5&gt;
GRASS GIS <http://grass.osgeo.org>

9

#1214: r.li.edgedensity: segmentation fault
------------------------------+---------------------------------------------
Reporter: neteler | Owner: grass-dev@…
     Type: defect | Status: new
Priority: normal | Milestone: 6.4.4
Component: Raster | Version: svn-releasebranch64
Keywords: r.li.edgedensity | Platform: Linux
      Cpu: x86-64 |
------------------------------+---------------------------------------------

Comment(by mmetz):

Replying to [comment:4 rashadkm]:
> Replying to [comment:3 hamish]:
> > Hi,
> >
> > you might test in grass7 where the server/client stuff has been
removed so r.li.daemon is simpler. If that works and 6.x doesn't, it
narrows down where to look.
> >
> edegedensity and patchdensity fails for me in grass70 and works in
grass65 and grass64
> svn revision: 58968
> location: nc_spm_08
> mapset: PERMANENT
>
{{{
r.li.patchdensity map=geology conf=geology_mov output=pdens_out
r.li.edgedensity map=geology conf=geology_mov output=edens_out
}}}
>
> geology_mov:
{{{
SAMPLINGFRAME 0|0|1|1
SAMPLEAREA -1|-1|0.03571428571428571|0.02631578947368421
MOVINGWINDOW
}}}
>

r.li.patchdensity and r.li.edgedensity pass the test with trunk r59072.

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/1214#comment:6&gt;
GRASS GIS <http://grass.osgeo.org>

10

#1214: r.li.edgedensity: segmentation fault
------------------------------+---------------------------------------------
Reporter: neteler | Owner: grass-dev@…
     Type: defect | Status: new
Priority: normal | Milestone: 6.4.4
Component: Raster | Version: svn-releasebranch64
Keywords: r.li.edgedensity | Platform: Linux
      Cpu: x86-64 |
------------------------------+---------------------------------------------

Comment(by neteler):

What is our backport policy here?

--
Ticket URL: <http://trac.osgeo.org/grass/ticket/1214#comment:7&gt;
GRASS GIS <http://grass.osgeo.org>

11

#1214: r.li.edgedensity: segmentation fault
------------------------------+---------------------------------------------
Reporter: neteler | Owner: grass-dev@…
     Type: defect | Status: new
Priority: normal | Milestone: 6.4.4
Component: Raster | Version: svn-releasebranch64
Keywords: r.li.edgedensity | Platform: Linux
      Cpu: x86-64 |
------------------------------+---------------------------------------------

Comment(by mmetz):

Replying to [comment:7 neteler]:
> What is our backport policy here?

The r.li modules should be backported, or else the r.li modules should be
deactivated in G6 because they are broken.

Do we want to keep the parallelization in G6?

--
Ticket URL: <http://trac.osgeo.org/grass/ticket/1214#comment:8&gt;
GRASS GIS <http://grass.osgeo.org>

12

#1214: r.li.edgedensity: segmentation fault
------------------------------+---------------------------------------------
Reporter: neteler | Owner: grass-dev@…
     Type: defect | Status: new
Priority: normal | Milestone: 6.4.4
Component: Raster | Version: svn-releasebranch64
Keywords: r.li.edgedensity | Platform: Linux
      Cpu: x86-64 |
------------------------------+---------------------------------------------

Comment(by neteler):

Replying to [comment:8 mmetz]:
> Replying to [comment:7 neteler]:
> > What is our backport policy here?
>
> The r.li modules should be backported, or else the r.li modules should
be deactivated in G6 because they are broken.
>
> Do we want to keep the parallelization in G6?

Since probably only "brute-force" backporting is possible (i.e. replace
the
current G6 version with trunk and then merge back the libgis calls), we
will not be able to keep the parallelization in G6.

--
Ticket URL: <http://trac.osgeo.org/grass/ticket/1214#comment:9&gt;
GRASS GIS <http://grass.osgeo.org>

13

#1214: r.li.edgedensity: segmentation fault
------------------------------+---------------------------------------------
Reporter: neteler | Owner: grass-dev@…
     Type: defect | Status: new
Priority: normal | Milestone: 6.4.4
Component: Raster | Version: svn-releasebranch64
Keywords: r.li.edgedensity | Platform: Linux
      Cpu: x86-64 |
------------------------------+---------------------------------------------

Comment(by mmetz):

Replying to [comment:9 neteler]:
> Replying to [comment:8 mmetz]:
> > Replying to [comment:7 neteler]:
> > > What is our backport policy here?
> >
> > The r.li modules should be backported, or else the r.li modules should
be deactivated in G6 because they are broken.
> >
> > Do we want to keep the parallelization in G6?
>
> Since probably only "brute-force" backporting is possible (i.e. replace
the
> current G6 version with trunk and then merge back the libgis calls), we
> will not be able to keep the parallelization in G6.

For the actual modules, I agree that a brute-force backport is the easiest
solution. The daemon could be updated by just backporting the relevant
changes which were not that many. Essentially it is only the fixes
regarding the IO cache, the handling of the computational region and the
creation of the r.li-specific mask. That would allow for testing the
parallelization, preferably with a moving window configuration.

--
Ticket URL: <http://trac.osgeo.org/grass/ticket/1214#comment:10&gt;
GRASS GIS <http://grass.osgeo.org>

14

#1214: r.li.edgedensity: segmentation fault
------------------------------+---------------------------------------------
Reporter: neteler | Owner: grass-dev@…
     Type: defect | Status: new
Priority: normal | Milestone: 6.4.4
Component: Raster | Version: svn-releasebranch64
Keywords: r.li.edgedensity | Platform: All
      Cpu: x86-64 |
------------------------------+---------------------------------------------
Changes (by neteler):

  * platform: Linux => All

Comment:

Replying to [comment:10 mmetz]:
> Replying to [comment:9 neteler]:
> > Replying to [comment:8 mmetz]:
> > > Replying to [comment:7 neteler]:
> > > > What is our backport policy here?
> > >
> > > The r.li modules should be backported, or else the r.li modules
should be deactivated in G6 because they are broken.
> > >
> > > Do we want to keep the parallelization in G6?
> >
> > Since probably only "brute-force" backporting is possible (i.e.
replace the
> > current G6 version with trunk and then merge back the libgis calls),
we
> > will not be able to keep the parallelization in G6.
>
> For the actual modules, I agree that a brute-force backport is the
easiest solution.

I have done so in r59304 (G6.5.svn) and in r59305 (G6.4.svn).

Open issues: the modules r.li.dominance, r.li.pielou, r.li.renyi,
r.li.shannon,
r.li.simpson are not yet producing proper output. Since they appear to be
similar
among each other, there might be the same issue to be fixed in all.
Help needed.

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/1214#comment:11&gt;
GRASS GIS <http://grass.osgeo.org>

15

#1214: r.li.edgedensity: segmentation fault
------------------------------+---------------------------------------------
Reporter: neteler | Owner: grass-dev@…
     Type: defect | Status: new
Priority: normal | Milestone: 6.4.4
Component: Raster | Version: svn-releasebranch64
Keywords: r.li.edgedensity | Platform: All
      Cpu: x86-64 |
------------------------------+---------------------------------------------

Comment(by mmetz):

Replying to [comment:11 neteler]:
>
> Open issues: the modules r.li.dominance, r.li.pielou, r.li.renyi,
r.li.shannon,
> r.li.simpson are not yet producing proper output. Since they appear to
be similar
> among each other, there might be the same issue to be fixed in all.
> Help needed.

I have cleaned up the backport to 6.4 a bit in r59598, then tested with
the spearfish example described in the TODO, both moving window and whole
region. The results are identical between G64 and G71. Can you test again
and provide the example that produces incorrect results, if the results
are still incorrect?

--
Ticket URL: <http://trac.osgeo.org/grass/ticket/1214#comment:12&gt;
GRASS GIS <http://grass.osgeo.org>

16

#1214: r.li.edgedensity: segmentation fault
------------------------------+---------------------------------------------
Reporter: neteler | Owner: grass-dev@…
     Type: defect | Status: new
Priority: normal | Milestone: 6.4.4
Component: Raster | Version: svn-releasebranch64
Keywords: r.li.edgedensity | Platform: All
      Cpu: x86-64 |
------------------------------+---------------------------------------------

Comment(by neteler):

Replying to [comment:12 mmetz]:
> I have cleaned up the backport to 6.4 a bit in r59598

I needed to add r59743 in order to avoid odd error messages if the input
map is not there. Still I get

{{{
GRASS 6.4.4svn (spearfish60):~ > g.gisenv set=DEBUG=1
GRASS 6.4.4svn (spearfish60):~ > r.li.edgedensity map=geology
conf=movwindow7 output=edens_out
D1/1: r.li.daemon pathSetup: [/home/neteler/.r.li/history/movwindow7]
Illegal filename. Character <> not allowed.
Illegal filename. Character <> not allowed.
Illegal filename. Character <> not allowed.
...
}}}

--
Ticket URL: <http://trac.osgeo.org/grass/ticket/1214#comment:13&gt;
GRASS GIS <http://grass.osgeo.org>

17

#1214: r.li.edgedensity: segmentation fault
------------------------------+---------------------------------------------
Reporter: neteler | Owner: grass-dev@…
     Type: defect | Status: new
Priority: normal | Milestone: 6.4.4
Component: Raster | Version: svn-releasebranch64
Keywords: r.li.edgedensity | Platform: All
      Cpu: x86-64 |
------------------------------+---------------------------------------------

Comment(by neteler):

After "make distclean" it runs fine. I added two new test scripts:

  * raster/r.li/r.li.testing_nc_asc.sh
  * raster/r.li/r.li.testing_sp_mov.sh

Whole maplayer versus moving window. Both produce identical results
in GRASS 6 and 7, respectively.

I think the bug(s) have been solved and the ticket can be closed.

--
Ticket URL: <http://trac.osgeo.org/grass/ticket/1214#comment:14&gt;
GRASS GIS <http://grass.osgeo.org>

18

#1214: r.li.edgedensity: segmentation fault
----------------------+-----------------------------------------------------
  Reporter: neteler | Owner: grass-dev@…
      Type: defect | Status: closed
  Priority: normal | Milestone: 6.4.4
Component: Raster | Version: svn-releasebranch64
Resolution: fixed | Keywords: r.li.edgedensity
  Platform: All | Cpu: x86-64
----------------------+-----------------------------------------------------
Changes (by neteler):

  * status: new => closed
  * resolution: => fixed

--
Ticket URL: <http://trac.osgeo.org/grass/ticket/1214#comment:15&gt;
GRASS GIS <http://grass.osgeo.org>