r.le.patch crashes with -c flag

[wilsonadam]

I am trying to run r.le.patch to create a map of separate 'patches' using the -c flag to drop the edges and only keep core areas of a certain size.

To recreate this:

g.region n=1 s=0 e=1 w=0 res=.01 ## Make some region
r.random.surface output=surface  ## create a raster to use as input
r.random input=surface n=10 raster_output=points ## create some random points
r.grow input=points radius=10 output=patch ## grow them to make 'patches'
r.le.patch -n map=patch sam=w co1=2 co2=c1 ## run r.le.patch with -n flag to identify the patches by number - it works fine
r.le.patch -c map=patch sam=w co1=2 co2=c1 ## run r.le.patch with -c flag to identify only 'core areas' - it crashes!

It segfaults with the error shown below. I am running the GRASS6.4.0RC5 checked out and compiled this morning on Fedora 11 2.6.30.9-90.fc11.x86_64

Any ideas? Am I doing something wrong or is this a bug? I've tried several settings for the co1 and c02 and it crashes with every combination I have tried.

Thanks for any help.

###########################################################

GRASS 6.4.0RC5 (CFR):/media/Data > r.le.patch -c map=patch sam=w co1=2 co2=c1  

PARAMETER CHOICES:
    MAP:      patch
    SAMPLE:      whole map        TRACING:  8 neighbor
    OUTPUT MAPS:
          interior
    CORE MEASURES:
          mean core size

R.LE.PATCH IS WORKING....;

*** glibc detected *** r.le.patch: double free or corruption (out): 0x0000000001c92be0 ***
======= Backtrace: =========
/lib64/libc.so.6[0x39e5e75a96]
r.le.patch(cell_clip+0x8fa)[0x417cea]
r.le.patch(cell_clip_drv+0x18c)[0x4180dc]
r.le.patch(patch_fore+0x98)[0x40c2d8]
r.le.patch(main+0x4fe)[0x40e61e]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x39e5e1ea2d]
r.le.patch[0x403109]
======= Memory map: ========
00400000-0041d000 r-xp 00000000 fd:00 341102                             /usr/local/grass-6.4.0RC5/bin/r.le.patch
0061d000-0061e000 rw-p 0001d000 fd:00 341102                             /usr/local/grass-6.4.0RC5/bin/r.le.patch
01c4c000-01caf000 rw-p 00000000 00:00 0                                  [heap]
39e5a00000-39e5a1f000 r-xp 00000000 fd:00 45132                          /lib64/ld-2.10.1.so
39e5c1e000-39e5c1f000 r--p 0001e000 fd:00 45132                          /lib64/ld-2.10.1.so
39e5c1f000-39e5c20000 rw-p 0001f000 fd:00 45132                          /lib64/ld-2.10.1.so
39e5e00000-39e5f64000 r-xp 00000000 fd:00 45133                          /lib64/libc-2.10.1.so
39e5f64000-39e6164000 ---p 00164000 fd:00 45133                          /lib64/libc-2.10.1.so
39e6164000-39e6168000 r--p 00164000 fd:00 45133                          /lib64/libc-2.10.1.so
39e6168000-39e6169000 rw-p 00168000 fd:00 45133                          /lib64/libc-2.10.1.so
39e6169000-39e616e000 rw-p 00000000 00:00 0
39e6200000-39e6282000 r-xp 00000000 fd:00 54274                          /lib64/libm-2.10.1.so
39e6282000-39e6482000 ---p 00082000 fd:00 54274                          /lib64/libm-2.10.1.so
39e6482000-39e6483000 r--p 00082000 fd:00 54274                          /lib64/libm-2.10.1.so
39e6483000-39e6484000 rw-p 00083000 fd:00 54274                          /lib64/libm-2.10.1.so
39e6600000-39e6602000 r-xp 00000000 fd:00 56013                          /lib64/libdl-2.10.1.so
39e6602000-39e6802000 ---p 00002000 fd:00 56013                          /lib64/libdl-2.10.1.so
39e6802000-39e6803000 r--p 00002000 fd:00 56013                          /lib64/libdl-2.10.1.so
39e6803000-39e6804000 rw-p 00003000 fd:00 56013                          /lib64/libdl-2.10.1.so
39e6a00000-39e6a15000 r-xp 00000000 fd:00 56006                          /lib64/libz.so.1.2.3
39e6a15000-39e6c14000 ---p 00015000 fd:00 56006                          /lib64/libz.so.1.2.3
39e6c14000-39e6c15000 rw-p 00014000 fd:00 56006                          /lib64/libz.so.1.2.3
39f0400000-39f0419000 r-xp 00000000 fd:00 116332                         /lib64/libgcc_s-4.4.1-20090729.so.1
39f0419000-39f0619000 ---p 00019000 fd:00 116332                         /lib64/libgcc_s-4.4.1-20090729.so.1
39f0619000-39f061a000 rw-p 00019000 fd:00 116332                         /lib64/libgcc_s-4.4.1-20090729.so.1
7f308a2da000-7f308f3ad000 r--p 00000000 fd:00 56067                      /usr/lib/locale/locale-archive
7f308f3ad000-7f308f3b0000 rw-p 00000000 00:00 0
7f308f3d2000-7f308f3da000 r-xp 00000000 fd:00 358068                     /usr/local/grass-6.4.0RC5/lib/libgrass_datetime.6.4.0RC5.so
7f308f3da000-7f308f5d9000 ---p 00008000 fd:00 358068                     /usr/local/grass-6.4.0RC5/lib/libgrass_datetime.6.4.0RC5.so
7f308f5d9000-7f308f5da000 rw-p 00007000 fd:00 358068                     /usr/local/grass-6.4.0RC5/lib/libgrass_datetime.6.4.0RC5.so
7f308f5da000-7f308f5db000 rw-p 00000000 00:00 0
7f308f5db000-7f308f62c000 r-xp 00000000 fd:00 358108                     /usr/local/grass-6.4.0RC5/lib/libgrass_gis.6.4.0RC5.so
7f308f62c000-7f308f82c000 ---p 00051000 fd:00 358108                     /usr/local/grass-6.4.0RC5/lib/libgrass_gis.6.4.0RC5.so
7f308f82c000-7f308f82e000 rw-p 00051000 fd:00 358108                     /usr/local/grass-6.4.0RC5/lib/libgrass_gis.6.4.0RC5.so
7f308f82e000-7f308f838000 rw-p 00000000 00:00 0
7fffcf185000-7fffcf19a000 rw-p 00000000 00:00 0                          [stack]
7fffcf1ee000-7fffcf1ef000 r-xp 0000000Aborted

It crashes with G_free() in trace.c line 339.

[neteler]

Here a backtrace:

GRASS 6.4.0svn (spearfish60):~ >  r.le.patch -c map=patch sam=w co1=2 co2=c1

PARAMETER CHOICES:
        MAP:      patch
        SAMPLE:   whole map     TRACING:  8 neighbor
        OUTPUT MAPS:
interior        
        CORE MEASURES: 
mean core size  

R.LE.PATCH IS WORKING....;

Aborted patch      10


GRASS 6.4.0svn (spearfish60):~ > gdb r.le.patch
GNU gdb 6.8-6mdv2009.1 (Mandriva Linux release 2009.1)
...
This GDB was configured as "x86_64-mandriva-linux-gnu"...  
(gdb) r -c map=patch sam=w co1=2 co2=c1  
Starting program: /home/neteler/grass64/dist.x86_64-unknown-linux-gnu/bin/r.le.patch -c map=patch sam=w co1=2 co2=c1

PARAMETER CHOICES:
        MAP:      patch
        SAMPLE:   whole map     TRACING:  8 neighbor
        OUTPUT MAPS:
interior        
        CORE MEASURES: 
mean core size  

R.LE.PATCH IS WORKING....;

Tracing patch      10
Program received signal SIGABRT, Aborted.
0x00007fe8a0f84a15 in raise () from /lib64/libc.so.6
(gdb) bt     
#0  0x00007fe8a0f84a15 in raise () from /lib64/libc.so.6
#1  0x00007fe8a0f86243 in abort () from /lib64/libc.so.6
#2  0x00007fe8a0fc59d0 in ?? () from /lib64/libc.so.6
#3  0x00007fe8a196b1fa in G_free (buf=0x249aae0) at alloc.c:129    
#4  0x0000000000417b49 in cell_clip_drv (col0=0, row0=0, ncols=100, nrows=100, value=0x0, index=0, radius=0)  
    at trace.c:339  
#5  0x000000000040d221 in whole_reg_driver () at driver.c:2816     
#6  0x0000000000403342 in patch_fore () at driver.c:115 
#7  0x000000000041014e in main (argc=6, argv=0x7fffe6d0f2d8) at main.c:197
(gdb) bt full
#0  0x00007fe8a0f84a15 in raise () from /lib64/libc.so.6
No symbol table info available.
#1  0x00007fe8a0f86243 in abort () from /lib64/libc.so.6
No symbol table info available.
#2  0x00007fe8a0fc59d0 in ?? () from /lib64/libc.so.6
No symbol table info available.
#3  0x00007fe8a196b1fa in G_free (buf=0x249aae0) at alloc.c:129    
No locals.   
#4  0x0000000000417b49 in cell_clip_drv (col0=0, row0=0, ncols=100, nrows=100, value=0x0, index=0, radius=0)  
    at trace.c:339  
        pat = (CELL **) 0x7fe8a197bc00
        pat_buf = (CELL *) 0x7fe8a1bc0a40
        cor_cell_buf = (CELL *) 0x24b2ab0
        cor_fcell_buf = (FCELL *) 0x7fffe6d0f180 
        buf = (DCELL **) 0x2470370 
        cor = (DCELL **) 0x249a790 
        cor_dcell_buf = (DCELL *) 0x7fe8a1ddf710 
        null_buf = (DCELL **) 0x2485580  
        i = 0
        j = 101  
        fd = 1   
        fe = 8   
        p = 6423704 
        infd = 7 
        centernull = 1         
        empty = 0
        hist_ok = 1 
        colr_ok = 1 
        cats_ok = 1 
        range_ok = 1
        mapset = 0x7fe8a1bc0a40 "neteler"        
        name = 0x24674a0 "patch"   
        list_head = (PATCH *) 0x0  
        hist = {mapid = "Wed Nov  4 20:31:52 2009", '\0' <repeats 55 times>, title = "patch", '\0' <repeats 74 times>,   
  mapset = "neteler", '\0' <repeats 72 times>, creator = "neteler", '\0' <repeats 72 times>,
  maptype = "raster", '\0' <repeats 73 times>, datsrc_1 = '\0' <repeats 79 times>, datsrc_2 = '\0' <repeats 79 times>,   
  keywrd = "generated by r.grow", '\0' <repeats 60 times>, edlinecnt = 1, edhist = { 
    "r.grow input=\"points\" output=\"patch\" radius=10 metric=\"euclidean\"", '\0' <repeats 14 times>,
    '\0' <repeats 79 times> <repeats 49 times>}} 
        cats = {ncats = 219, num = 255, title = 0x24ba700 "Random points on [surface in neteler]", fmt = 0x24ba8b0 "",   
  m1 = 0, a1 = 0, m2 = 0, a2 = 0, q = {truncate_only = 0, round_only = 0, defaultDRuleSet = 1685287777,
    defaultCRuleSet = 0, infiniteLeftSet = 0, infiniteRightSet = 0, cRangeSet = -65536, maxNofRules = 250, 
    nofRules = 219, defaultDMin = 2.7027177092469472e-82, defaultDMax = 6.9483966104968404e-310, defaultCMin = 0,        
    defaultCMax = 0, infiniteDLeft = 0, infiniteDRight = 3.914178569747262e+180, infiniteCLeft = 23, infiniteCRight = 0, 
    dMin = 1, dMax = 255, cMin = 0, cMax = 218, table = 0x24b4350, fp_lookup = {vals = 0x0, rules = 0x7fffe6d0df10,      
      nalloc = -422519216, active = 0, inf_dmin = 2.1290593012604334e-317, inf_dmax = 6.9533349326523867e-310,
      inf_min = 4206800, inf_max = 0}}, labels = 0x24b07d0, marks = 0x24b0fe0, nalloc = 256, last_marked_rule = -1}      
        newcats = {ncats = 0, num = 0, title = 0x24b00c0 "Random points on [surface in neteler]", fmt = 0x0, m1 = 0,     
  a1 = 0, m2 = 0, a2 = 0, q = {truncate_only = 0, round_only = 0, defaultDRuleSet = 38184240, defaultCRuleSet = 0,       
    infiniteLeftSet = 0, infiniteRightSet = 0, cRangeSet = -422519248, maxNofRules = 0, nofRules = 0, defaultDMin = 0,   
    defaultDMax = 6.9533349325994229e-310, defaultCMin = -422518352, defaultCMax = 32767,
    infiniteDLeft = -nan(0xfffffffffffff), infiniteDRight = 6.9533349326547583e-310, infiniteCLeft = -422518352,         
    infiniteCRight = 32767, dMin = 6.953334932613652e-310, dMax = 6.9483969725536792e-310, cMin = 0, cMax = 0,
    table = 0x0, fp_lookup = {vals = 0x7fffe6d0e180, rules = 0x7fe8a0fb9619, nalloc = -72515583, active = 0,  
      inf_dmin = 6.9533349326547583e-310, inf_dmax = 6.9533349326547583e-310, inf_min = -422518352, inf_max = 32767}},   
  labels = 0x0, marks = 0x7fffe6d0e1db, nalloc = 0, last_marked_rule = -1}
        stats = {node = 0x24b00f0, tlen = 10, N = 3, curp = 0, null_data_count = 8532, curoffset = -422518784}
        colr = {version = 0, shift = 0, invert = 0, is_float = 0, null_set = 0, null_red = 232 '\ufffd',    
  null_grn = 127 '\177', null_blu = 0 '\0', undef_set = 0, undef_red = 0 '\0', undef_grn = 0 '\0', undef_blu = 0 '\0',   
  fixed = {rules = 0x24bb7b0, n_rules = 1, lookup = {red = 0x1a19aa2a0 <Address 0x1a19aa2a0 out of bounds>,
      grn = 0x7fe8a19aa2a0 "MASK", blu = 0x246a530 "-3.461977 -3.461977 to -3.461977", set = 0x7fffe6d0ee20 "",          
      nalloc = -1583890387, active = 0}, fp_lookup = {vals = 0x0, rules = 0x7fe8a1bc0a40, nalloc = 0, active = 0},       
    min = 1, max = 255}, modular = {rules = 0x0, n_rules = 0, lookup = {red = 0x7fffe6d0df10 "",       
      grn = 0x7fffe6d0de50 "\200\ufffd\ufffd\ufffd\ufffd\177", blu = 0x0, set = 0x7fe8a19b101c "", nalloc = 1, active = 0}, fp_lookup = {    
      vals = 0x7fffe6d0d950, rules = 0xd, nalloc = 0, active = 0}, min = 0, max = -1}, cmin = 1, cmax = 255}
        range = {min = 76, max = 171, first_time = 0}
        fprange = {min = 2.1290593012604334e-317, max = 6.9483969595155832e-310, first_time = 0}
        quant = {truncate_only = -1583694900, round_only = 32744, defaultDRuleSet = -1583694895,
  defaultCRuleSet = 32744, infiniteLeftSet = -422519552, infiniteRightSet = 32767, cRangeSet = 38188368,
  maxNofRules = 0, nofRules = 38171648, defaultDMin = 1.8865940164224833e-316, defaultDMax = 6.9533349327978397e-310,
  defaultCMin = -1583818750, defaultCMax = 32744, infiniteDLeft = 6.9533349325962609e-310,
  infiniteDRight = 2.1219957904712067e-314, infiniteCLeft = 38188368, infiniteCRight = 0,
  dMin = 1.8859378972448062e-316, dMax = 6.9483969725914258e-310, cMin = -1583694895, cMax = 32744,
  table = 0x5002467400, fp_lookup = {vals = 0x246a880, rules = 0x7fffe6d0db60, nalloc = 4206800, active = 0,
    inf_dmin = 6.9533349328713566e-310, inf_dmax = 0, inf_min = 0, inf_max = 0}}
        data_type = 0
#5  0x000000000040d221 in whole_reg_driver () at driver.c:2816
        i = -422514224
        j = 32767
        regcnt = 0
        found = 38171664
        fr = 0
        nrows = 100
        ncols = 100
        ptrfirst = (REGLIST *) 0x7fe8a1bc0a40
        ptrthis = (REGLIST *) 0x24674a0
        ptrnew = (REGLIST *) 0xfefefefefefefeff
        row_buf = (CELL *) 0x2470370
#6  0x0000000000403342 in patch_fore () at driver.c:115
No locals.
#7  0x000000000041014e in main (argc=6, argv=0x7fffe6d0f2d8) at main.c:197
        module = (struct GModule *) 0x7fe8a1bc0f40

[neteler]

The crash persists in current 6.4.svn, it fails on G_free() in trace.c, line 765

source:grass/branches/releasebranch_6_4/raster/r.le/r.le.patch/trace.c#L765​

[mmetz]

Replying to neteler:

The crash persists in current 6.4.svn, it fails on G_free() in trace.c, line 765

source:grass/branches/releasebranch_6_4/raster/r.le/r.le.patch/trace.c#L765​

One problem is that memory is allocated for ncols but then ncols + 3 entries are accessed, causing memory corruption. Furthermore, there are various for (i = 1; i < nrows + 1; i++) which also exceed allocated memory. The r.le.* modules are deprecated and deactivated in trunk; it is recommended to use the r.li.* modules instead.

Markus M