[GRASS-dev] v.net.visibility memory leak? - was Re: [GRASS-user]
traveling salesman problem in air
Markus Metz
markus.metz.giswork at googlemail.com
Thu Apr 16 02:28:48 EDT 2009
Markus Neteler wrote:
> (moving to grass-dev)
>
> [Martina - we need to investigate a bit]
>
> On Wed, Apr 15, 2009 at 10:42 PM, Martina Schäfer
> <Martina.Schafer at ebc.uu.se> wrote:
>
>> Interesting discussion!! I've created the centroids but unfortunately, the
>> visibility network module repeatedly crashed (I am using GRASS 6.4 on Mac
>> OS, but tried on Windows XP as well) with the message "out of memory".
>>
>
> I have run valgrind to check for a memory leak (Linux 64 bit box):
> Some funky "uninitialised byte(s)" problem appears... (inline also a
> debug msg?):
>
Some leaks in the vector libs could disappear if
Vect_set_release_support() is called just before closing vectors in
v.net.visibility. Maybe the output of valgrind becomes a bit shorter and
more readable.
Markus M
>
> GRASS 6.5.svn (spearfish60): > CMD="v.net.visibility input=roads
> output=graph --o"
> GRASS 6.5.svn (spearfish60): > valgrind --tool=memcheck
> --leak-check=yes --show-reachable=yes $CMD --o
> ==3496== Memcheck, a memory error detector.
> ==3496== Copyright (C) 2002-2007, and GNU GPL'd, by Julian Seward et al.
> ==3496== Using LibVEX rev 1854, a library for dynamic binary translation.
> ==3496== Copyright (C) 2004-2007, and GNU GPL'd, by OpenWorks LLP.
> ==3496== Using valgrind-3.3.1, a dynamic binary instrumentation framework.
> ==3496== Copyright (C) 2000-2007, and GNU GPL'd, by Julian Seward et al.
> ==3496== For more details, rerun with: -v
> ==3496==
> ==3496== Syscall param write(buf) points to uninitialised byte(s)
> ==3496== at 0x7035D70: write (in /lib64/libc-2.8.so)
> ==3496== by 0x6FD6EE9: _IO_file_write (in /lib64/libc-2.8.so)
> ==3496== by 0x6FD7DF8: _IO_do_write (in /lib64/libc-2.8.so)
> ==3496== by 0x6FD89F6: _IO_switch_to_get_mode (in /lib64/libc-2.8.so)
> ==3496== by 0x6FD736F: _IO_file_seekoff (in /lib64/libc-2.8.so)
> ==3496== by 0x6FCCDA9: ftell (in /lib64/libc-2.8.so)
> ==3496== by 0x5D41F4D: dig_ftell (file.c:40)
> ==3496== by 0x5D42963: dig__write_head (head.c:56)
> ==3496== by 0x4E57FE4: V1_open_new_nat (open_nat.c:127)
> ==3496== by 0x4E57434: Vect_open_new (open.c:565)
> ==3496== by 0x402EAF: main (main.c:85)
> ==3496== Address 0x4028009 is not stack'd, malloc'd or (recently) free'd
> Building topology for vector map <graph>...
> Registering primitives...
> 330643 primitives registered
> 661286 vertices registered
> primitives: 402.000000
> Building areas...
> 100%
> 0 areas built
> 0 isles built
> areas: 1.000000
> Attaching islands...
> isles: 0.000000
> Attaching centroids...
> 100%
> centroids: 1.000000
> areas to cidx: 0.000000 <<--- should this be G_debug()?
> Number of nodes: 4491
> Number of primitives: 330643
> Number of points: 0
> Number of lines: 330643
> Number of boundaries: 0
> Number of centroids: 0
> Number of areas: 0
> Number of isles: 0
> ==3496==
> ==3496== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2 from 1)
> ==3496== malloc/free: in use at exit: 489,152,702 bytes in 2,067,875 blocks.
> ==3496== malloc/free: 4,047,776 allocs, 1,979,901 frees, 1,604,422,635
> bytes allocated.
> ==3496== For counts of detected errors, rerun with: -v
> ==3496== searching for pointers to 2,067,875 not-freed blocks.
> ==3496== checked 73,330,480 bytes.
> ==3496==
> ==3496==
> ==3496== 192 bytes in 8 blocks are possibly lost in loss record 1 of 21
> ==3496== at 0x4C2136E: malloc (vg_replace_malloc.c:207)
> ==3496== by 0x529603E: G__malloc (alloc.c:41)
> ==3496== by 0x4E3E213: Vect__new_cats_struct (cats.c:62)
> ==3496== by 0x4E3E1C4: Vect_new_cats_struct (cats.c:44)
> ==3496== by 0x404EB4: report (visibility.c:212)
> ==3496== by 0x404E5B: handle (visibility.c:198)
> ==3496== by 0x4050E7: construct_visibility (visibility.c:278)
> ==3496== by 0x4030EF: main (main.c:125)
> ==3496==
> ==3496==
> ==3496== 256 bytes in 8 blocks are still reachable in loss record 2 of 21
> ==3496== at 0x4C2136E: malloc (vg_replace_malloc.c:207)
> ==3496== by 0x4E4F2F2: Vect__new_line_struct (line.c:69)
> ==3496== by 0x4E4F2A8: Vect_new_line_struct (line.c:59)
> ==3496== by 0x404EAB: report (visibility.c:211)
> ==3496== by 0x404C70: handle (visibility.c:176)
> ==3496== by 0x4050E7: construct_visibility (visibility.c:278)
> ==3496== by 0x4030EF: main (main.c:125)
> ==3496==
> ==3496==
> ==3496== 480 bytes in 15 blocks are possibly lost in loss record 3 of 21
> ==3496== at 0x4C2136E: malloc (vg_replace_malloc.c:207)
> ==3496== by 0x4E4F2F2: Vect__new_line_struct (line.c:69)
> ==3496== by 0x4E4F2A8: Vect_new_line_struct (line.c:59)
> ==3496== by 0x404EAB: report (visibility.c:211)
> ==3496== by 0x404C70: handle (visibility.c:176)
> ==3496== by 0x4050E7: construct_visibility (visibility.c:278)
> ==3496== by 0x4030EF: main (main.c:125)
> ==3496==
> ==3496==
> ==3496== 480 bytes in 1 blocks are still reachable in loss record 4 of 21
> ==3496== at 0x4C2136E: malloc (vg_replace_malloc.c:207)
> ==3496== by 0x5296135: G__realloc (alloc.c:109)
> ==3496== by 0x4E46602: Vect_add_dblink (field.c:226)
> ==3496== by 0x4E47333: Vect_read_dblinks (field.c:645)
> ==3496== by 0x4E56D61: Vect__open_old (open.c:344)
> ==3496== by 0x4E57029: Vect_open_old (open.c:415)
> ==3496== by 0x402E5F: main (main.c:81)
> ==3496==
> ==3496==
> ==3496== 2,048 bytes in 4 blocks are definitely lost in loss record 5 of 21
> ==3496== at 0x4C2136E: malloc (vg_replace_malloc.c:207)
> ==3496== by 0x5F545D6: RTreeNewNode (node.c:49)
> ==3496== by 0x5F5364C: RTreeNewIndex (index.c:29)
> ==3496== by 0x5D4B522: dig_spidx_init (spindex.c:36)
> ==3496== by 0x5D43C94: dig_init_plus (plus.c:94)
> ==3496== by 0x4E564B2: Vect__open_old (open.c:146)
> ==3496== by 0x4E57029: Vect_open_old (open.c:415)
> ==3496== by 0x402E5F: main (main.c:81)
> ==3496==
> ==3496==
> ==3496== 4,800 bytes in 6 blocks are indirectly lost in loss record 6 of 21
> ==3496== at 0x4C1F144: calloc (vg_replace_malloc.c:397)
> ==3496== by 0x5D3FAF5: dig__frealloc (allocation.c:144)
> ==3496== by 0x5D3F991: dig__alloc_space (allocation.c:83)
> ==3496== by 0x5D4D3C9: dig_alloc_points (struct_alloc.c:239)
> ==3496== by 0x4E5B200: Vect__Read_line_nat (read_nat.c:309)
> ==3496== by 0x4E5AD24: V2_read_line_nat (read_nat.c:138)
> ==3496== by 0x4E5A9E3: Vect_read_line (read.c:106)
> ==3496== by 0x403403: count (main.c:200)
> ==3496== by 0x402FE6: main (main.c:108)
> ==3496==
> ==3496==
> ==3496== 33,700 bytes in 85 blocks are still reachable in loss record 7 of 21
> ==3496== at 0x4C1F144: calloc (vg_replace_malloc.c:397)
> ==3496== by 0x5D3F976: dig__alloc_space (allocation.c:81)
> ==3496== by 0x5D4983D: buf_alloc (portable.c:55)
> ==3496== by 0x5D49B0E: dig__fread_port_L (portable.c:150)
> ==3496== by 0x5D4872D: dig_Rd_Plus_head (plus_struct.c:614)
> ==3496== by 0x4E579D6: Vect_open_topo (open.c:722)
> ==3496== by 0x4E5693A: Vect__open_old (open.c:229)
> ==3496== by 0x4E57029: Vect_open_old (open.c:415)
> ==3496== by 0x402E5F: main (main.c:81)
> ==3496==
> ==3496==
> ==3496== 38,440 bytes in 1,356 blocks are still reachable in loss
> record 8 of 21
> ==3496== at 0x4C2136E: malloc (vg_replace_malloc.c:207)
> ==3496== by 0x4C214F7: realloc (vg_replace_malloc.c:429)
> ==3496== by 0x5D4D0A8: dig_alloc_nodes (struct_alloc.c:99)
> ==3496== by 0x5D44166: dig_load_plus (plus.c:290)
> ==3496== by 0x4E57AC5: Vect_open_topo (open.c:751)
> ==3496== by 0x4E5693A: Vect__open_old (open.c:229)
> ==3496== by 0x4E57029: Vect_open_old (open.c:415)
> ==3496== by 0x402E5F: main (main.c:81)
> ==3496==
> ==3496==
> ==3496== 40,008 bytes in 1 blocks are still reachable in loss record 9 of 21
> ==3496== at 0x4C214A1: realloc (vg_replace_malloc.c:429)
> ==3496== by 0x5D4D0A8: dig_alloc_nodes (struct_alloc.c:99)
> ==3496== by 0x5D46D50: dig_add_node (plus_node.c:116)
> ==3496== by 0x5D461D1: add_line (plus_line.c:55)
> ==3496== by 0x5D46379: dig_add_line (plus_line.c:114)
> ==3496== by 0x4E3CB9B: Vect_build_nat (build_nat.c:538)
> ==3496== by 0x4E3AD22: Vect_build_partial (build.c:134)
> ==3496== by 0x4E3AC15: Vect_build (build.c:55)
> ==3496== by 0x40314C: main (main.c:132)
> ==3496==
> ==3496==
> ==3496== 223,200 bytes in 558 blocks are possibly lost in loss record 10 of 21
> ==3496== at 0x4C1F144: calloc (vg_replace_malloc.c:397)
> ==3496== by 0x5D3F976: dig__alloc_space (allocation.c:81)
> ==3496== by 0x5D4D415: dig_alloc_points (struct_alloc.c:248)
> ==3496== by 0x4E4F3CA: Vect_copy_xyz_to_pnts (line.c:118)
> ==3496== by 0x404F16: report (visibility.c:219)
> ==3496== by 0x404C70: handle (visibility.c:176)
> ==3496== by 0x4050E7: construct_visibility (visibility.c:278)
> ==3496== by 0x4030EF: main (main.c:125)
> ==3496==
> ==3496==
> ==3496== 248,016 bytes in 5,167 blocks are still reachable in loss
> record 11 of 21
> ==3496== at 0x4C2136E: malloc (vg_replace_malloc.c:207)
> ==3496== by 0x5D4CF59: dig_alloc_node (struct_alloc.c:44)
> ==3496== by 0x5D46D93: dig_add_node (plus_node.c:123)
> ==3496== by 0x5D461D1: add_line (plus_line.c:55)
> ==3496== by 0x5D46379: dig_add_line (plus_line.c:114)
> ==3496== by 0x4E3CB9B: Vect_build_nat (build_nat.c:538)
> ==3496== by 0x4E3AD22: Vect_build_partial (build.c:134)
> ==3496== by 0x4E3AC15: Vect_build (build.c:55)
> ==3496== by 0x40314C: main (main.c:132)
> ==3496==
> ==3496==
> ==3496== 449,309 bytes in 66 blocks are still reachable in loss record
> 12 of 21
> ==3496== at 0x4C2136E: malloc (vg_replace_malloc.c:207)
> ==3496== by 0x529603E: G__malloc (alloc.c:41)
> ==3496== by 0x52CE929: G_store (store.c:36)
> ==3496== by 0x52C29D9: G_set_program_name (progrm_nme.c:52)
> ==3496== by 0x52AEAD2: G__gisinit (gisinit.c:51)
> ==3496== by 0x402CD7: main (main.c:42)
> ==3496==
> ==3496==
> ==3496== 2,645,144 bytes in 4,491 blocks are still reachable in loss
> record 13 of 21
> ==3496== at 0x4C214A1: realloc (vg_replace_malloc.c:429)
> ==3496== by 0x5D4CFF9: dig_node_alloc_line (struct_alloc.c:72)
> ==3496== by 0x5D46B28: dig_node_add_line (plus_node.c:56)
> ==3496== by 0x5D46079: add_line (plus_line.c:44)
> ==3496== by 0x5D46379: dig_add_line (plus_line.c:114)
> ==3496== by 0x4E3CB9B: Vect_build_nat (build_nat.c:538)
> ==3496== by 0x4E3AD22: Vect_build_partial (build.c:134)
> ==3496== by 0x4E3AC15: Vect_build (build.c:55)
> ==3496== by 0x40314C: main (main.c:132)
> ==3496==
> ==3496==
> ==3496== 2,645,144 bytes in 4,491 blocks are still reachable in loss
> record 14 of 21
> ==3496== at 0x4C214A1: realloc (vg_replace_malloc.c:429)
> ==3496== by 0x5D4D033: dig_node_alloc_line (struct_alloc.c:77)
> ==3496== by 0x5D46B28: dig_node_add_line (plus_node.c:56)
> ==3496== by 0x5D4622F: add_line (plus_line.c:64)
> ==3496== by 0x5D46379: dig_add_line (plus_line.c:114)
> ==3496== by 0x4E3CB9B: Vect_build_nat (build_nat.c:538)
> ==3496== by 0x4E3AD22: Vect_build_partial (build.c:134)
> ==3496== by 0x4E3AC15: Vect_build (build.c:55)
> ==3496== by 0x40314C: main (main.c:132)
> ==3496==
> ==3496==
> ==3496== 2,648,008 bytes in 1 blocks are still reachable in loss
> record 15 of 21
> ==3496== at 0x4C214A1: realloc (vg_replace_malloc.c:429)
> ==3496== by 0x5D4D15B: dig_alloc_lines (struct_alloc.c:133)
> ==3496== by 0x5D46344: dig_add_line (plus_line.c:110)
> ==3496== by 0x4E3CB9B: Vect_build_nat (build_nat.c:538)
> ==3496== by 0x4E3AD22: Vect_build_partial (build.c:134)
> ==3496== by 0x4E3AC15: Vect_build (build.c:55)
> ==3496== by 0x40314C: main (main.c:132)
> ==3496==
> ==3496==
> ==3496== 4,020,168 bytes in 3 blocks are still reachable in loss
> record 16 of 21
> ==3496== at 0x4C214A1: realloc (vg_replace_malloc.c:429)
> ==3496== by 0x5296148: G__realloc (alloc.c:111)
> ==3496== by 0x52A4EB2: set_env (env.c:156)
> ==3496== by 0x52A4C44: read_env (env.c:104)
> ==3496== by 0x52A54CE: G__getenv (env.c:317)
> ==3496== by 0x52A5410: G_getenv (env.c:271)
> ==3496== by 0x52B36A0: G_location (location.c:63)
> ==3496== by 0x52B36B8: G__location_path (location.c:78)
> ==3496== by 0x52B3644: G_location_path (location.c:41)
> ==3496== by 0x52AEB0B: G__gisinit (gisinit.c:57)
> ==3496== by 0x402CD7: main (main.c:42)
> ==3496==
> ==3496==
> ==3496== 7,937,917 (7,937,869 direct, 48 indirect) bytes in 330,646
> blocks are definitely lost in loss record 17 of 21
> ==3496== at 0x4C2136E: malloc (vg_replace_malloc.c:207)
> ==3496== by 0x529603E: G__malloc (alloc.c:41)
> ==3496== by 0x4E3E213: Vect__new_cats_struct (cats.c:62)
> ==3496== by 0x4E3E1C4: Vect_new_cats_struct (cats.c:44)
> ==3496== by 0x404EB4: report (visibility.c:212)
> ==3496== by 0x404B61: handle (visibility.c:164)
> ==3496== by 0x4050E7: construct_visibility (visibility.c:278)
> ==3496== by 0x4030EF: main (main.c:125)
> ==3496==
> ==3496==
> ==3496== 26,517,440 bytes in 331,468 blocks are still reachable in
> loss record 18 of 21
> ==3496== at 0x4C2136E: malloc (vg_replace_malloc.c:207)
> ==3496== by 0x5D4D0F9: dig_alloc_line (struct_alloc.c:114)
> ==3496== by 0x5D45F40: add_line (plus_line.c:27)
> ==3496== by 0x5D46379: dig_add_line (plus_line.c:114)
> ==3496== by 0x4E3CB9B: Vect_build_nat (build_nat.c:538)
> ==3496== by 0x4E3AD22: Vect_build_partial (build.c:134)
> ==3496== by 0x4E3AC15: Vect_build (build.c:55)
> ==3496== by 0x40314C: main (main.c:132)
> ==3496==
> ==3496==
> ==3496== 407,100,768 (10,579,968 direct, 396,520,800 indirect) bytes
> in 330,624 blocks are definitely lost in loss record 19 of 21
> ==3496== at 0x4C2136E: malloc (vg_replace_malloc.c:207)
> ==3496== by 0x4E4F2F2: Vect__new_line_struct (line.c:69)
> ==3496== by 0x4E4F2A8: Vect_new_line_struct (line.c:59)
> ==3496== by 0x404EAB: report (visibility.c:211)
> ==3496== by 0x404B61: handle (visibility.c:164)
> ==3496== by 0x4050E7: construct_visibility (visibility.c:278)
> ==3496== by 0x4030EF: main (main.c:125)
> ==3496==
> ==3496==
> ==3496== 34,601,984 bytes in 67,582 blocks are still reachable in loss
> record 20 of 21
> ==3496== at 0x4C2136E: malloc (vg_replace_malloc.c:207)
> ==3496== by 0x5F545D6: RTreeNewNode (node.c:49)
> ==3496== by 0x5F56AF6: RTreeSplitNode (split_q.c:313)
> ==3496== by 0x5F54E52: RTreeAddBranch (node.c:201)
> ==3496== by 0x5F53BA3: RTreeInsertRect2 (index.c:121)
> ==3496== by 0x5F5398A: RTreeInsertRect2 (index.c:102)
> ==3496== by 0x5F5398A: RTreeInsertRect2 (index.c:102)
> ==3496== by 0x5F5398A: RTreeInsertRect2 (index.c:102)
> ==3496== by 0x5F5398A: RTreeInsertRect2 (index.c:102)
> ==3496== by 0x5F5398A: RTreeInsertRect2 (index.c:102)
> ==3496== by 0x5F5398A: RTreeInsertRect2 (index.c:102)
> ==3496== by 0x5F53D81: RTreeInsertRect1 (index.c:162)
> ==3496==
> ==3496==
> ==3496== 396,516,048 bytes in 991,294 blocks are indirectly lost in
> loss record 21 of 21
> ==3496== at 0x4C1F144: calloc (vg_replace_malloc.c:397)
> ==3496== by 0x5D3F976: dig__alloc_space (allocation.c:81)
> ==3496== by 0x5D4D3C9: dig_alloc_points (struct_alloc.c:239)
> ==3496== by 0x4E4F3CA: Vect_copy_xyz_to_pnts (line.c:118)
> ==3496== by 0x404F16: report (visibility.c:219)
> ==3496== by 0x404C70: handle (visibility.c:176)
> ==3496== by 0x4050E7: construct_visibility (visibility.c:278)
> ==3496== by 0x4030EF: main (main.c:125)
> ==3496==
> ==3496== LEAK SUMMARY:
> ==3496== definitely lost: 18,519,885 bytes in 661,274 blocks.
> ==3496== indirectly lost: 396,520,848 bytes in 991,300 blocks.
> ==3496== possibly lost: 223,872 bytes in 581 blocks.
> ==3496== still reachable: 73,888,097 bytes in 414,720 blocks.
> ==3496== suppressed: 0 bytes in 0 blocks.
>
> Looks like some memory leak?
> E.g.,
> data_structures.c: stack = G_malloc(size * sizeof(struct Point));
>
> but there is no G_free(stack).
>
> In visibility.c I also see two malloc() calls instead of G_malloc().
>
> Markus
> _______________________________________________
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>
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