[gmx-developers] uninitialized data

[hessb at mpip-mainz.mpg.de]

Hi,

Could you mail me the tpr file that gives this valgrind problem
and the one that gives the walls problem?

Berk

> Also I'm getting this from time to time..which seems very scary! Any
> ideas???
>
> ==25865== Use of uninitialised value of size 8
> ==25865==    at 0x5168C4: add_gbond (mshift.c:82)
> ==25865==    by 0x5169D6: mk_igraph (mshift.c:113)
> ==25865==    by 0x51761E: mk_graph_ilist (mshift.c:331)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x516831: add_gbond (mshift.c:76)
> ==25865==    by 0x5169B6: mk_igraph (mshift.c:112)
> ==25865==    by 0x51761E: mk_graph_ilist (mshift.c:331)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Use of uninitialised value of size 8
> ==25865==    at 0x516880: add_gbond (mshift.c:81)
> ==25865==    by 0x5169B6: mk_igraph (mshift.c:112)
> ==25865==    by 0x51761E: mk_graph_ilist (mshift.c:331)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Use of uninitialised value of size 8
> ==25865==    at 0x5168C4: add_gbond (mshift.c:82)
> ==25865==    by 0x5169B6: mk_igraph (mshift.c:112)
> ==25865==    by 0x51761E: mk_graph_ilist (mshift.c:331)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x516831: add_gbond (mshift.c:76)
> ==25865==    by 0x5169D6: mk_igraph (mshift.c:113)
> ==25865==    by 0x51761E: mk_graph_ilist (mshift.c:331)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Use of uninitialised value of size 8
> ==25865==    at 0x516880: add_gbond (mshift.c:81)
> ==25865==    by 0x5169D6: mk_igraph (mshift.c:113)
> ==25865==    by 0x51761E: mk_graph_ilist (mshift.c:331)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x51739A: determine_graph_parts (mshift.c:278)
> ==25865==    by 0x517635: mk_graph_ilist (mshift.c:336)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x5311F0: save_realloc (smalloc.c:164)
> ==25865==    by 0x51719F: compact_graph (mshift.c:248)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x65362CB: realloc (malloc.c:3542)
> ==25865==    by 0x53121E: save_realloc (smalloc.c:177)
> ==25865==    by 0x51719F: compact_graph (mshift.c:248)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x65362E6: realloc (malloc.c:3551)
> ==25865==    by 0x53121E: save_realloc (smalloc.c:177)
> ==25865==    by 0x51719F: compact_graph (mshift.c:248)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x6535B5B: _int_realloc (malloc.c:4635)
> ==25865==    by 0x6536410: realloc (malloc.c:3604)
> ==25865==    by 0x53121E: save_realloc (smalloc.c:177)
> ==25865==    by 0x51719F: compact_graph (mshift.c:248)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x6535B6E: _int_realloc (malloc.c:4644)
> ==25865==    by 0x6536410: realloc (malloc.c:3604)
> ==25865==    by 0x53121E: save_realloc (smalloc.c:177)
> ==25865==    by 0x51719F: compact_graph (mshift.c:248)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x6535BAA: _int_realloc (malloc.c:4653)
> ==25865==    by 0x6536410: realloc (malloc.c:3604)
> ==25865==    by 0x53121E: save_realloc (smalloc.c:177)
> ==25865==    by 0x51719F: compact_graph (mshift.c:248)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x6535D0A: _int_realloc (malloc.c:4745)
> ==25865==    by 0x6536410: realloc (malloc.c:3604)
> ==25865==    by 0x53121E: save_realloc (smalloc.c:177)
> ==25865==    by 0x51719F: compact_graph (mshift.c:248)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Use of uninitialised value of size 8
> ==25865==    at 0x6DD0D13: (within /lib/libc-2.8.90.so)
> ==25865==    by 0x6DD3F53: vfprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x6DDC007: fprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x51720E: compact_graph (mshift.c:253)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x6DD0D1D: (within /lib/libc-2.8.90.so)
> ==25865==    by 0x6DD3F53: vfprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x6DDC007: fprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x51720E: compact_graph (mshift.c:253)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x6DD3FD4: vfprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x6DDC007: fprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x51720E: compact_graph (mshift.c:253)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x6DD4729: vfprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x6DDC007: fprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x51720E: compact_graph (mshift.c:253)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x6DD322D: vfprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x6DDC007: fprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x51720E: compact_graph (mshift.c:253)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Use of uninitialised value of size 8
> ==25865==    at 0x6DD0D13: (within /lib/libc-2.8.90.so)
> ==25865==    by 0x6DD3F53: vfprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x6DDC007: fprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x517224: compact_graph (mshift.c:255)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x6DD0D1D: (within /lib/libc-2.8.90.so)
> ==25865==    by 0x6DD3F53: vfprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x6DDC007: fprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x517224: compact_graph (mshift.c:255)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x6DD3FD4: vfprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x6DDC007: fprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x517224: compact_graph (mshift.c:255)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x6DD4729: vfprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x6DDC007: fprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x517224: compact_graph (mshift.c:255)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x6DD322D: vfprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x6DDC007: fprintf (in /lib/libc-2.8.90.so)
> ==25865==    by 0x517224: compact_graph (mshift.c:255)
> ==25865==    by 0x5176BE: mk_graph_ilist (mshift.c:351)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x517744: mk_graph_ilist (mshift.c:361)
> ==25865==    by 0x517830: mk_graph (mshift.c:382)
> ==25865==    by 0x4275A5: do_md (md.c:672)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> starting mdrun 'Electrolyte on gold 111 surface in water'
> 5000 steps,     10.0 ps.
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x51847B: first_colour (mshift.c:561)
> ==25865==    by 0x5186CF: mk_mshift (mshift.c:634)
> ==25865==    by 0x4A769C: do_force (sim_util.c:476)
> ==25865==    by 0x42938E: do_md (md.c:1116)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x5183F3: mk_grey (mshift.c:515)
> ==25865==    by 0x51876A: mk_mshift (mshift.c:645)
> ==25865==    by 0x4A769C: do_force (sim_util.c:476)
> ==25865==    by 0x42938E: do_md (md.c:1116)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x51847B: first_colour (mshift.c:561)
> ==25865==    by 0x51865B: mk_mshift (mshift.c:619)
> ==25865==    by 0x4A769C: do_force (sim_util.c:476)
> ==25865==    by 0x42938E: do_md (md.c:1116)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x4C9222: do_walls (wall.c:148)
> ==25865==    by 0x46D428: do_force_lowlevel (force.c:1591)
> ==25865==    by 0x4A7D10: do_force (sim_util.c:562)
> ==25865==    by 0x42938E: do_md (md.c:1116)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ==25865==
> ==25865== Conditional jump or move depends on uninitialised value(s)
> ==25865==    at 0x4C923A: do_walls (wall.c:148)
> ==25865==    by 0x46D428: do_force_lowlevel (force.c:1591)
> ==25865==    by 0x4A7D10: do_force (sim_util.c:562)
> ==25865==    by 0x42938E: do_md (md.c:1116)
> ==25865==    by 0x4269FA: mdrunner (md.c:426)
> ==25865==    by 0x42C579: main (mdrun.c:492)
> ^C==25865==
> ==25865== ERROR SUMMARY: 36882 errors from 30 contexts (suppressed: 130
> from 2)
> ==25865== malloc/free: in use at exit: 0 bytes in 0 blocks.
> ==25865== malloc/free: 0 allocs, 0 frees, 0 bytes allocated.
> ==25865== For counts of detected errors, rerun with: -v
> ==25865== All heap blocks were freed -- no leaks are possible.
>
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