[gmx-developers] Re: memory problem?

[Michael Shirts]

Ignore previous email -- it's just crashing, apparently going off the
end of the tabulated function table.  I changed something else since a
previous strange memory error.  Back later if required. . .

On Thu, Nov 19, 2009 at 6:27 PM, Michael Shirts <mrshirts at gmail.com> wrote:
> I'm getting a weird crash that only shows up occasionally -- changing
> things like ifdefs can turn it on or off.  When I find a situation it
> occurs in,
> and I valgrid it, I'm getting something like this:
>
> ==58808== Invalid read of size 8
> ==58808==    at 0x27DAB7: nb_kernel332_ia32_sse2.nb332_unroll_loop (in
> /Users/mrshirts/work/gromacs_allv/git/gromacs_mrs/src//ke\
> rnel/mdrun)
> ==58808==    by 0x2A3C1B: do_nonbonded (in
> /Users/mrshirts/work/gromacs_allv/git/gromacs_mrs/src//kernel/mdrun)
> ==58808==    by 0x630E9: do_force_lowlevel (in
> /Users/mrshirts/work/gromacs_allv/git/gromacs_mrs/src//kernel/mdrun)
> ==58808==    by 0xBC1C2: do_force (in
> /Users/mrshirts/work/gromacs_allv/git/gromacs_mrs/src//kernel/mdrun)
> ==58808==    by 0x17102: do_md (in
> /Users/mrshirts/work/gromacs_allv/git/gromacs_mrs/src//kernel/mdrun)
> ==58808==    by 0x125FD: mdrunner (in
> /Users/mrshirts/work/gromacs_allv/git/gromacs_mrs/src//kernel/mdrun)
> ==58808==    by 0x1119C: mdrunner_threads (in
> /Users/mrshirts/work/gromacs_allv/git/gromacs_mrs/src//kernel/mdrun)
> ==58808==    by 0x1C163: main (in
> /Users/mrshirts/work/gromacs_allv/git/gromacs_mrs/src//kernel/mdrun)
> ==58808==  Address 0x16bba60 is 9,248 bytes inside a block of size 33,600 free'd
> ==58808==    at 0x563035: free (vg_replace_malloc.c:325)
> ==58808==    by 0x1441AD: save_free (in
> /Users/mrshirts/work/gromacs_allv/git/gromacs_mrs/src//kernel/mdrun)
> ==58808==    by 0xC774A: done_tabledata (in
> /Users/mrshirts/work/gromacs_allv/git/gromacs_mrs/src//kernel/mdrun)
> ==58808==    by 0xC9650: make_tables (in
> /Users/mrshirts/work/gromacs_allv/git/gromacs_mrs/src//kernel/mdrun)
> ==58808==    by 0x605D0: make_nbf_tables (in
> /Users/mrshirts/work/gromacs_allv/git/gromacs_mrs/src//kernel/mdrun)
> ==58808==    by 0x62329: init_forcerec (in
> /Users/mrshirts/work/gromacs_allv/git/gromacs_mrs/src//kernel/mdrun)
> ==58808==    by 0x11E48: mdrunner (in
> /Users/mrshirts/work/gromacs_allv/git/gromacs_mrs/src//kernel/mdrun)
> ==58808==    by 0x1119C: mdrunner_threads (in
> /Users/mrshirts/work/gromacs_allv/git/gromacs_mrs/src//kernel/mdrun)
> ==58808==    by 0x1C163: main (in
> /Users/mrshirts/work/gromacs_allv/git/gromacs_mrs/src//kernel/mdrun)
>
> I haven't touched any of these files in my edits, and no other
> valgrind errors appear before this.  Looking over the code, I don't
> see anything particularly wrong with done_tabledata, which frees three
> tabledata arrays that appear to always be allocated first.  Any ideas?
>
> Best,
> Michael
>