Hi Ethan, Here are the contents of the valgrind log file after running the following command:
valgrind --tool=memcheck --leak-check=yes --num-callers=20 --log-file=valgrind.log /programs/coot-Linux-x86_64-centos-6-gtk2-python/bin/coot Doesn't mean much to me, but perhaps you or Paul might get some clues? Thanks, Scott ==13497== Memcheck, a memory error detector ==13497== Copyright (C) 2002-2010, and GNU GPL'd, by Julian Seward et al. ==13497== Using Valgrind-3.6.0 and LibVEX; rerun with -h for copyright info ==13497== Command: /programs/coot-Linux-x86_64-centos-6-gtk2-python/bin/coot ==13497== Parent PID: 12940 ==13497== ==13500== ==13500== HEAP SUMMARY: ==13500== in use at exit: 59,581 bytes in 1,782 blocks ==13500== total heap usage: 2,944 allocs, 1,162 frees, 113,746 bytes allocated ==13500== ==13500== LEAK SUMMARY: ==13500== definitely lost: 0 bytes in 0 blocks ==13500== indirectly lost: 0 bytes in 0 blocks ==13500== possibly lost: 0 bytes in 0 blocks ==13500== still reachable: 59,581 bytes in 1,782 blocks ==13500== suppressed: 0 bytes in 0 blocks ==13500== Reachable blocks (those to which a pointer was found) are not shown. ==13500== To see them, rerun with: --leak-check=full --show-reachable=yes ==13500== ==13500== For counts of detected and suppressed errors, rerun with: -v ==13500== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 6 from 6) ==13497== ==13497== HEAP SUMMARY: ==13497== in use at exit: 70,808 bytes in 1,810 blocks ==13497== total heap usage: 5,637 allocs, 3,827 frees, 228,367 bytes allocated ==13497== ==13497== 16 bytes in 1 blocks are definitely lost in loss record 125 of 469 ==13497== at 0x4C26FDE: malloc (vg_replace_malloc.c:236) ==13497== by 0x465E32: xmalloc (in /bin/bash) ==13497== by 0x42413D: ??? (in /bin/bash) ==13497== by 0x424EA8: yyparse (in /bin/bash) ==13497== by 0x41D2E9: parse_command (in /bin/bash) ==13497== by 0x46AB67: parse_string (in /bin/bash) ==13497== by 0x41E24C: xparse_dolparen (in /bin/bash) ==13497== by 0x44D8EC: ??? (in /bin/bash) ==13497== by 0x44859D: ??? (in /bin/bash) ==13497== by 0x44A2BB: ??? (in /bin/bash) ==13497== by 0x44A451: expand_string_assignment (in /bin/bash) ==13497== by 0x44538A: ??? (in /bin/bash) ==13497== by 0x44572E: ??? (in /bin/bash) ==13497== by 0x44A0F5: ??? (in /bin/bash) ==13497== by 0x42E9CE: ??? (in /bin/bash) ==13497== by 0x42FF42: execute_command_internal (in /bin/bash) ==13497== by 0x430BED: execute_command (in /bin/bash) ==13497== by 0x41D535: reader_loop (in /bin/bash) ==13497== by 0x41CCF8: main (in /bin/bash) ==13497== ==13497== LEAK SUMMARY: ==13497== definitely lost: 16 bytes in 1 blocks ==13497== indirectly lost: 0 bytes in 0 blocks ==13497== possibly lost: 0 bytes in 0 blocks ==13497== still reachable: 70,792 bytes in 1,809 blocks ==13497== suppressed: 0 bytes in 0 blocks ==13497== Reachable blocks (those to which a pointer was found) are not shown. ==13497== To see them, rerun with: --leak-check=full --show-reachable=yes ==13497== ==13497== For counts of detected and suppressed errors, rerun with: -v ==13497== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 6 from 6) On Aug 14, 2012, at 2:32 PM, Ethan Merritt wrote: > On Tuesday, August 14, 2012 01:06:46 pm you wrote: >> Hello, >> I just downloaded the latest coot (4322) and attempted to luanch on a new >> CentOS 6 machine. Coot was none too happy. >> >> Here is the output. >> >> I'm not sure how to turn on debugging or core dumps, but if that would be >> useful I can redo this. > > Try running the program under valgrind. > It will be very slow, but when it hits the problem point the valgrind log will > tell you, or more to the point - tell the developers, where in the program > the offending memory chunk was allocated. > > The command would be something like > valgrind --tool=memcheck --leak-check=yes --num-callers=20 > --log-file=valgrind.log /full/path/to/coot > > Note that you need to use the full path for the coot executable. > An alias will not work. > > > Ethan ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 sibyls.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 cell 510.206.4418 desk 510.495.2697 beamline 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
smime.p7s
Description: S/MIME cryptographic signature
