On 12/07/15 14:32, David van der Spoel wrote: > Hi, > > I compiled a fresh OB clone but get SEGV on a number of programs, > including babel. > % babel -ig98 decane-g4.log -osdf koko.sdf > Segmentation fault
Forget this for now, it may be an apple issue anyway as it does work on Linux contrary to what I stated earlier. > > and > > % valgrind !! > valgrind babel -ig98 decane-g4.log -osdf koko.sdf > ==27734== Memcheck, a memory error detector > ==27734== Copyright (C) 2002-2012, and GNU GPL'd, by Julian Seward et al. > ==27734== Using Valgrind-3.8.1 and LibVEX; rerun with -h for copyright info > ==27734== Command: babel -ig98 decane-g4.log -osdf koko.sdf > ==27734== > ==27734== Invalid write of size 1 > ==27734== at 0x3DF1C0E35A: _dl_signal_error (in /lib64/ld-2.12.so) > ==27734== by 0x3DF1C0E4D9: _dl_signal_cerror (in /lib64/ld-2.12.so) > ==27734== by 0x3DF1C0A319: _dl_lookup_symbol_x (in /lib64/ld-2.12.so) > ==27734== by 0x3DF1C0E03F: _dl_fixup (in /lib64/ld-2.12.so) > ==27734== by 0x3DF1C14804: _dl_runtime_resolve (in /lib64/ld-2.12.so) > ==27734== by 0x40A41A: main (babel.cpp:318) > ==27734== Address 0x7feff6a80 is not stack'd, malloc'd or (recently) free'd > ==27734== > ==27734== Invalid read of size 8 > ==27734== at 0x3DF1C1721D: __longjmp (in /lib64/ld-2.12.so) > ==27734== by 0x6163656400383966: ??? > ==27734== by 0x6F6C2E34672D656D: ??? > ==27734== by 0x6664736F2D0066: ??? > ==27734== by 0x6664732E6F6B6F6A: ??? > ==27734== by 0x70733D52455354FF: ??? > ==27734== by 0x4E474F4C006C656E: ??? > ==27734== by 0x656F70733D454D40: ??? > ==27734== by 0x2F3D454D4F48006B: ??? > ==27734== by 0x6F70732F656D6F67: ??? > ==27734== by 0x3D48544150006C64: ??? > ==27734== by 0x70732F656D6F682E: ??? > ==27734== Address 0x7feff6a88 is not stack'd, malloc'd or (recently) free'd > > > Happens on both Linux and OSX with gcc >= 4.8 > Clues? > -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------------------------------------------------------ Don't Limit Your Business. Reach for the Cloud. GigeNET's Cloud Solutions provide you with the tools and support that you need to offload your IT needs and focus on growing your business. Configured For All Businesses. Start Your Cloud Today. https://www.gigenetcloud.com/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
