Re: [OpenBabel-Devel] git version of OB broken?
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.sehttp://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
Re: [OpenBabel-Devel] git version of OB broken?
On 15/07/15 19:29, Geoffrey Hutchison wrote: Forget this for now, it may be an apple issue anyway as it does work on Linux contrary to what I stated earlier. I'm using Mac / Clang and can't reproduce this. I know David Koes also develops on Mac. Did you run make install on Mac? Have you tried clang instead of gcc-4.8? -Geoff clang indeed solves the problem, thanks! -- 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.sehttp://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
Re: [OpenBabel-Devel] git version of OB broken?
Can you provide a test case? On 12 July 2015 at 13:32, David van der Spoel sp...@xray.bmc.uu.se 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 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.sehttp://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 -- 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
Re: [OpenBabel-Devel] git version of OB broken?
On 13/07/15 10:35, Noel O'Boyle wrote: Can you provide a test case? http://folding.bmc.uu.se/decane-g4.log.gz On 12 July 2015 at 13:32, David van der Spoel sp...@xray.bmc.uu.se 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 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.sehttp://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 -- 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.sehttp://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
Re: [OpenBabel-Devel] git version of OB broken?
It seems the error below was introduced by this commit according to git bisect commit d34579511061a09ac7ea873294fa85c3eaff875e Author: dkoes dk...@pitt.edu Date: Sun Jun 14 15:21:05 2015 -0400 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 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.sehttp://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
[OpenBabel-Devel] git version of OB broken?
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 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.sehttp://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
