Hi,
Yes, i do, and the offline gdb output that you sent is even more
evidence (since it shows again that the seg fault occurs before
antechamber proper has started).
scott
On Mon, Jan 29, 2018 at 08:35:45PM +0000, Yuan Hu wrote:
>
> Those libesets_pac.so is located in the antivirus software.
> I'm using ESET NOD32 Antivirus 4.
> Do you think that library file is the culprit?
> Thanks.
>
> $locate libesets_pac
> /opt/eset/esets/lib/libesets_pac.so
> /opt/eset/esets/lib32/libesets_pac.so
> /usr/lib/libesets_pac.so
> /usr/lib64/libesets_pac.so
>
> Best,
> Yuan
>
>
> -----Original Message-----
> From: Scott Brozell [mailto:sbrozell.rci.rutgers.edu]
> Sent: Monday, January 29, 2018 2:56 PM
> To: AMBER Mailing List
> Subject: EXT: Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
>
> This appears to not be a direct antechamber issue.
> I cannot find a machine with libesets_pac, which looks to play a critical role in the problem. Let's take this off list.
>
> scott
>
> On Fri, Jan 26, 2018 at 08:15:53PM +0000, Yuan Hu wrote:
> >
> > Yes. It turned out to be same.
> > See the gdb result below:
> >
> > # gdb /usr/local/software/amber16/bin/to_be_dispatched/antechamber
> >
> > GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-100.el7 Reading symbols
> > from /usr/local/software/amber16/bin/to_be_dispatched/antechamber...done.
> > (gdb) run
> >
> > Starting program:
> > /usr/local/software/amber16/bin/to_be_dispatched/antechamber
> > [Thread debugging using libthread_db enabled] Using host libthread_db
> > library "/lib64/libthread_db.so.1".
> >
> > Program received signal SIGSEGV, Segmentation fault.
> > _IO_fgets (buf=0x7fffffffd9f0 ".\333\377\377\377\177", n=160, fp=0x0) at iofgets.c:50
> > 50 _IO_acquire_lock (fp);
> > (gdb) where
> > #0 _IO_fgets (buf=0x7fffffffd9f0 ".\333\377\377\377\177", n=160,
> > fp=0x0) at iofgets.c:50
> > #1 0x000000000040fff7 in connect (connect_file=0x7 <Address 0x7 out of bounds>, atomnum=10924368, atom=0x6e, bondnum=0xa6b150, bond=0xa6b150, maxbond=0)
> > at rotate.c:901
> > #2 0x00007ffff7e953d1 in ?? () from /lib64/libesets_pac.so
> > #3 0x00007ffff7e894ce in ?? () from /lib64/libesets_pac.so
> > #4 0x00007ffff7e896cc in ?? () from /lib64/libesets_pac.so
> > #5 0x00007ffff7e8a77e in ?? () from /lib64/libesets_pac.so
> > #6 0x00007ffff7e8589a in ?? () from /lib64/libesets_pac.so
> > #7 0x00007ffff7e859c8 in ?? () from /lib64/libesets_pac.so
> > #8 0x00007ffff7eb0dc6 in ?? () from /lib64/libesets_pac.so
> > #9 0x0000000000000001 in ?? ()
> > #10 0x0000000000000001 in ?? ()
> > #11 0x00007fffffffe448 in ?? ()
> > #12 0x00007ffff7e8389b in ?? () from /lib64/libesets_pac.so
> > #13 0x00007fffffffe448 in ?? ()
> > #14 0x00007ffff7dea47f in call_init (env=0x7fffffffe458,
> > argv=0x7fffffffe3d0, argc=-134475776, l=0x7ffff7ff9658) at
> > dl-init.c:67
> > #15 _dl_init (main_map=0x7ffff7ffe150, argc=-134475776,
> > argv=0x7fffffffe3d0, env=0x7fffffffe458) at dl-init.c:131
> > #16 0x00007ffff7ddc1aa in _dl_start_user () from
> > /lib64/ld-linux-x86-64.so.2
> > #17 0x0000000000000001 in ?? ()
> > #18 0x00007fffffffe6ae in ?? ()
> > #19 0x0000000000000000 in ?? ()
> > (gdb)
> >
> >
> > Best,
> > Yuan
> >
> >
> > -----Original Message-----
> > From: Scott Brozell [mailto:sbrozell.rci.rutgers.edu]
> > Sent: Friday, January 26, 2018 3:09 PM
> > To: AMBER Mailing List
> > Subject: EXT: Re: [AMBER] Amber16 installation: Segmentation fault
> > (core dumped) error when execute antechamber
> >
> > [EXTERNAL]
> >
> > Hi,
> >
> > 1. So the teLeap and antechamber ldd's are the same on each machine.
> >
> > 2.
> > If you cannot find the core file then
> > gdb /usr/local/software/amber16/bin/to_be_dispatched/antechamber
> > gdb> run
> > gdb> where
> >
> > scott
> >
> > On Fri, Jan 26, 2018 at 07:50:44PM +0000, Yuan Hu wrote:
> > > 1. ldd -v bin/teLeap
> > >
> > > ===> Machine 1: antechamber has segmentation fault
> > >
> > > linux-vdso.so.1 => (0x00007ffcacaa1000)
> > > libesets_pac.so => /lib64/libesets_pac.so (0x00007f89744db000)
> > > libm.so.6 => /lib64/libm.so.6 (0x00007f89741d9000)
> > > libc.so.6 => /lib64/libc.so.6 (0x00007f8973e16000)
> > > libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f8973bfa000)
> > > libdl.so.2 => /lib64/libdl.so.2 (0x00007f89739f5000)
> > > /lib64/ld-linux-x86-64.so.2 (0x00007f8974658000)
> > >
> > > Version information:
> > > ./teLeap:
> > > libm.so.6 (GLIBC_2.2.5) => /lib64/libm.so.6
> > > libc.so.6 (GLIBC_2.3) => /lib64/libc.so.6
> > > libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
> > > libc.so.6 (GLIBC_2.7) => /lib64/libc.so.6
> > > libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
> > > /lib64/libesets_pac.so:
> > > libdl.so.2 (GLIBC_2.2.5) => /lib64/libdl.so.2
> > > ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
> > > libpthread.so.0 (GLIBC_2.2.5) => /lib64/libpthread.so.0
> > > libc.so.6 (GLIBC_2.3) => /lib64/libc.so.6
> > > libc.so.6 (GLIBC_2.3.3) => /lib64/libc.so.6
> > > libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
> > > /lib64/libm.so.6:
> > > ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
> > > libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
> > > libc.so.6 (GLIBC_PRIVATE) => /lib64/libc.so.6
> > > /lib64/libc.so.6:
> > > ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
> > > ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
> > > /lib64/libpthread.so.0:
> > > ld-linux-x86-64.so.2 (GLIBC_2.2.5) => /lib64/ld-linux-x86-64.so.2
> > > ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
> > > ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
> > > libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
> > > libc.so.6 (GLIBC_2.3.2) => /lib64/libc.so.6
> > > libc.so.6 (GLIBC_PRIVATE) => /lib64/libc.so.6
> > > libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
> > > /lib64/libdl.so.2:
> > > ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
> > > libc.so.6 (GLIBC_PRIVATE) => /lib64/libc.so.6
> > > libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
> > >
> > > ===> Machine 2: antechamber has no problem
> > >
> > > linux-vdso.so.1 => (0x00007ffd209fc000)
> > > libm.so.6 => /lib64/libm.so.6 (0x00007f0b4d3b2000)
> > > libc.so.6 => /lib64/libc.so.6 (0x00007f0b4cff0000)
> > > /lib64/ld-linux-x86-64.so.2 (0x00007f0b4d6cc000)
> > >
> > > Version information:
> > > ./teLeap:
> > > libm.so.6 (GLIBC_2.2.5) => /lib64/libm.so.6
> > > libc.so.6 (GLIBC_2.3) => /lib64/libc.so.6
> > > libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
> > > libc.so.6 (GLIBC_2.7) => /lib64/libc.so.6
> > > libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
> > > /lib64/libm.so.6:
> > > ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
> > > libc.so.6 (GLIBC_2.14) => /lib64/libc.so.6
> > > libc.so.6 (GLIBC_PRIVATE) => /lib64/libc.so.6
> > > libc.so.6 (GLIBC_2.2.5) => /lib64/libc.so.6
> > > /lib64/libc.so.6:
> > > ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
> > > ld-linux-x86-64.so.2 (GLIBC_PRIVATE) =>
> > > /lib64/ld-linux-x86-64.so.2
> > >
>
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Received on Mon Jan 29 2018 - 14:00:02 PST
