Hi,
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 - 12:00:02 PST
