Scott,
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
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<
http://www.gnu.org/software/gdb/bugs/>...
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
>
> 2. I didn't see any core* files dumped into the folder.
>
> $gdb /usr/local/software/amber16/bin/to_be_dispatched/antechamber
> core*
>
> GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-100.el7 Copyright (C)
> 2013 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later
> <http://gnu.org/licenses/gpl.html>
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law. Type "show copying"
> and "show warranty" for details.
> This GDB was configured as "x86_64-redhat-linux-gnu".
> For bug reporting instructions, please see:
> <http://www.gnu.org/software/gdb/bugs/>...
> Reading symbols from /usr/local/software/amber16/bin/to_be_dispatched/antechamber...done.
> /usr/local/software/amber16/bin/core*: No such file or directory.
> (gdb) where
> No stack.
> (gdb)
>
>
> Yuan
>
>
> -----Original Message-----
> From: Scott Brozell [mailto:sbrozell.rci.rutgers.edu]
> Sent: Friday, January 26, 2018 1:41 PM
> To: AMBER Mailing List
> Subject: EXT: Re: [AMBER] Amber16 installation: Segmentation fault
> (core dumped) error when execute antechamber
>
> [EXTERNAL]
>
> Hi,
>
> 1.
> There are a surprising number of differences. I do not see an ahh-haa one however. Using bin/teLeap instead of antechamber do you see similar differences between the two machines ?
>
> 2.
> Although this smells increasingly like an issue with your workstation, please try these steps which i shortsightedly omitted before.
> Note that core* denotes the core file dumped.
>
> gdb /usr/local/software/amber16/bin/to_be_dispatched/antechamber core*
> gdb> where
>
> scott
>
> On Fri, Jan 26, 2018 at 01:17:29PM +0000, Yuan Hu wrote:
> > 1. The ldd information is as follow:
> >
> > ===> Machine 1: antechamber has segmentation fault $ldd -v antechamber
> > linux-vdso.so.1 => (0x00007ffc0edbd000)
> > libesets_pac.so => /lib64/libesets_pac.so (0x00007f9a90816000)
> > libm.so.6 => /lib64/libm.so.6 (0x00007f9a90514000)
> > libc.so.6 => /lib64/libc.so.6 (0x00007f9a90151000)
> > libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f9a8ff35000)
> > libdl.so.2 => /lib64/libdl.so.2 (0x00007f9a8fd30000)
> > /lib64/ld-linux-x86-64.so.2 (0x00007f9a90993000)
> >
> > Version information:
> > ./antechamber:
> > 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_2.7) => /lib64/libc.so.6
> > libc.so.6 (GLIBC_2.14) => /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 $ldd -v antechamber
> > linux-vdso.so.1 => (0x00007ffd6ab25000)
> > libm.so.6 => /lib64/libm.so.6 (0x00007f475ee5c000)
> > libc.so.6 => /lib64/libc.so.6 (0x00007f475ea9a000)
> > /lib64/ld-linux-x86-64.so.2 (0x00007f475f176000)
> >
> > Version information:
> > ./antechamber:
> > 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_2.7) => /lib64/libc.so.6
> > libc.so.6 (GLIBC_2.14) => /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
> >
> >
> > 2. Run debug version of antechamber. Not working. See the on-screen output:
> >
> > [root.machine1 antechamber]# echo $AMBERHOME
> > /usr/local/software/amber16
> > [root.machine1 antechamber]# make clean /bin/rm -f *.o acdoctor
> > am1bcc antechamber atomtype bondtype charmmgen database espgen match
> > match_atomname parmcal parmchk parmchk2 prepgen residuegen respgen
> > translate test-penalties test-int-part test-combination
> > [root.machine1 antechamber]# make install AMBERBUILDFLAGS='-g -O0'
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o acdoctor.o acdoctor.c
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o eprintf.o eprintf.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 acdoctor.o eprintf.o \
> > -L/usr/local/software/amber16/lib -lcifparse -lm -o acdoctor cp
> > acdoctor /usr/local/software/amber16/bin/to_be_dispatched/acdoctor
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o am1bcc.o am1bcc.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 am1bcc.o eprintf.o \
> > -lm -o am1bcc
> > cp am1bcc /usr/local/software/amber16/bin/to_be_dispatched/am1bcc
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o antechamber.o antechamber.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 antechamber.o eprintf.o \
> > -L/usr/local/software/amber16/lib -lcifparse -lm -o antechamber
> > cp antechamber /usr/local/software/amber16/bin/to_be_dispatched/antechamber
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o atomtype.o atomtype.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 \
> > atomtype.o eprintf.o -lm -o atomtype cp atomtype
> > /usr/local/software/amber16/bin/to_be_dispatched/atomtype
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o bondtype.o bondtype.c
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o ncsu-penalties.o ncsu-penalties.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 \
> > bondtype.o eprintf.o ncsu-penalties.o -lm -o bondtype cp
> > bondtype /usr/local/software/amber16/bin/to_be_dispatched/bondtype
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o charmmgen.o charmmgen.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 \
> > charmmgen.o eprintf.o -lm -o charmmgen cp charmmgen
> > /usr/local/software/amber16/bin/to_be_dispatched/charmmgen
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o database.o database.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 \
> > database.o eprintf.o -lm -o database cp database
> > /usr/local/software/amber16/bin/to_be_dispatched/database
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o espgen.o espgen.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 \
> > espgen.o eprintf.o -lm -o espgen cp espgen
> > /usr/local/software/amber16/bin/to_be_dispatched/espgen
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o match.o match.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 \
> > eprintf.o match.o -lm -o match
> > cp match /usr/local/software/amber16/bin/to_be_dispatched/match
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o match_atomname.o match_atomname.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 \
> > match_atomname.o eprintf.o -lm -o match_atomname cp
> > match_atomname /usr/local/software/amber16/bin/to_be_dispatched/match_atomname
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o parmcal.o parmcal.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 \
> > eprintf.o parmcal.o -lm -o parmcal cp parmcal
> > /usr/local/software/amber16/bin/to_be_dispatched/parmcal
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o parmchk.o parmchk.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 \
> > parmchk.o eprintf.o -lm -o parmchk cp parmchk
> > /usr/local/software/amber16/bin/to_be_dispatched/parmchk
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o parmchk2.o parmchk2.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 \
> > parmchk2.o eprintf.o -lm -o parmchk2 cp parmchk2
> > /usr/local/software/amber16/bin/to_be_dispatched/parmchk2
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o prepgen.o prepgen.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 \
> > eprintf.o prepgen.o -lm -o prepgen cp prepgen
> > /usr/local/software/amber16/bin/to_be_dispatched/prepgen
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o residuegen.o residuegen.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 \
> > residuegen.o eprintf.o -lm -o residuegen cp residuegen
> > /usr/local/software/amber16/bin/to_be_dispatched/residuegen
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o respgen.o respgen.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 \
> > respgen.o eprintf.o -lm -o respgen cp respgen
> > /usr/local/software/amber16/bin/to_be_dispatched/respgen
> > gcc -c -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -o translate.o translate.c
> > gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN -g -O0 -g -O0 -g -O0 -g -O0 \
> > translate.o eprintf.o -lm -o translate cp translate
> > /usr/local/software/amber16/bin/to_be_dispatched/translate
> > SFX= BINDIR=/usr/local/software/amber16/bin sh patch.sh
> > [root.machine1 antechamber]# ls -l
> > /usr/local/software/amber16/bin/to_be_dispatched/antechamber
> > -rwxr-xr-x. 1 root root 423854 Jan 26 08:09
> > /usr/local/software/amber16/bin/to_be_dispatched/antechamber
> > [root.machine1 antechamber]#
> > /usr/local/software/amber16/bin/to_be_dispatched/antechamber
> > Segmentation fault (core dumped)
> >
> >
> > Best,
> > Yuan
> >
> >
> > -----Original Message-----
> > From: Scott Brozell [mailto:sbrozell.rci.rutgers.edu]
> > Sent: Thursday, January 25, 2018 1:51 PM
> > To: AMBER Mailing List
> > Subject: EXT: Re: [AMBER] Amber16 installation: Segmentation fault
> > (core dumped) error when execute antechamber
> >
> > [EXTERNAL]
> >
> > Hi,
> >
> > 1.
> > What is different between your two workstations?
> > (Run ldd on the workstation that works and compare to below.)
> >
> > On Wed, Jan 24, 2018 at 01:19:13PM +0000, Yuan Hu wrote:
> > > $ldd /usr/local/software/amber16/bin/to_be_dispatched/antechamber
> > > linux-vdso.so.1 => (0x00007ffcba57b000)
> > > libesets_pac.so => /usr/lib64/libesets_pac.so (0x00007f268172e000)
> > > libm.so.6 => /usr/lib64/libm.so.6 (0x00007f268142c000)
> > > libc.so.6 => /usr/lib64/libc.so.6 (0x00007f2681069000)
> > > libpthread.so.0 => /usr/lib64/libpthread.so.0 (0x00007f2680e4d000)
> > > libdl.so.2 => /usr/lib64/libdl.so.2 (0x00007f2680c48000)
> > > /lib64/ld-linux-x86-64.so.2 (0x00007f268188a000)
> >
> > 2.
> > On the broken workstation a debug version of antechamber, run it, and send the output including the stack trace:
> >
> > cd AmberTools/src/antechamber/
> > make clean
> > make install AMBERBUILDFLAGS='-g -O0'
> > ls -l /usr/local/software/amber16/bin/to_be_dispatched/antechamber
> > /usr/local/software/amber16/bin/to_be_dispatched/antechamber
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Received on Fri Jan 26 2018 - 12:30:04 PST
