Hi Scott,
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
scott
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Received on Fri Jan 26 2018 - 05:30:04 PST
