Just tried the binary version AmberTools17, and same segmentation fault.
-Yuan
-----Original Message-----
From: Hai Nguyen [mailto:nhai.qn.gmail.com]
Sent: Friday, January 26, 2018 2:10 PM
To: AMBER Mailing List
Subject: EXT: Re: [AMBER] Amber16 installation: Segmentation fault (core dumped) error when execute antechamber
[EXTERNAL]
Also,
may be try binary distribution version of AT17 to see if antechamber work.
If that work, then compare two versions would help.
Hai
On Fri, Jan 26, 2018 at 1:40 PM, Scott Brozell <sbrozell.rci.rutgers.edu>
wrote:
> 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 - 12:00:02 PST
