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 - 11:00:03 PST
