[gmx-developers] Debugging using gdb

[Mark Abraham]

On 24/09/2011 9:43 AM, Shachi Katira wrote:
> Dear GROMACS developers,
>
> I'm trying to modify the pull code and have encountered a segmentation 
> fault in the process. I need some help running GROMACS with gdb. When 
> I execute mdrun with gdb, on using 'backtrace' I get
>
> (gdb) backtrace full
> #0  _nb_kernel030_x86_64_sse2.nb030_unroll_loop () at 
> nb_kernel030_x86_64_sse2.s:329
> No locals.
> #1  0x3fdbf7e25d753ea9 in ?? ()
> No symbol table info available.
> #2  0x3fdbf7e25d753ea9 in ?? ()
> No symbol table info available.
> #3  0x3fda979e858aa137 in ?? ()
> No symbol table info available.
> #4  0x3fda979e858aa137 in ?? ()
> No symbol table info available.
> #5  0x40160678c8dd1923 in ?? ()
> No symbol table info available.
> #6  0x40160678c8dd1923 in ?? ()
> No symbol table info available.
> #7  0x4092e38cfdd6e1f8 in ?? ()
> No symbol table info available.
> #8  0x3fea3c3849a97e50 in ?? ()
> No symbol table info available.
> #9  0xc0c168adf977afb2 in ?? ()
> No symbol table info available.
> #10 0xbfa833e2faac1228 in ?? ()
> No symbol table info available.
> #11 0x407e54df4b25981d in ?? ()
> No symbol table info available.
> #12 0xbff026a42edd354c in ?? ()
> No symbol table info available.
> #13 0x4000000000000000 in ?? ()
> No symbol table info available.
> #14 0x4000000000000000 in ?? ()
> No symbol table info available.
> #15 0x409f400000000000 in ?? ()
> No symbol table info available.
> #16 0x409f400000000000 in ?? ()
> No symbol table info available.
> #17 0x3fcb98201cd5f99c in ?? ()
> No symbol table info available.
> #18 0x0000000000000000 in ?? ()
> No symbol table info available.
>
>
> Is it possible to obtain more information from backtrace? Are the 
> libraries being stripped?

Yes. Not by GROMACS.
>
> Details:
> I compiled the modified code using
> > ./configure CC=gcc --prefix=/home/shachi/gromacs-4.5.1.o 
> --enable-double --with-fft=fftw3 --without-x --enable-debug 
> --program-suffix=_p
> > export CFLAGS=-g (even though --enable-debug should already add this)

--enable-debug doesn't do anything AFAICR. Neither does make look at 
environment variables. Set your CFLAGS before configure, and this should 
work. You will see the -g flag in the make output when it calls the 
compiler, if things are working right.

> > make
> >make install
>
> Additionally, I modified the configure script to remove all '-O2' and 
> '-O3' flags so that gdb doesn't get confused.

Also wise.

Mark

>
> I invoked gdb using
> > gdb --args mdrun_p -s holer1k1beta1.tpr -v
>
>
>
> Thanks.
>
> --Shachi
>
>

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