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On 24/09/2011 9:43 AM, Shachi Katira wrote:
<blockquote
cite="mid:CAA3wwwq9PWTBtPm9xr344Dziy-EPZoZ3w97Gv5vARmbs1A=NYA@mail.gmail.com"
type="cite">
<div dir="ltr">Dear GROMACS developers,
<div><br>
</div>
<div>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</div>
<div><br>
</div>
<div>
<div>(gdb) backtrace full</div>
<div>#0 _nb_kernel030_x86_64_sse2.nb030_unroll_loop () at
nb_kernel030_x86_64_sse2.s:329</div>
<div>No locals.</div>
<div>#1 0x3fdbf7e25d753ea9 in ?? ()</div>
<div>No symbol table info available.</div>
<div>#2 0x3fdbf7e25d753ea9 in ?? ()</div>
<div>No symbol table info available.</div>
<div>#3 0x3fda979e858aa137 in ?? ()</div>
<div>No symbol table info available.</div>
<div>#4 0x3fda979e858aa137 in ?? ()</div>
<div>No symbol table info available.</div>
<div>#5 0x40160678c8dd1923 in ?? ()</div>
<div>No symbol table info available.</div>
<div>#6 0x40160678c8dd1923 in ?? ()</div>
<div>No symbol table info available.</div>
<div>#7 0x4092e38cfdd6e1f8 in ?? ()</div>
<div>No symbol table info available.</div>
<div>#8 0x3fea3c3849a97e50 in ?? ()</div>
<div>No symbol table info available.</div>
<div>#9 0xc0c168adf977afb2 in ?? ()</div>
<div>No symbol table info available.</div>
<div>#10 0xbfa833e2faac1228 in ?? ()</div>
<div>No symbol table info available.</div>
<div>#11 0x407e54df4b25981d in ?? ()</div>
<div>No symbol table info available.</div>
<div>#12 0xbff026a42edd354c in ?? ()</div>
<div>No symbol table info available.</div>
<div>#13 0x4000000000000000 in ?? ()</div>
<div>No symbol table info available.</div>
<div>#14 0x4000000000000000 in ?? ()</div>
<div>No symbol table info available.</div>
<div>#15 0x409f400000000000 in ?? ()</div>
<div>No symbol table info available.</div>
<div>#16 0x409f400000000000 in ?? ()</div>
<div>No symbol table info available.</div>
<div>#17 0x3fcb98201cd5f99c in ?? ()</div>
<div>No symbol table info available.</div>
<div>#18 0x0000000000000000 in ?? ()</div>
<div>No symbol table info available.</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Is it possible to obtain more information from backtrace?
Are the libraries being stripped?</div>
</div>
</blockquote>
<br>
Yes. Not by GROMACS.<br>
<blockquote
cite="mid:CAA3wwwq9PWTBtPm9xr344Dziy-EPZoZ3w97Gv5vARmbs1A=NYA@mail.gmail.com"
type="cite">
<div dir="ltr">
<div><br>
</div>
<div>Details:</div>
<div>I compiled the modified code using </div>
<div>> ./configure CC=gcc
--prefix=/home/shachi/gromacs-4.5.1.o --enable-double
--with-fft=fftw3 --without-x --enable-debug
--program-suffix=_p</div>
<div>> export CFLAGS=-g (even though --enable-debug should
already add this)</div>
</div>
</blockquote>
<br>
--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.<br>
<br>
<blockquote
cite="mid:CAA3wwwq9PWTBtPm9xr344Dziy-EPZoZ3w97Gv5vARmbs1A=NYA@mail.gmail.com"
type="cite">
<div dir="ltr">
<div>> make</div>
<div>>make install</div>
<div><br>
</div>
<div>Additionally, I modified the configure script to remove all
'-O2' and '-O3' flags so that gdb doesn't get confused.</div>
</div>
</blockquote>
<br>
Also wise.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:CAA3wwwq9PWTBtPm9xr344Dziy-EPZoZ3w97Gv5vARmbs1A=NYA@mail.gmail.com"
type="cite">
<div dir="ltr">
<div><br>
</div>
<div>I invoked gdb using </div>
<div>> gdb --args mdrun_p -s holer1k1beta1.tpr -v</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Thanks.</div>
<div><br>
</div>
<div>--Shachi</div>
</div>
<br>
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