[EMBOSS] Problem in profiling water and needle programs in the EMBOSS package

[Vivek Menon]

I still get these error messages.
BFD: needle(.rela.plt): relocation 101 has invalid symbol index 0
BFD: needle(.rela.plt): relocation 102 has invalid symbol index 0
BFD: needle(.rela.plt): relocation 103 has invalid symbol index 0
BFD: needle(.rela.plt): relocation 104 has invalid symbol index 0
BFD: needle(.rela.plt): relocation 105 has invalid symbol index 0

Based on your previous message, I deleted the directory and did a
fresh install with
./configure --prefix=$HOME --with-gccprofilling --disable-shared
make install
-bash-3.00$ ls
bin  include  lib  share

cd bin
./water
gprof water gmon.out >gprof_water_ecoli1.txt
.......Error messages...
The gprof file is created now and I see these error messages. The whoe
point in my profiling water is to determine the functions utilizing
max. CPU time and function calls.
is this information affected by the error messages or by creating
static libraries?

Thanks once again.
Vivek


On 4/12/07, ajb at ebi.ac.uk <ajb at ebi.ac.uk> wrote:
> You probably also need to 'make clean' and then configure again,
> this time also adding '--disable-shared' on the configuration
> line. That will cause static libraries to be used.
>
> HTH
>
> Alan
>
>
> > Thanks for the info.
> > I reconfigured the package with options --prefix=$HOME and
> > --with-gccprofiling.
> > I executed the water program from the bin directory and this is what I
> > got:
> > -bash-3.00$ gprof water gmon.out > gprof_water_ecoli01.txt
> > BFD: water(.rela.plt): relocation 0 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 1 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 2 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 3 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 4 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 5 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 6 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 7 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 8 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 9 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 10 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 11 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 12 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 13 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 14 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 15 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 16 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 17 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 18 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 19 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 20 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 21 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 22 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 23 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 24 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 25 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 26 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 27 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 28 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 29 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 30 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 31 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 32 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 33 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 34 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 35 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 36 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 37 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 38 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 39 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 40 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 41 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 42 has invalid symbol index 0
> > BFD: water(.rela.plt): relocation 43 has invalid symbol index 0
> > --------------------------
> >
> > what's going wrong now?? BTW I am using a linux-powerpc ppc64 machine.
> > Thanks,
> > Vivek
> >
> > On 4/12/07, ajb at ebi.ac.uk <ajb at ebi.ac.uk> wrote:
> >> That is likely to be because, unless you do a 'make install' the files
> >> in the 'emboss' directory are libtool scripts that call the true
> >> executables (which are held in the 'emboss/.libs' subdirectory after
> >> compilation).
> >>
> >> You may get away with typing:
> >>   gprof .libs/water gmon.out > gprof_water_ecoli01.txt
> >>
> >> on some systems/configurations. However, the recommended way is
> >> to use --prefix when you configure emboss (e.g.
> >> --prefix=/usr/local/emboss)
> >> and do a 'make install'. Then use the true executable in (e.g.)
> >> /usr/local/emboss/bin
> >>
> >> HTH
> >>
> >> Alan
> >>
> >>
> >> > Hello all,
> >> > I am having issues compiling the water and needle programs from the
> >> > EMBOSS package.
> >> > 1. I configured the package with --with-gccprofiling option which
> >> > ensured that all the CFLAGS and LDFLAGS are set with -pg option.
> >> > -bash-3.00$ ./water
> >> > Smith-Waterman local alignment.
> >> > Input sequence: ../../ncbi/build/myquery.txt
> >> > Second sequence(s): ../../ncbi/build/ecoli.nt
> >> > Gap opening penalty [10.0]:
> >> > Gap extension penalty [0.5]:
> >> > Output alignment [test1.water]:
> >> > 2. the gmon.out file is created, however I get the foll. message
> >> > -bash-3.00$ gprof water gmon.out > gprof_water_ecoli01.txt
> >> > gprof: water: not in a.out format
> >> >
> >> > has anyone had this problem??
> >> > Thanks in advance,
> >> > Vivek
> >> > _______________________________________________
> >> > EMBOSS mailing list
> >> > EMBOSS at lists.open-bio.org
> >> > http://lists.open-bio.org/mailman/listinfo/emboss
> >> >
> >>
> >>
> >>
> >
>
>
>