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

[Vivek Menon]

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
> >
>
>
>