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

[ajb at ebi.ac.uk]

Hello Vivek,

> 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

Then I'd guess that there are some ppc64 ELF problems on your linux ppc64
system. I can now only suggest that any available
updates are applied to your linux ppc64 distribution - there were some
ppc64 binutils package ELF problems with symbol tables last year I see. If
that isn't
possible then try to gain access to a linux x86 or x86_64 system.


> Based on your previous message, I deleted the directory and did a
> fresh install with
> ./configure --prefix=$HOME --with-gccprofilling --disable-shared

I think you meant --with-gccprofile

> 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.

What you are doing is correct, and indeed works without error on Linux x86
and x86_64
systems (I have just tried it on Fedora 32bit and 64bit distros).

> is this information affected by the error messages or by creating
> static libraries?

If sensible-looking profiling information is being produced in
gprof_water_ecoli1.txt then it is not
going to be affected by using static libraries (and likely not by
relocation errors - but I'd be happier if the errors weren't there).

HTH

Alan