I think Octave is doing a lot of malloc/free operations, probably more than we need, and which is related to the creation of temporary objects such as returning octave_value objects or octave_value_list objects from functions.  That is going to be hard to quickly fix.

The one thing that does strike me is the __nss_database_lookup which is taking 7.4% of the time.  Is this a consequence of having remote directories on the PATH for Octave?  That seems like a lot of database lookups.

I used the following script to benchmark the calling overhead in Octave.

N = 1e6;

tic;
for i = 1:N
  ## Empty for loop body
endfor
bm1 = toc

function NOP ()
endfunction

tic;
for i = 1:N
  ## Call NOP subfunction
  NOP ();
endfor
bm2 = toc

tic;
for i = 1:N
  ## Call C++ emptyoct function
  emptyoct();
endfor
bm3 = toc

The accompanying emptyoct.cc file is

#include <octave/oct.h>

DEFUN_DLD (emptyoct, args, nargout,
           "emptyoct does nothing, and should be fast")
{
  return ovl (octave_value ());
}

The results were

bm1 = 0.074267
bm2 = 2.2344
bm3 = 1.2721

Even with C++ there is a fair amount of overhead.