jacobwilliams / pikaia Goto Github PK

Dear Jacob,
many thanks for the updated pikaia code.

I am just playing a bit around with it and trying to start it parallel with openmp by adding
some cpu consuming dummy code in the Rosenbrock function (the plan is to apply pikaia to some "real world problem") and

a) in pikaya subroutine after "!Compute initial (random but bounded) phenotypes" comment line

      !$omp parallel do private(ip)
      do ip=istart,me%np
         do k=1,me%n
            oldph(k,ip)=urand()  !from [0,1] ! urand not thread safe!
         end do
         call me%ff(oldph(:,ip),fitns(ip))
      end do
      !$omp end parallel do

(have also set omp_set_nested(.false.) in the example to avoid splitting k loop... )

b) in newpop after "!replace population" comment line

      !$omp parallel do private(i)
      do i=1,me%np

         oldph(:,i)=newph(:,i)

         !get fitness using caller's fitness function
         call me%ff(oldph(:,i),fitns(i))

      end do
      !$omp end parallel do

It seems to bring something (not much but anyway) but I have got also 3 more questions related to the problem:

1. Are there any other good places to do openmp threads in the code? (mb I haven't found them?)
2. Should Fortran built-in random generator and urand() function be parts of private objects for each openmp thread? I.e. do we need to replace this random_number with something more portable and related to OOP ?
3. I cannot ensure reproducibility of calculation in modified version using openmp threads. This seems to be connected with 2? Or there is some kind of limitation at the algorithm level?

The mersenne-twister module has been split off into a separate FPM package: https://github.com/jacobwilliams/mersenne-twister-fortran

Make that an FPM dependency.

I just clone and tested this project using fpm (version 0.4.0), as follows:

fpm build
fpm test

and got the following error:

At line 809 of file ././src/pikaia_module.f90
Fortran runtime error: Index '0' of dimension 1 of array 'stackl' below lower bound of 1

Error termination. Backtrace:
#0  0x7f6f65ab57c2 in ???
#1  0x7f6f65ab6289 in ???
#2  0x7f6f65ab689a in ???
#3  0x40a854 in rqsort
	at ././src/pikaia_module.f90:809
#4  0x406665 in __pikaia_module_MOD_rnkpop
	at ././src/pikaia_module.f90:1243
#5  0x40d6a4 in __pikaia_module_MOD_pikaia
	at ././src/pikaia_module.f90:515
#6  0x40bbfe in __pikaia_module_MOD_solve_with_pikaia
	at ././src/pikaia_module.f90:650
#7  0x401a28 in pikaia_test
	at src/tests/pikaia_test.f90:75
#8  0x403836 in main
	at src/tests/pikaia_test.f90:10
<ERROR> Execution failed for object " pikaia_test "
<ERROR>*cmd_run*:stopping due to failed executions
STOP 1

This happens in the subroutine rqsort, and I am not sure how to solve it.

https://github.com/weixing1531/pikaia/tree/Binary
I wrote a subclass named pikaia_binary_class.
In the class, I change the definition of array gn.
integer(IB),dimension(me%n),intent(out) :: gn
operate the array gn in subroutine cross,mutate,encode,decode with using fortran's BIT INTRINSIC PROCEDURES ,then save memory and increase speed.