Performance: Writing to stdout vs output_unit

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1

The problem

Hi, as I am trying to improve the performance of the test Reverse Complement from the Benchmark Game, I can use two different methods to write to standard output.

As the first (the fastest) method spends less time I feel tented to use it, but, it is not so portable as the second one.

Do you know how to get the best of both methods. Thank you

Note: I am using gfortran 9.3.0 and Linux

My results

TIME fast procedure:    6.27586031    
TIME slow procedure:    15.6404552

The code

program write_test
    use, intrinsic :: iso_fortran_env
    implicit none

    integer:: file_id, i 
    real:: time_fast(0:1), time_slow(0:1)
    integer, parameter:: iterations = 5e7
    character(len=7), parameter:: s = "Fortran"

    !-----------------------------------------------
    ! Faster procedure
    !-----------------------------------------------
    call cpu_time(time_fast(0))
    open(newunit=file_id, file="/dev/stdout", form="unformatted", access="stream")
    do i = 1, iterations
        write (file_id) s
    end do
    close(file_id)
    call cpu_time(time_fast(1))

    ! ----------------------------------------------
    ! Slower procedure
    ! ----------------------------------------------
    call cpu_time(time_slow(0))
    open(unit=output_unit)
    do i = 1, iterations
        write (output_unit, "(a)") s
    end do
    call cpu_time(time_slow(1))

    ! ----------------------------------------------
    ! Show results
    ! ----------------------------------------------
    print *, "TIME fast procedure: ",time_fast(1)-time_fast(0)
    print *, "TIME slow procedure: ",time_slow(1)-time_slow(0)
end program write_test
3

I looked through the description for the Reverse Complement code (having written such code in Fortran in the past), and the requirements basically mandate poorly written code. I would ignore their suggestions and just write a code that accomplishes the task and makes sense in Fortran.

The unit OUTPUT_UNIT should be connected to the same file that C calls stdout.

4

My goal is to improve the Fortran results in that test, but I am not able to use output_unit as unformatted using gfortran, so I am looking for other solutions.

After working on some benchmarks I realized they are not useful tools, as the constraints are too artificial.

Note: usually I get better results with gfortran than with ifort, I am not sure why

1 Like
5

In pure Fortran, you have no choice but to use write/print with the large associated overheads.

If you’re willing to use c interop for your benchmark and since you are only outputting a string in this example (which requires no parsing/conversion), you can call the c function puts:


program write_test
    use iso_c_binding, only: c_char, c_null_char
    implicit none

    integer:: i, r 
    real:: time_fast(0:1), time_slow(0:1)
    integer, parameter:: iterations = 5e7
    character(len=7), parameter:: s = "Fortran"
    
    interface
      function puts(str) result(r) bind(C,name="puts")
        import
        character(kind=c_char), dimension(*) :: str
        integer :: r
      end function puts
    end interface

    !-----------------------------------------------
    ! Faster procedure
    !-----------------------------------------------
    call cpu_time(time_fast(0))
    do i = 1, iterations
        r = puts(s//c_null_char)
    end do
    call cpu_time(time_fast(1))

    ! ----------------------------------------------
    ! Slower procedure
    ! ----------------------------------------------
    call cpu_time(time_slow(0))
    open(unit=output_unit)
    do i = 1, iterations
        write (output_unit, "(a)") s
    end do
    call cpu_time(time_slow(1))

    ! ----------------------------------------------
    ! Show results
    ! ----------------------------------------------
    print *, "TIME fast procedure: ",time_fast(1)-time_fast(0)
    print *, "TIME slow procedure: ",time_slow(1)-time_slow(0)
end program write_test

On my machine this has a similar performance to your original using unformatted output.
This is faster because, as @pmk pointed out, there’s a lot of overhead in the write routine, even compared to c printf.

I use c interop so ubiquitously in Fortran that I don’t consider it invalid for a benchmark, but this opinion is likely not shared by all.

2 Likes
6

Indeed. OUTPUT_UNIT is the same unit as * in Fortran, and is explicitly for sequential formatted output. So gfortran is doing the right thing. OTOH, processing a FASTA file like this usually results in another FASTA file written to a normal disk file, not to stdout. I guess you could try writing the output unformatted to disk, including new_line characters at the end of each “line” and then ‘cat’ the result sending it to the screen.

1 Like
7

I am afraid that one of the constraints of this benchmarksgame states that you have to read from stdin and write to stdout in this way:

$ ./test <input.fasta >output.fasta