Hi Jason,
reduced the given example to a minimum, should toggle P8.45.
It doesn't work.
Log of make:
root@beaglebone-ln:/media/SD32/home/ln/Programme/Puls_neu/source# make
CC    puls_gen.c
"puls_gen.c", line 82: warning #112-D: statement is unreachable
"puls_gen.c", line 70: warning #179-D: variable "i" was declared but never 
referenced
"puls_gen.c", line 70: warning #179-D: variable "j" was declared but never 
referenced
LD    gen/puls_gen.obj
CC    puls_gen.c
"puls_gen.c", line 82: warning #112-D: statement is unreachable
"puls_gen.c", line 70: warning #179-D: variable "i" was declared but never 
referenced
"puls_gen.c", line 70: warning #179-D: variable "j" was declared but never 
referenced
LD    gen/decay95.obj
-    Generated firmwares are : gen/puls_gen.out gen/decay95.out
root@beaglebone-ln:/media/SD32/home/ln/Programme/Puls_neu/source#* 
config-pin overlay cape-universala*
root@beaglebone-ln:/media/SD32/home/ln/Programme/Puls_neu/source# *config-pin 
p8.45 pruout*
root@beaglebone-ln:/media/SD32/home/ln/Programme/Puls_neu/source# *config-pin 
-q p8.45*
*P8_45 Mode: pruout*
root@beaglebone-ln:/media/SD32/home/ln/Programme/Puls_neu/source# make run
-    copying firmware file gen/puls_gen.out to /lib/firmware/am335x-pru1-fw
/bin/sh: 1: cannot create /sys/bus/platform/drivers/pru-rproc/unbind: 
Permission denied
/bin/sh: 1: cannot create /sys/bus/platform/drivers/pru-rproc/bind: 
Permission denied
-    rebooting pru core 0
-    pru core 1 is now loaded with gen/puls_gen.out
root@beaglebone-ln:/media/SD32/home/ln/Programme/Puls_neu/source#

My C-code:
#include <stdint.h>
#include <pru_cfg.h>
#include <pru_ctrl.h>
#include "resource_table_empty.h"

#define    INS_PER_US 200           // 5ns per instruction
#define INS_PER_DELAY_LOOP 2     // two instructions per delay loop
#define DELAY_CYCLES_US (INS_PER_US / INS_PER_DELAY_LOOP)

#define GPIO1 0x4804C000
#define GPIO_CLEARDATAOUT 0x190
#define GPIO_SETDATAOUT 0x194
#define USR0 (1<<21)
#define USR1 (1<<22)
#define USR2 (1<<23)
#define USR3 (1<<24)
unsigned int volatile * const GPIO1_CLEAR = (unsigned int *) (GPIO1 + 
GPIO_CLEARDATAOUT);
unsigned int volatile * const GPIO1_SET = (unsigned int *) (GPIO1 + 
GPIO_SETDATAOUT);

volatile register unsigned int __R30;
volatile register unsigned int __R31;
#define PRU0_GPIO (1<<2)

#ifndef DECAY_RATE
#define DECAY_RATE 100
#endif
#ifndef DELAY_CYCLES
#define DELAY_CYCLES DELAY_CYCLES_US
#endif

const int decay = DECAY_RATE;

void main(void) {
    int i, j;

    /* Clear SYSCFG[STANDBY_INIT] to enable OCP master port */
    CT_CFG.SYSCFG_bit.STANDBY_INIT = 0;


        //




*        while (1)        {         __R30 |= 0x00000001;          // toggle 
P8_45         __R30 &= 0xFFFFFFFE;        }*
    __halt();
}
Makefile is attached.

At the moment it works .... and I know why .... I can do the next step.
What is wrong or missing?

Thanks for help and have a good day

Kasimir

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Attachment: Makefile
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