STM32: Loading programs to different flash locations

You should stop and reconsider the way you plan to get this work.
In order to get this done, you need a separate project per program type (bootloader, application A and B). Each must have a unique linker script, determining a unique entry point and vector table. Do not fiddle with IROM1 - use a linker script instead!
In addition to that, you will need a variable/RAM location, defined in the bootloader, indicating whether application B failed - such a variable must not be initialized to 0 upon startup of the bootloader (look up ZI and UNINIT elements in linker scripts).

Thank you Tamir, very helpful. I do not have much experience with linker scripts, but I will take the time to learn and report back.

Another import point of interest: In the bootloader, before jumping to application, disable the interrupts and clear the pending ones. In the application initialization procedure, remap the vector table - then enable the interrupts.

The .hex file reflects where binary data should be placed in memory - any memory.
Unless you need to write more than one type of memory, you could make you life much easier by converting the .hex file into a .bin type file and handling this one in the bootloader - which is basically the same program code/data content stripped on addressing data. This is useful if you always need to write your data to a constant address in memory.
You can find many free programs to convert a .hex file to a binary. You could of course add parsing a .hex file in your program but that seems rather an overkill for simple cases.

Update: I am able to flash the program into Partition A (@address 0x8060000) and verify it with a CRC check. The program runs anything in while loop fine (LED3 toggling, UART); however, the LED2 toggling based off of a timer interrupt does not work. When I flash the program normally (ie not with my bootloader) it works 100%, including LED2 toggling.

Below I include the jump function/linker file for the bootloader application at 0x8000000 and the main.c/linker file for the application at 0x8060000:

@@@@@@@@@@@@@@@@@@@@ JUMP FUNCTION IN BOOTLOADER PROGRAM AT 0x8000000 @@@@@@@@@@@@@@@@@

void ApplicationManager::RunActivePartition()
{ JumpToApplication = (void (*)(void)) (*((uint32_t *) (active_partition.address + 4)));

/* Reset RCC clock configuration */ HAL_RCC_DeInit();

/* Disable and reset systick timer */ SysTick->CTRL= 0; SysTick->LOAD = 0; SysTick->VAL = 0;

/* Disable all interrupts */ __disable_irq();

/* Set vector table offset register */ SetVectorTable(MemoryInfo::BTLR_ADDRESS, MemoryInfo::PARTITION_A_OFFSET_FROM_BTLR);

/* STM32 needs the stack pointer to start at the beginning of ** the application in flash. This must happen last */ __set_MSP(*(uint32_t*) active_partition.address);

JumpToApplication();

/*************** Other things I have tried ***************/ /* Remap system memory */ // SYSCFG->MEMRMP = SYSCFG_MEMRMP_MEM_MODE_0; //

// /* Clear pending interrupts */ // uint32_t isrflags = READ_REG(huart->Instance->SR); // Clears some UART interrupt

/* Disable peripheral clocks */ // __HAL_RCC_GPIOA_CLK_DISABLE(); // __HAL_RCC_GPIOB_CLK_DISABLE(); // __HAL_RCC_GPIOC_CLK_DISABLE(); // __HAL_RCC_GPIOD_CLK_DISABLE(); // __HAL_RCC_GPIOG_CLK_DISABLE(); // __HAL_RCC_GPIOH_CLK_DISABLE();

// __HAL_UART_DISABLE(&huart3);

// __HAL_RCC_PWR_CLK_DISABLE();

/*************** What I want to add when more basic implementation works ***************/ // /* Relocate vector interrupt table to RAM */ // CopyVectorInterruptTable();

// /* TODO: Patch VIT with bootloader interrupt handlers (ex: hard fault handler) */ // PatchVectorInterruptTable();

// if (!CopyandPatchOkay()) // { // LOG_DEBUG("Vector interrupt table not probably copied and/or patched \n"); // } // else // { // LOG_DEBUG("Device ready to jump into application \n"); // }
}

@@@@@@@@@@@@@@@@@@@@ LINKER FILE FOR APPLICATION (BOOTLOADER) 0x8000000 @@@@@@@@@@@@@@@@@

/* Highest address of the user mode stack */
_estack = 0x20010000; /* end of RAM */
/* Generate a link error if heap and stack don't fit into RAM */
_Min_Heap_Size = 0x200; /* required amount of heap */
_Min_Stack_Size = 0x400; /* required amount of stack */

/* Specify the memory areas */
MEMORY
{ RAM (xrw) : ORIGIN = 0x20000000, LENGTH = 192K
CCMRAM (rw) : ORIGIN = 0x10000000, LENGTH = 64K
FLASH (rx) : ORIGIN = 0x8000000, LENGTH = 2048K
}

@@@@@@@@@@@@@@@@@@@@@@@@ APPLICATION TO JUMP TO AT 0x8060000 @@@@@@@@@@@@@@@@@@@@

void HAL_TIM_PeriodElapsedCallback(TIM_HandleTypeDef *htim10)
{ HAL_GPIO_TogglePin(LD2_GPIO_Port, LD2_Pin);
} /* USER CODE END 0 */

/** * @brief The application entry point. * @retval int */
int main(void)
{ /* USER CODE BEGIN 1 */

/* USER CODE END 1 */

/* MCU Configuration--------------------------------------------------------*/

/* Reset of all peripherals, Initializes the Flash interface and the Systick. */ HAL_Init();

/* USER CODE BEGIN Init */

/* USER CODE END Init */

/* Configure the system clock */ SystemClock_Config();

/* USER CODE BEGIN SysInit */

/* USER CODE END SysInit */

/* Initialize all configured peripherals */ MX_GPIO_Init(); MX_USART3_UART_Init(); MX_TIM10_Init(); /* USER CODE BEGIN 2 */ uint32_t count = 0; HAL_TIM_Base_Start_IT(&htim10); /* USER CODE END 2 */

/* Infinite loop */ /* USER CODE BEGIN WHILE */ while (1) { for (uint32_t i=0; i < 100000; i++); HAL_GPIO_TogglePin(LD3_GPIO_Port, LD3_Pin); _printf("Hi %d \n", count); count++; /* USER CODE END WHILE */

/* USER CODE BEGIN 3 */ } /* USER CODE END 3 */
}

@@@@@@@@@@@@@@@@@@@@ LINKER FILE FOR APPLICATION (BLINKY) 0x8060000 @@@@@@@@@@@@@@@@@

/* Highest address of the user mode stack */
_estack = 0x20010000; /* end of RAM */
/* Generate a link error if heap and stack don't fit into RAM */
_Min_Heap_Size = 0x200; /* required amount of heap */
_Min_Stack_Size = 0x400; /* required amount of stack */

/* Specify the memory areas */
MEMORY
{ RAM (xrw) : ORIGIN = 0x20000000, LENGTH = 192K
CCMRAM (rw) : ORIGIN = 0x10000000, LENGTH = 64K
FLASH (rx) : ORIGIN = 0x8060000, LENGTH = 1024K
}

I see you are disabling interrupts in the bootloader. Are you ever enabling them again?