STM32-E407 doesn’t work on PIO

The black_f407zg is not the proper target / variant for it. The original board has an 8Mhz crystal for HSE on it. The arduino code (variant.cpp) in C:\Users\<home>\.platformio\packages\framework-arduinoststm32\variants\BLACK_F407XX\variant.cpp has code which initializes the PLL parameters (multipliers and divisors M,N,P,Q) as follows

WEAK void SystemClock_Config(void)
{

  RCC_OscInitTypeDef RCC_OscInitStruct;
  RCC_ClkInitTypeDef RCC_ClkInitStruct;

  /**Configure the main internal regulator output voltage
  */
  __HAL_RCC_PWR_CLK_ENABLE();

  __HAL_PWR_VOLTAGESCALING_CONFIG(PWR_REGULATOR_VOLTAGE_SCALE1);

  /**Initializes the CPU, AHB and APB busses clocks
  */
  RCC_OscInitStruct.OscillatorType = RCC_OSCILLATORTYPE_HSE;
  RCC_OscInitStruct.HSEState = RCC_HSE_ON;
  RCC_OscInitStruct.PLL.PLLState = RCC_PLL_ON;
  RCC_OscInitStruct.PLL.PLLSource = RCC_PLLSOURCE_HSE;
  RCC_OscInitStruct.PLL.PLLM = 8;
  RCC_OscInitStruct.PLL.PLLN = 336;
  RCC_OscInitStruct.PLL.PLLP = RCC_PLLP_DIV2;
  RCC_OscInitStruct.PLL.PLLQ = 7;
  if (HAL_RCC_OscConfig(&RCC_OscInitStruct) != HAL_OK) {
    _Error_Handler(__FILE__, __LINE__);
  }

  /**Initializes the CPU, AHB and APB busses clocks
  */
  RCC_ClkInitStruct.ClockType = RCC_CLOCKTYPE_HCLK | RCC_CLOCKTYPE_SYSCLK
                                | RCC_CLOCKTYPE_PCLK1 | RCC_CLOCKTYPE_PCLK2;
  RCC_ClkInitStruct.SYSCLKSource = RCC_SYSCLKSOURCE_PLLCLK;
  RCC_ClkInitStruct.AHBCLKDivider = RCC_SYSCLK_DIV1;
  RCC_ClkInitStruct.APB1CLKDivider = RCC_HCLK_DIV4;
  RCC_ClkInitStruct.APB2CLKDivider = RCC_HCLK_DIV2;

  if (HAL_RCC_ClockConfig(&RCC_ClkInitStruct, FLASH_LATENCY_5) != HAL_OK) {
    _Error_Handler(__FILE__, __LINE__);
  }
}

Which matches the parameters to get a full 168MHz SYSCLK for the Cortex-M4F core and the peripherals.

Your Olimex board however however has a 12MHz crystal (see schematics page 27)

Without altering the PLL parameters we now get a higher-than-allowed HCLK.

So you are operating your microcontroller out-of-specs and that won’t even boot. The following PLL initialization code is needed:

void SystemClock_Config(void)
{
  RCC_OscInitTypeDef RCC_OscInitStruct = {0};
  RCC_ClkInitTypeDef RCC_ClkInitStruct = {0};

  /** Configure the main internal regulator output voltage 
  */
  __HAL_RCC_PWR_CLK_ENABLE();
  __HAL_PWR_VOLTAGESCALING_CONFIG(PWR_REGULATOR_VOLTAGE_SCALE1);
  /** Initializes the CPU, AHB and APB busses clocks 
  */
  RCC_OscInitStruct.OscillatorType = RCC_OSCILLATORTYPE_HSE;
  RCC_OscInitStruct.HSEState = RCC_HSE_ON;
  RCC_OscInitStruct.PLL.PLLState = RCC_PLL_ON;
  RCC_OscInitStruct.PLL.PLLSource = RCC_PLLSOURCE_HSE;
  RCC_OscInitStruct.PLL.PLLM = 6;
  RCC_OscInitStruct.PLL.PLLN = 168;
  RCC_OscInitStruct.PLL.PLLP = RCC_PLLP_DIV2;
  RCC_OscInitStruct.PLL.PLLQ = 7;
  if (HAL_RCC_OscConfig(&RCC_OscInitStruct) != HAL_OK)
  {
    _Error_Handler(__FILE__, __LINE__);
  }
  /** Initializes the CPU, AHB and APB busses clocks 
  */
  RCC_ClkInitStruct.ClockType = RCC_CLOCKTYPE_HCLK|RCC_CLOCKTYPE_SYSCLK
                              |RCC_CLOCKTYPE_PCLK1|RCC_CLOCKTYPE_PCLK2;
  RCC_ClkInitStruct.SYSCLKSource = RCC_SYSCLKSOURCE_PLLCLK;
  RCC_ClkInitStruct.AHBCLKDivider = RCC_SYSCLK_DIV1;
  RCC_ClkInitStruct.APB1CLKDivider = RCC_HCLK_DIV4;
  RCC_ClkInitStruct.APB2CLKDivider = RCC_HCLK_DIV2;

  if (HAL_RCC_ClockConfig(&RCC_ClkInitStruct, FLASH_LATENCY_5) != HAL_OK)
  {
    _Error_Handler(__FILE__, __LINE__);
  }
}

Which brings your MCU to top-speed with valid params on a 12MHz crystal.

So you should test this by doing this local modification to your variant.cpp in the path I have noted above.

I further found it strange that Platformio’s board JSON file references the wrong linker file

However, the BLACK_F407XX folder does contain a ldscript.ld which is valid for this microcontroller and it should be used. Double check that in the compile commands (pio run -v).