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I am interfacing MPU6050 with Arduino using Simulink S-function builder. I'm implementing MPU6050_DMP6 code in Simulink s-function builder by following this video. By following this tutorial I implemented the S-function as: I set sample time 0.05 in s-function builder block and number of discrete state=1 and sample mode = 1. in the libraries tab I put the following code:

#include <math.h>
#ifndef MATLAB_MEX_FILE
int counter=0;
#include <Arduino.h>
#include "I2Cdev.h"
#include "I2Cdev.cpp"

#include "helper_3dmath.h"
#include "MPU6050_6Axis_MotionApps20.h"
#include "MPU6050.h" // not necessary if using MotionApps include file
#include "MPU6050.cpp" // not necessary if using MotionApps include file
// Arduino Wire library is required if I2Cdev I2CDEV_ARDUINO_WIRE implementation
// is used in I2Cdev.h
#if I2CDEV_IMPLEMENTATION == I2CDEV_ARDUINO_WIRE
    #include "Wire.h"
    #include "Wire.cpp"
    #include "utility/twi.h"
    #include "utility/twi.c"
#endif
// class default I2C address is 0x68
// specific I2C addresses may be passed as a parameter here
// AD0 low = 0x68 (default for SparkFun breakout and InvenSense evaluation board)
// AD0 high = 0x69
MPU6050 mpu;

#define OUTPUT_READABLE_YAWPITCHROLL

// uncomment "OUTPUT_READABLE_REALACCEL" if you want to see acceleration
// components with gravity removed. This acceleration reference frame is
// not compensated for orientation, so +X is always +X according to the
// sensor, just without the effects of gravity. If you want acceleration
// compensated for orientation, us OUTPUT_READABLE_WORLDACCEL instead.
//#define OUTPUT_READABLE_REALACCEL

// uncomment "OUTPUT_READABLE_WORLDACCEL" if you want to see acceleration
// components with gravity removed and adjusted for the world frame of
// reference (yaw is relative to initial orientation, since no magnetometer
// is present in this case). Could be quite handy in some cases.
//#define OUTPUT_READABLE_WORLDACCEL

// uncomment "OUTPUT_TEAPOT" if you want output that matches the
// format used for the InvenSense teapot demo
//#define OUTPUT_TEAPOT

#define INTERRUPT_PIN 2  // use pin 2 on Arduino Uno & most boards
#define LED_PIN 13 // (Arduino is 13, Teensy is 11, Teensy++ is 6)
bool blinkState = false;

// MPU control/status vars
bool dmpReady = false;  // set true if DMP init was successful
uint8_t mpuIntStatus;   // holds actual interrupt status byte from MPU
uint8_t devStatus;      // return status after each device operation (0 = success, !0 = error)
uint16_t packetSize;    // expected DMP packet size (default is 42 bytes)
uint16_t fifoCount;     // count of all bytes currently in FIFO
uint8_t fifoBuffer[64]; // FIFO storage buffer

// orientation/motion vars
Quaternion q;           // [w, x, y, z]         quaternion container
VectorInt16 aa;         // [x, y, z]            accel sensor measurements
VectorInt16 aaReal;     // [x, y, z]            gravity-free accel sensor measurements
VectorInt16 aaWorld;    // [x, y, z]            world-frame accel sensor measurements
VectorFloat gravity;    // [x, y, z]            gravity vector
float euler[3];         // [psi, theta, phi]    Euler angle container
float ypr[3];           // [yaw, pitch, roll]   yaw/pitch/roll container and gravity vector

// packet structure for InvenSense teapot demo
uint8_t teapotPacket[14] = { '$', 0x02, 0,0, 0,0, 0,0, 0,0, 0x00, 0x00, '\r', '\n' };



// ================================================================
// ===               INTERRUPT DETECTION ROUTINE                ===
// ================================================================

volatile bool mpuInterrupt = false;     // indicates whether MPU interrupt pin has gone high
void dmpDataReady() {
    mpuInterrupt = true;
}
#endif

in the discrete update tab I have implemented following code:

if (xD[0]!=1){    
#ifndef MATLAB_MEX_FILE
       // join I2C bus (I2Cdev library doesn't do this automatically)
#if I2CDEV_IMPLEMENTATION == I2CDEV_ARDUINO_WIRE
        Wire.begin();
        Wire.setClock(400000); // 400kHz I2C clock. Comment this line if having compilation difficulties
    #elif I2CDEV_IMPLEMENTATION == I2CDEV_BUILTIN_FASTWIRE
        Fastwire::setup(400, true);
    #endif

    // initialize serial communication
    // (115200 chosen because it is required for Teapot Demo output, but it's
    // really up to you depending on your project)
    Serial2.begin(115200);
//     while (!Serial); // wait for Leonardo enumeration, others continue immediately

    // NOTE: 8MHz or slower host processors, like the Teensy @ 3.3v or Ardunio
    // Pro Mini running at 3.3v, cannot handle this baud rate reliably due to
    // the baud timing being too misaligned with processor ticks. You must use
    // 38400 or slower in these cases, or use some kind of external separate
    // crystal solution for the UART timer.

    // initialize device
    Serial2.println(F("Initializing I2C devices..."));
    mpu.initialize();
    pinMode(INTERRUPT_PIN, INPUT);
    // verify connection
    Serial2.println(F("Testing device connections..."));
    Serial2.println(mpu.testConnection() ? F("MPU6050 connection successful") : F("MPU6050 connection failed"));

    // wait for ready
   // Serial2.println(F("\nSend any character to begin DMP programming and demo: "));
   // while (Serial2.available() && Serial2.read()); // empty buffer
   // while (!Serial2.available());                 // wait for data
   // while (Serial2.available() && Serial2.read()); // empty buffer again

    // load and configure the DMP
    Serial2.println(F("Initializing DMP..."));
    devStatus = mpu.dmpInitialize();

    // supply your own gyro offsets here, scaled for min sensitivity
    mpu.setXGyroOffset(220);
    mpu.setYGyroOffset(76);
    mpu.setZGyroOffset(-85);
    mpu.setZAccelOffset(1788); // 1688 factory default for my test chip

    // make sure it worked (returns 0 if so)
    if (devStatus == 0) {
        // turn on the DMP, now that it's ready
        Serial2.println(F("Enabling DMP..."));
        mpu.setDMPEnabled(true);
        // enable Arduino interrupt detection
        Serial2.println(F("Enabling interrupt detection (Arduino external interrupt 0)..."));
        attachInterrupt(digitalPinToInterrupt(INTERRUPT_PIN), dmpDataReady, RISING);
        mpuIntStatus = mpu.getIntStatus();
        // set our DMP Ready flag so the main loop() function knows it's okay to use it
        Serial2.println(F("DMP ready! Waiting for first interrupt..."));
        dmpReady = true;

        // get expected DMP packet size for later comparison
        packetSize = mpu.dmpGetFIFOPacketSize();
    } else {
        // ERROR!
        // 1 = initial memory load failed
        // 2 = DMP configuration updates failed
        // (if it's going to break, usually the code will be 1)
        Serial2.print(F("DMP Initialization failed (code "));
        Serial2.print(devStatus);
        Serial2.println(F(")"));
    }       
    #endif 

  xD[0]=1;
 }

and in output tab I have implemented this code:

if (xD[0]==1){
    #ifndef MATLAB_MEX_FILE
// if programming failed, don't try to do anything
    if (!dmpReady) {               
        return;
    }

    // wait for MPU interrupt or extra packet(s) available
    while (!mpuInterrupt && fifoCount < packetSize) {
        // other program behavior stuff here
        // .
        // .
        // .
        // if you are really paranoid you can frequently test in between other
        // stuff to see if mpuInterrupt is true, and if so, "break;" from the
        // while() loop to immediately process the MPU data
        // .
        // .
        // .
    }

    // reset interrupt flag and get INT_STATUS byte
    mpuInterrupt = false;
    mpuIntStatus = mpu.getIntStatus();

    // get current FIFO count
    fifoCount = mpu.getFIFOCount();
    // check for overflow (this should never happen unless our code is too inefficient)
    if ((mpuIntStatus & 0x10) || fifoCount == 1024) {
        // reset so we can continue cleanly
        mpu.resetFIFO();        
        // otherwise, check for DMP data ready interrupt (this should happen frequently)
    } else if (mpuIntStatus & 0x02) {
        // wait for correct available data length, should be a VERY short wait
        while (fifoCount < packetSize) fifoCount = mpu.getFIFOCount();       
        // read a packet from FIFO
        mpu.getFIFOBytes(fifoBuffer, packetSize);

        // track FIFO count here in case there is > 1 packet available
        // (this lets us immediately read more without waiting for an interrupt)
        fifoCount -= packetSize;

#ifdef OUTPUT_READABLE_QUATERNION
        // display quaternion values in easy matrix form: w x y z
        mpu.dmpGetQuaternion(&q, fifoBuffer);
        // Serial.print("quat\t");
        // Serial.print(q.w);
        // Serial.print("\t");
        // Serial.print(q.x);
        // Serial.print("\t");
        // Serial.print(q.y);
        // Serial.print("\t");
        // Serial.println(q.z);
#endif

#ifdef OUTPUT_READABLE_EULER
        // display Euler angles in degrees
//         mpu.dmpGetQuaternion(&q, fifoBuffer);
//         mpu.dmpGetEuler(euler, &q);
//         Serial.print("euler\t");
//         Serial.print(euler[0] * 180/M_PI);
//         Serial.print("\t");
//         Serial.print(euler[1] * 180/M_PI);
//         Serial.print("\t");
//         Serial.println(euler[2] * 180/M_PI);
#endif

#ifdef OUTPUT_READABLE_YAWPITCHROLL
        // display Euler angles in degrees
        mpu.dmpGetQuaternion(&q, fifoBuffer);
        mpu.dmpGetGravity(&gravity, &q);
        mpu.dmpGetYawPitchRoll(ypr, &q, &gravity);
        *roll = ypr[0] * 180/M_PI;
        *pitch = ypr[1] * 180/M_PI;
        *yaw = ypr[2] * 180/M_PI;
        Serial2.print("ypr\t");
        Serial2.print(ypr[0] * 180/M_PI);
        Serial2.print("\t");
        Serial2.print(ypr[1] * 180/M_PI);
        Serial2.print("\t");
        Serial2.println(ypr[2] * 180/M_PI);
#endif

#ifdef OUTPUT_READABLE_REALACCEL
        // display real acceleration, adjusted to remove gravity
        mpu.dmpGetQuaternion(&q, fifoBuffer);
        mpu.dmpGetAccel(&aa, fifoBuffer);
        mpu.dmpGetGravity(&gravity, &q);
        mpu.dmpGetLinearAccel(&aaReal, &aa, &gravity);
        // Serial.print("areal\t");
        // Serial.print(aaReal.x);
        // Serial.print("\t");
        // Serial.print(aaReal.y);
        // Serial.print("\t");
        // Serial.println(aaReal.z);
#endif

#ifdef OUTPUT_READABLE_WORLDACCEL
        // display initial world-frame acceleration, adjusted to remove gravity
        // and rotated based on known orientation from quaternion
        mpu.dmpGetQuaternion(&q, fifoBuffer);
        mpu.dmpGetAccel(&aa, fifoBuffer);
        mpu.dmpGetGravity(&gravity, &q);
        mpu.dmpGetLinearAccel(&aaReal, &aa, &gravity);
        mpu.dmpGetLinearAccelInWorld(&aaWorld, &aaReal, &q);
        // Serial.print("aworld\t");
        // Serial.print(aaWorld.x);
        // Serial.print("\t");
        // Serial.print(aaWorld.y);
        // Serial.print("\t");
        // Serial.println(aaWorld.z);
#endif

#ifdef OUTPUT_TEAPOT
        // display quaternion values in InvenSense Teapot demo format:
        teapotPacket[2] = fifoBuffer[0];
        teapotPacket[3] = fifoBuffer[1];
        teapotPacket[4] = fifoBuffer[4];
        teapotPacket[5] = fifoBuffer[5];
        teapotPacket[6] = fifoBuffer[8];
        teapotPacket[7] = fifoBuffer[9];
        teapotPacket[8] = fifoBuffer[12];
        teapotPacket[9] = fifoBuffer[13];
        Serial.write(teapotPacket, 14);
        teapotPacket[11]++; // packetCount, loops at 0xFF on purpose
#endif

        // blink LED to indicate activity
        // blinkState = !blinkState;
        // digitalWrite(LED_PIN, blinkState);
    }

#endif   
}

The solver I'm using is fixed-step discrete solver.

I build the S-function and then the model successfully. When I run the simulation in the external mode using Arduino mega there are jump and glitches in the output raw, pitch and roll angles as shown in the figures However, when I plotted the same code through Arduino IDE and monitor data on serial plotter there is no glitches and jumps in angles. I have also change the baud rate to 115200, solver to auto and sample time of s-function but the problem remain to persist. Any help would be appreciated! Thanks in advance!

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Measurement sometime lost due to serial communications between Arduino and Simulink. So raw data have some glitches in output values. In order to solve the issue, we have to use state estimation to solve this problem.

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To add to the answer above, you are limited by the serial speed of the USB, i.e. USB 2.0 is around 12 Mbps, as well as what your hardware can manage. Also, Simulink uses about 25% of each time step simply for maintaining communication and it is unclear how bandwidth is used by this. A simple rule of thumb is to work out how much data you are trying to log and at what frequency as this should give you an idea if you are trying to log too much and hence Simulink won't catch all the data and you end up with the blip you have in the scope. For context, I have been making a wheel speed calculation algorithm and was losing data simply because it wasn't possible to log the volume of data I wanted at high frequency (i.e. 5000 Hz). If you think about logging 3 int8 values at 5000 Hz you are talking 120 kkps, this should give some idea as to how this can get out of control with more signals or larger data types like double.

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