[ejpostema]

Hi All,

I am creating a UDF to use an velocity profile from MRI as a boundary condition. I read the velocity profile from a CSV, which contain 30 13x16 matrices. So there a 30 velocity profiles depending on time. I interpolate between the points in a later stage.

I wrote a DEFINE_INIT function to read in the data, but I get an error in fluent when I execute this function on demand (to test it).

Node 9: Process 3868: Received signal SIGSEGV.

==============================================================================
MPI Application rank 0 exited before MPI_Finalize() with status 2
 The fl process could not be started.

I have copy the same code to test it. And I am able to compile and read the CSV file within codeblocks. I don't know what is going wrong here

THis is my DEFINE_INIT functions

DEFINE_INIT(read_csv,d)//, fname)
{
	char buffer[500];
	int i, j, k;
	int num;
	float x, y, z, pixelspace;
	FILE *file = fopen("C:\\Data\\Astrid\\CFD\\Flow_matlab_files\\test1.csv", "r");
	{
		fscanf(file, "%f %f %f %f", &x, &y, &z, &pixelspace);
		for (k = 0; k < TIMESTEP; k++)
		{
			for (i = 0; i < HEIGHT; i++)
			{
				for (j = 0; j < WIDTH; j++)
				{
					fscanf(file, "%d", &num);
					numArray[k][i][j] = num;
				}
			}
		}
	}
	//construct x and y coordinates
	for (i = 0; i <= WIDTH; i++)
	{
		xCor[i] = x + pixelspace*i;
	}
	for (i = 0; i <= HEIGHT; i++)
	{
		yCor[i] = y + pixelspace*i;
	}
	
}

[pakk]

You are doing parallel, it would help to first try it in serial mode.

And I am able to compile and read the CSV file within codeblocks

What is codeblocks?

Nowhere in your code you define what numArray, xCor or yCor are. I can infer that they are arrays, but are they big enough?

DEFINE_INIT(read_csv,d)//, fname)

What is this? Why the two slashes and the fname?

Your 8th line is a {, but that does not make any sense... There is no for-loop or if-clause or anything similar to start a block...

[ejpostema]

Originally Posted by pakk

You are doing parallel, it would help to first try it in serial mode.


What is codeblocks?

Nowhere in your code you define what numArray, xCor or yCor are. I can infer that they are arrays, but are they big enough?

Sorry, yeah I define those arrays earlier, posted only a piece of the code. Only posted the init function. They are big enough and are defined correctly (as an int)

Codeblocks is an IDE (like visual studio). So I started a project there where I coded the same function as above (without define init). I am able to compile it and execute the function. So I used it to test this part of the code

Originally Posted by pakk

DEFINE_INIT(read_csv,d)//, fname)

What is this? Why the two slashes and the fname?

oh some leftover. I commented something out, you can ignore it. Sorry for the inconvience

Originally Posted by pakk

Your 8th line is a {, but that does not make any sense... There is no for-loop or if-clause or anything similar to start a block...

I think I saw that in an example. Will see if it works to remove those (within codeblocks it does not matter)

[pakk]

Originally Posted by ejpostema

oh some leftover. I commented something out, you can ignore it. Sorry for the inconvience

I can ignore it, but the compiler will not ignore it.
This is not the correct way to use comments: you should use /* this style */. The style with two //-es is not proper c-style, although many compilers accept it.

[ejpostema]

Originally Posted by pakk

I can ignore it, but the compiler will not ignore it.
This is not the correct way to use comments: you should use /* this style */. The style with two //-es is not proper c-style, although many compilers accept it.

Thnx for the feedback. I have removed those lines and curly braceless you mentioned as well.

I get a segmentation fault now. Will check for some more bugs

[pakk]

Segmentation faults really suggest that your arrays are not big enough. They should be at least the following size:

float xCor[WIDTH];
float yCor[HEIGHT];
int numArray[TIMESTEP][HEIGHT][WIDTH];

Debug your code by adding messages, to see how far your code got. I did this below, along with slightly reordering your code.

DEFINE_INIT(read_csv,d)
{
	char buffer[500];
	int i, j, k;
	int num;
	float x, y, z, pixelspace;
	FILE *file = fopen("C:\\Data\\Astrid\\CFD\\Flow_matlab_files\\test1.csv", "r");
	if (!file) {Message("Error opening file.\n"); exit(1);}

	fscanf(file, "%f %f %f %f", &x, &y, &z, &pixelspace);
	Message("First line read.\n");

	/*construct x and y coordinates*/
	for (j = 0; j <= WIDTH; j++)
	{
		xCor[j] = x + pixelspace*j;
	}
	for (i = 0; i <= HEIGHT; i++)
	{
		yCor[i] = y + pixelspace*i;
	}
	Message("Coordinates constructed.\n");

	for (k = 0; k < TIMESTEP; k++)
	{
		for (i = 0; i < HEIGHT; i++)
		{
			for (j = 0; j < WIDTH; j++)
			{
				fscanf(file, "%d", &num);
				numArray[k][i][j] = num;
			}
		}
		Message("Timestep %d read correctly.\n",k);
	}
	Message("Finished reading timesteps.\n");
}

[ejpostema]

I left this problem for a while, since I had some other prioritues (some abstract deadlines).

I talked with somebody who has some better understanding on this stuff than me. He adviced me to break the code up into smaller pieces. First get on thing to work within fluent and then add the other stuff. Great advice so that is what I did.
Anyway I a now just focussing on the interpolation and have hardcode one matrix into my code. I'll add the other stuff later.

I am now getting this error message: 'MPI Application rank 3 exited before MPI_Finalize() with status -1073741819'

Does anyone understand what this means or what is wrong? thanks a lot in advance, I am the only one in my department with a bit of C knowledge

#include "udf.h" /*file that contains definitions for define functions and fluent operations*/

DEFINE_PROFILE(inlet_velocity, th, index)
{
	Message("ENTERED INLET_VELOCITY FUNCTION.\n");
	/*Declaration of constants*/
	float numArray[12][15];
	int pixelSize = 0.0000769;
	float MRIx = -0.0005;
	float MRIy = -0.0005;
	float MRIz = -0.0066797900;
	float xCor[12];
	float yCor[15];
	/*float dist[207]; /* xCor times yCor*/
	float posVector[ND_ND];  /* an array for the coordinates */
	float x, y, z, r;
	float x2x1, y2y1, x2x, y2y, yy1, xx1;
	float q11, q12, q21, q22;
	int i, j;
	/*float a, b, c, d, aa, bb, cc, dd;*/
	int ax, ay, bx, by, cx, cy, dx, dy;
	float x1, x2, x3, x4, y1, y2, y3, y4;
	/*int px1, px2, px3, px4, py1, py2, py3, py4;*/
	float vel;
	face_t f; // f is a face thread index
	float t = CURRENT_TIME;
	float nodeDistance;
	float distance0;
	float distance1;
	float distance2;
	float distance3;

	Message("FINISHED DECLARING VARIABLES.\n");
	/* Create the matrix with MRI flow velocity
	hardcoded for testing purposes, needs to be changed in the future */
	/* row 0 */
	numArray[0][0] = 0;
	numArray[0][1] = 0;
	numArray[0][2] = 0;
	numArray[0][3] = 0;
	numArray[0][4] = 0;
	numArray[0][5] = 0;
	numArray[0][6] = 0;
	numArray[0][7] = 0;
	numArray[0][8] = 0;
	numArray[0][9] = 0;
	numArray[0][10] = 0;
	numArray[0][11] = 0;
	numArray[0][12] = 0;

	/* row 1 */
	numArray[1][0] = 0;
	numArray[1][1] = 0;
	numArray[1][2] = 0;
	numArray[1][3] = 101;
	numArray[1][4] = 101;
	numArray[1][5] = 80;
	numArray[1][6] = 87;
	numArray[1][7] = 96;
	numArray[1][8] = 87;
	numArray[1][9] = 78;
	numArray[1][10] = 0;
	numArray[1][11] = 0;
	numArray[1][12] = 0;

	/* row 2 */
	numArray[2][0] = 0;
	numArray[2][1] = 0;
	numArray[2][2] = 0;
	numArray[2][3] = 73;
	numArray[2][4] = 93;
	numArray[2][5] = 87;
	numArray[2][6] = 93;
	numArray[2][7] = 89;
	numArray[2][8] = 88;
	numArray[2][9] = 87;
	numArray[2][10] = 106;
	numArray[2][11] = 137;
	numArray[2][12] = 0;

	/* row 3 */
	numArray[3][0] = 0;
	numArray[3][1] = 0;
	numArray[3][2] = 0;
	numArray[3][3] = 77;
	numArray[3][4] = 90;
	numArray[3][5] = 103;
	numArray[3][6] = 106;
	numArray[3][7] = 98;
	numArray[3][8] = 92;
	numArray[3][9] = 88;
	numArray[3][10] = 88;
	numArray[3][11] = 79;
	numArray[3][12] = 0;

	/* row 4 */
	numArray[4][0] = 0;
	numArray[4][1] = 0;
	numArray[4][2] = 91;
	numArray[4][3] = 94;
	numArray[4][4] = 100;
	numArray[4][5] = 113;
	numArray[4][6] = 119;
	numArray[4][7] = 110;
	numArray[4][8] = 92;
	numArray[4][9] = 81;
	numArray[4][10] = 81;
	numArray[4][11] = 67;
	numArray[4][12] = 0;

	/* row 5 */
	numArray[5][0] = 0;
	numArray[5][1] = 0;
	numArray[5][2] = 107;
	numArray[5][3] = 112;
	numArray[5][4] = 112;
	numArray[5][5] = 117;
	numArray[5][6] = 121;
	numArray[5][7] = 115;
	numArray[5][8] = 94;
	numArray[5][9] = 73;
	numArray[5][10] = 79;
	numArray[5][11] = 101;
	numArray[5][12] = 0;

	/* row 6 */
	numArray[6][0] = 0;
	numArray[6][1] = 90;
	numArray[6][2] = 109;
	numArray[6][3] = 121;
	numArray[6][4] = 118;
	numArray[6][5] = 115;
	numArray[6][6] = 115;
	numArray[6][7] = 111;
	numArray[6][8] = 98;
	numArray[6][9] = 85;
	numArray[6][10] = 80;
	numArray[6][11] = 92;
	numArray[6][12] = 0;

	/* row 7 */
	numArray[7][0] = 0;
	numArray[7][1] = 98;
	numArray[7][2] = 107;
	numArray[7][3] = 120;
	numArray[7][4] = 120;
	numArray[7][5] = 118;
	numArray[7][6] = 117;
	numArray[7][7] = 112;
	numArray[7][8] = 101;
	numArray[7][9] = 94;
	numArray[7][10] = 84;
	numArray[7][11] = 71;
	numArray[7][12] = 0;

	/* row 8 */
	numArray[8][0] = 0;
	numArray[8][1] = 105;
	numArray[8][2] = 110;
	numArray[8][3] = 117;
	numArray[8][4] = 122;
	numArray[8][5] = 123;
	numArray[8][6] = 121;
	numArray[8][7] = 115;
	numArray[8][8] = 102;
	numArray[8][9] = 98;
	numArray[8][10] = 93;
	numArray[8][11] = 70;
	numArray[8][12] = 0;

	/* row 9 */
	numArray[9][0] = 0;
	numArray[9][1] = 106;
	numArray[9][2] = 111;
	numArray[9][3] = 115;
	numArray[9][4] = 121;
	numArray[9][5] = 122;
	numArray[9][6] = 119;
	numArray[9][7] = 116;
	numArray[9][8] = 103;
	numArray[9][9] = 89;
	numArray[9][10] = 95;
	numArray[9][11] = 83;
	numArray[9][12] = 0;

	/* row 10 */
	numArray[10][0] = 0;
	numArray[10][1] = 0;
	numArray[10][2] = 105;
	numArray[10][3] = 110;
	numArray[10][4] = 115;
	numArray[10][5] = 116;
	numArray[10][6] = 118;
	numArray[10][7] = 117;
	numArray[10][8] = 100;
	numArray[10][9] = 75;
	numArray[10][10] = 75;
	numArray[10][11] = 81;
	numArray[10][12] = 0;

	/* row 11 */
	numArray[11][0] = 0;
	numArray[11][1] = 0;
	numArray[11][2] = 96;
	numArray[11][3] = 100;
	numArray[11][4] = 102;
	numArray[11][5] = 108;
	numArray[11][6] = 114;
	numArray[11][7] = 108;
	numArray[11][8] = 91;
	numArray[11][9] = 70;
	numArray[11][10] = 61;
	numArray[11][11] = 76;
	numArray[11][12] = 0;

	/* row 12 */
	numArray[12][0] = 0;
	numArray[12][1] = 0;
	numArray[12][2] = 0;
	numArray[12][3] = 85;
	numArray[12][4] = 87;
	numArray[12][5] = 94;
	numArray[12][6] = 98;
	numArray[12][7] = 94;
	numArray[12][8] = 85;
	numArray[12][9] = 75;
	numArray[12][10] = 71;
	numArray[12][11] = 0;
	numArray[12][12] = 0;

	/* row 13 */
	numArray[13][0] = 0;
	numArray[13][1] = 0;
	numArray[13][2] = 0;
	numArray[13][3] = 70;
	numArray[13][4] = 86;
	numArray[13][5] = 82;
	numArray[13][6] = 79;
	numArray[13][7] = 83;
	numArray[13][8] = 93;
	numArray[13][9] = 95;
	numArray[13][10] = 0;
	numArray[13][11] = 0;
	numArray[13][12] = 0;

	/* row 14 */
	numArray[14][0] = 0;
	numArray[14][1] = 0;
	numArray[14][2] = 0;
	numArray[14][3] = 0;
	numArray[14][4] = 0;
	numArray[14][5] = 89;
	numArray[14][6] = 78;
	numArray[14][7] = 84;
	numArray[14][8] = 106;
	numArray[14][9] = 108;
	numArray[14][10] = 0;
	numArray[14][11] = 0;
	numArray[14][12] = 0;

	/* row 15 */
	numArray[15][0] = 0;
	numArray[15][1] = 0;
	numArray[15][2] = 0;
	numArray[15][3] = 0;
	numArray[15][4] = 0;
	numArray[15][5] = 0;
	numArray[15][6] = 0;
	numArray[15][7] = 0;
	numArray[15][8] = 0;
	numArray[15][9] = 0;
	numArray[15][10] = 0;
	numArray[15][11] = 0;
	numArray[15][12] = 0;

	Message("FINISHED CREATION OF VENC MATRIX.\n");
	/* reconstruct the x and y coordinates of the venc matrix*/
	for (i = 0; i <= 12; i++)
	{
		xCor[i] = MRIx + pixelSize*i;
	}
	for (i = 0; i <= 15; i++)
	{
		yCor[i] = MRIy + pixelSize*i;
	}
	Message("Coordinates constructed.\n");

	begin_f_loop(f, th)
	{
		Message("BEGIN LOOP.\n");
		F_CENTROID(posVector, f, th);
		/* CHANGE THIS FOR THE REAL PROGRAM: x = PosVector[0]!!!*/
		x = posVector[1];	/* x coordinate */
		y = posVector[2];   /* y coordinate */
		z = posVector[0];	/* z coordinate */
		
		/* calculate the distances between the face and the points in the venc matrix */

		for (i = 0; i <= 12; i++)
		{
			
			for (j = 0; j <= 15; j++)
			{
				nodeDistance = sqrt((xCor[i] - x)*(xCor[i] - x) + (yCor[j] - y)*(yCor[j] - y));
				
				if (i == 0 && j == 0)
				{
					distance0 = nodeDistance;
					distance1 = nodeDistance;
					distance2 = nodeDistance;
					distance3 = nodeDistance;
				}
				else
				{
					if (nodeDistance < distance0)
					{
						distance0 = nodeDistance;
						ax = i;
						ay = j;
					}
					else if (nodeDistance < distance1)
					{
						distance1 = nodeDistance;
						bx = i;
						by = j;
					}
					else if (nodeDistance < distance2)
					{
						distance2 = nodeDistance;
						cx = i;
						cy = j;
					}
					else if (nodeDistance < distance3)
					{
						distance3 = nodeDistance;
						dx = i;
						dy = j; 
					}
				}
			}
		}

		q11 = numArray[ax][ay];
		q12 = numArray[bx][by];
		q21 = numArray[cx][cy];
		q22 = numArray[dx][dy];

		/*bilinear interpolation */
		x2x1 = xCor[bx] - xCor[ax];
		y2y1 = yCor[by] - yCor[ay];
		x2x = xCor[bx] - x;
		y2y = yCor[by] - y;
		xx1 = x - xCor[ax];
		yy1 = y - yCor[ay];

		vel = 1.0 / (x2x1 * y2y1) * (
			q11 * x2x * y2y +
			q21 * xx1 * y2y +
			q12 * x2x * yy1 +
			q22 * xx1 * yy1
			);

		vel = vel / 1000.0;

		/* give velocity to face*/
		F_PROFILE(f, th, index) = vel;
	}
	end_f_loop(f, th)
}

[pakk]

In general: debug in serial mode, not in parallel. In parallel, you will get MPI-warnings that are not so meaningful, in serial you have a bigger chance of seeing something useful.

More specific:

You define numArray:

float numArray[12][15];

This means the first index can run from 0 to 11, and the second index from 0-14.

But in your code, you assign it up to

numArray[15][12] = 0;

Note two things:
1. The order of 12 and 15 is reversed;
2. You try to assign more floats in your array than assigned.

One way to solve this: define your numArray differently:

float numArray[16][13];

This is the first problem I saw, I stopped looking after this.

[ejpostema]

Thanks, I feel stupid. haha.

Checked the code and fixed some more errors like that. I am now getting a divergence error, which probably means I am getting closer

I'll look into it

[ejpostema]

So taking a bit more care about the code itself I managed to complete de UDF.

there are some problems with the coordinates. I can solve a self made 3d tube, but not any other surfaces

I'll post it here when I have finished it.
Thanks