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Edgar Gabriel
COSC 6374
Parallel Computation
Debugging MPI applications
Edgar Gabriel
Spring 2009
COSC 6374 – Parallel ComputationEdgar Gabriel
Hint for the Homework
- Allocating 2-D matrices in C, Method 1
- default method recommended in all C books
- Problem: &(A[i][NCOLUMNS-1]+1) ≠ &(A[i+1][0])
/* Method 1 to allocate a 2D matrix */ A = ( double *) malloc ( NROWS * sizeof ( double )); for ( i=0; i<NROWS; i++ ) { A[i] = (double) malloc (NCOLUMNSsizeof(double )); }
/* How to free a 2D matrix allocated with Method 1 */ for ( i=0; i<NROWS; i++ ) { free ( A[i] ); } free (A);
COSC 6374 – Parallel ComputationEdgar Gabriel
Hint for the Homework
- Allocating 2-D matrices in C, Method 2
/* Method 2 to allocate a 2D matrix / A = ( double ) malloc ( NROWS * sizeof ( double )); A[0] = (double) malloc (NROWSNCOLUMNSsizeof(double)); for ( i=1; i<NROWS; i++ ) { A[i] = &(A[0]+iNCOLUMNS); }
/* How to free a 2D matrix allocated with Method 2 */ free (A[0]); free (A);
COSC 6374 – Parallel ComputationEdgar Gabriel
Hint for the Homework
- Comparing now the two methods + a statically defined
matrix of dimensions 4x
Method 1 A= 0x602010 A[0]= 0x &(A[0][0]) = 0x &(A[1][0]) = 0x &(A[2][0]) = 0x602a &(A[3][0]) = 0x602f Matrix A has been freed Method 2 A = 0x602010 A[0] = 0x &(A[0][0]) = 0x &(A[1][0]) = 0x &(A[2][0]) = 0x602a &(A[3][0]) = 0x602f Matrix A has freed Static matrix B = 0x7fff8ade7b00 B[0] = 0x7fff8ade7b &(B[0][0]) = 0x7fff8ade7b &(B[1][0]) = 0x7fff8ade &(B[2][0]) = 0x7fff8ade &(B[3][0]) = 0x7fff8ade8a
COSC 6374 – Parallel ComputationEdgar Gabriel
Using a debugger
- For a source file to be visible in the debugger, you have
to compile the source code with the –g option, e.g.
gabriel@salmon>mpicc –g –o test test.c
- Avoid using optimization flags, such as –O3 when you would like to debug the code
- Two types of debugger
- Command line debugger, such as gdb
- Graphical debuggers, such as ddd (which is a GUI to gdb)
COSC 6374 – Parallel ComputationEdgar Gabriel
Start
app.
Load application into the debugger
Debugger points to the problem
Show the value of a variable when the problem occurred
Show source code of app.
COSC 6374 – Parallel ComputationEdgar Gabriel
gdb commands
- Setting breakpoints: debugger stops execution at the
specified line. Example
(gdb) break errexample.c:
(gdb) break myfunc
- Stepping through the source code
(gdb) next (skips subroutines/functions) (gdb) step (enters subroutines/functions)
- Continue execution (not step by step anymore)
(gdb) cont
(gdb) quit
COSC 6374 – Parallel ComputationEdgar Gabriel
COSC 6374 – Parallel ComputationEdgar Gabriel
Attaching to a
process
to processes
which you would
like to debug
COSC 6374 – Parallel ComputationEdgar Gabriel
Debugging parallel applications (III)
- Some MPI libraries support the startup of a debugger in
the mpirun command, including Open MPI
mpirun –np 2 ddd ./colltest
- only if all processes are running locally
- Starts one ddd session per process
- Not useful for large numbers of processes
