= Code Debugging =
Ideally, code should be debuged on your desktop computer before being moved to a cluster environment. There are a number of debugging techniques, which you can learn from the internet.

== print ==
Insert 'print' into the source code.

in C/C++
{{{#!c 
 /* check */
#ifdef DEBUG
  if (info == 0) printf("successfully done\n"); 
#endif
}}}

in Fortran
{{{#!fortran
#ifdef debug
    if (info == 0) then
       print *,"successfully done"
    endif
#endif
}}}

Compile with ''-DDEBUG'' option
{{{
icc -g -pg -DDEBUG -c stokeslet2d.c
}}}

Makefile
{{{#!make
#
# CCS WORKSHOP
# Stokes Flow in a Cavity
#
# Makefile
#
#
TARGET = ex32s ex32m
#
ALL: $(TARGET)
#
CC = icc
 
#CFLAGS = -O3
CFLAGS = -g -pg -DDEBUG
#
#
#
SRC_EX32c = ex32.c stokeslet2d.c gmres.c
#
#
MKL_SQ_LIBS = -L$(MKLROOT)/lib/intel64/ \
	-I$(MKLROOT)/mkl/include \
	-Wl,--start-group \
	$(MKLROOT)/lib/intel64/libmkl_intel_lp64.a \
	$(MKLROOT)/lib/intel64/libmkl_sequential.a \
	$(MKLROOT)/lib/intel64/libmkl_core.a \
	-Wl,--end-group \
	-lpthread
#
MKL_MT_LIBS = -L$(MKLROOT)/lib/intel64/ \
	-I$(MKLROOT)/mkl/include \
	-Wl,--start-group \
	$(MKLROOT)/lib/intel64/libmkl_intel_lp64.a \
	$(MKLROOT)/lib/intel64/libmkl_intel_thread.a \
	$(MKLROOT)/lib/intel64/libmkl_core.a \
	-Wl,--end-group \
	-liomp5 \
	-lpthread
#
#
#
OBJ_EX32c = $(SRC_EX32c:.c=.o)
#
#
ex32s : $(OBJ_EX32c)
	$(CC) $(CFLAGS) -o $@ $(OBJ_EX32c) $(MKL_SQ_LIBS)
 
ex32m : $(OBJ_EX32c)
	$(CC) $(CFLAGS) -o $@ $(OBJ_EX32c) $(MKL_MT_LIBS)
 
#
#
%.o : %.c
	$(CC) $(CFLAGS) -c $<
 
#
clean:	
	rm -f *.o $(TARGET)
}}}

== GDB ==
You can use '''GDB''' on CCS cluster. [[http://www.gnu.org/software/gdb/|GDB]]

To debug with '''GDB''', submit an interactive job. [[https://wiki.hpc.tulane.edu/trac/wiki/cypress/using#SubmittingInteractiveJobs|See here]]

Compiling with '''-g''' option
{{{
 icc -g -pg -DDEBUG -c stokeslet2d.c
}}}
run '''gdb'''
{{{
user@host>gdb ./ex32s 
GNU gdb (GDB) Red Hat Enterprise Linux (7.2-56.el6)
Copyright (C) 2010 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /ccs-autofs/u01/fuji/LabWork/FlowInCavity/ex32s...done.
(gdb) 
}}}

show source by command, list '''line#'''
{{{
(gdb) list 44
39	    printf("Usage:%s [Depth of Cavity]\n",argv[0]);
40	    exit(-1);
41	  }
42	
43	  /* get inputed depth */
44	  dp = atof(argv[1]);
45	
46	  /* # of particles in depth */
47	  numpdepth = (int)(dp / EPSILON + 0.5);
48	  
(gdb)
}}}
set breakpoint by command, '''b line#'''
{{{
(gdb) b 47
Breakpoint 1 at 0x4044c2: file ex32.c, line 47.
(gdb) 
}}}
'''run [command line option]'''
{{{
(gdb) run 5
Starting program: /ccs-autofs/u01/fuji/LabWork/FlowInCavity/ex32s 1
[Thread debugging using libthread_db enabled]

Breakpoint 1, main (argc=2, argv=0x7fffffffd5c8) at ex32.c:47
47	  numpdepth = (int)(dp / EPSILON + 0.5);
Missing separate debuginfos, use: debuginfo-install glibc-2.12-1.80.el6_3.3.x86_64
(gdb) 
}}}

print values
{{{
(gdb) p dp
$1 = 5
(gdb) p numpdepth
$2 = 0
(gdb) 
}}}

continue one step
{{{
(gdb) next
50	  numpwidth = (int)(1.0 / EPSILON + 0.5);
(gdb) p numpdepth
$3 = 1000
(gdb) 
}}}

exit
{{{
(gdb) quit
A debugging session is active.

	Inferior 1 [process 6222] will be killed.

Quit anyway? (y or n) y
}}}