Changes between Initial Version and Version 1 of cypress/Programming/CodeDebugging

Timestamp:

08/19/15 17:02:48 (9 years ago)

Author:

fuji

Comment:

—

cypress/Programming/CodeDebugging

@@ +1 @@
+= 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
+}}}