I only list few functions and commands that I use them to find bugs in R and C. I will come back to explain them when I have time. #### Debug in R - <a href="./reference/debug/Rdebug.pdf">Rdebug.pdf</a> - I lost the original of this file. Please tell me where this good slide came from if you knew. - <a href="./reference/debug/R-debug-tools.pdf">R-debug-tools.pdf</a> - Roger D. Peng, UCLA, Department of Statistics. #### Debug in C - <a href="http://www.gnu.org/software/ddd/" target="_blank">ddd</a> - Linux command: <code>nm</code>, <code>ld</code>, <code>gprof</code>. - <a href="http://valgrind.org/" target="_blank">valgrind</a> Quick Example: ``` SHELL> gcc -g -o a.out *.c SHELL> valgrind --show-reachable=yes --leak-check=full a.out SHELL> valgrind --track-origins=yes ./a.out SHELL> gcc -pg -o a.out *.c SHELL> ./a.out SHELL> gprof > a.prof ``` #### Debug in R call C - <a href="http://valgrind.org/" target="_blank">valgrind</a> Quick Example: ``` SHELL> gcc -shared -g -o a.so *.c SHELL> R -d "valgrind --show-reachable=yes --tool=memcheck --leak-check=full" \ --vanilla < a.r SHELL> R -d "valgrind --track-origins=yes" --vanilla < a.r ``` Here, "a.r" should load "a.so" at the first. - <a href="http://bioconductor.fhcrc.org/workshops/2010/AdvancedR/using-gdb-with-R.mov" target="_blank">Debugging with GDB</a> #### Debug in MPI for R call C - <a href="http://valgrind.org/" target="_blank">valgrind</a> Quick Example: ``` SHELL> gcc -shared -g -o a.so *.c SHELL> mpiexec -np 2 R -d \ "valgrind --show-reachable=yes --tool=memcheck --leak-check=full --log-file=a.log" \ --vanilla -f a.r SHELL> mpiexec -np 2 R -d \ "valgrind --track-origins=yes --log-file=a.log" \ --vanilla -f a.r ``` Here, "a.so" is a MPI application, "a.r" should load "a.so" at the first, and the output file "a.log" has the tracing results. --- <div w3-include-html="../preamble_tail_date.html"></div>