Debugging

How to debug a crash in issm.exe?

If there is crash during the solve phase, we strongly suggest using Valgrind. Install Valgrind using one of the script in the directory ${ISSM_DIR}/externalpackages/valgrind. Valgrind will subsequently be embedded in ISSM and can detect segmentation faults as well as memory leaks. To do so, set the model debugging field to 1 and use only one CPU,

md.debug.valgrind = 1;
md.cluster.np = 1;

in your script, or, simply set,

valgrind = true;

in src/m/classes/debug.m to apply run Valgrind on all subsequently-run scripts. Launch the solution sequence and read the errlog file that it outputs.

When a build includes Boost

If your build includes the Boost C++ libraries, there are additional configuration steps needed to overcome a conflict when running Valgrind. Either,

  1. install Valgrind with externalpackages/valgrind/install-<OS>.sh
  2. set #define BOOST_MATH_PROMOTE_DOUBLE_POLICY false in externalpackages/valgrind/src/boost/math/tools/user.hpp before running bootstrap.sh and b2 install
  3. if you are using Dakota, this will need to be reinstalled as well

Interfaces

How to debug a MATLAB crash?

If there is a crash that is not in issm.exe (sometimes shown as by PETSc’s error manager), one should also use Valgrind. Use the following command,

matlab -nojvm -nosplash -r "your matlab commands" -D"valgrind --error-limit=no --tool=memcheck -v --log-file=valgrind.log"

Valgrind’s output file valgrind.log should help (look for Invalid read and Invalid write).

How to debug a Python crash?

If there is a crash that is not in issm.exe (sometimes shown as by PETSc’s error manager), one should also use Valgrind. Use the following command:

valgrind  --error-limit=no --tool=memcheck -v --log-file=valgrind.log python -E -tt ./yourpythonscript.py

Valgrind’s output file valgrind.log should help (look for Invalid read and Invalid write).

NOTE: if line numbers are not displayed for Mac users, add the following option --dsymutil=yes