troubleshooting.md

Troubleshooting Notes

🔵 My output appears to be out of order: errors are not printed exactly when they occur

If you redirect stdout and stderr to a file, you may notice that stderr lines are out-of-order with respect to the stdout lines; for example:

myAnalysisProgram                    # stdout and stderr print when they happen; ordering appears correct

myAnalysisProgram |& tee output.txt  # stderr prints when it happens, but stdout only prints when its buffer is full;
                                     # ordering appears mixed up

To redirect output to a file with the ordering preserved, run your executable with stdout unbuffered:

stdbuf -o0 myAnalysisProgram |& tee output.txt

Note

stdbuf on macOS may be installed as gstdbuf, from the Homebrew package coreutils.

🔵 I got a crash, but the stack trace (or debugger) is not telling me exactly where

Enable debugging symbols by setting the Iguana build option buildtype to 'debug', then rebuild. Assuming you're in your build directory, run:

meson configure -Dbuildtype=debug

Then rebuild (meson compile and/or meson install).

Remember to revert this change and rebuild/re-install, so that Iguana runs with full optimization when you are processing large data sets (-Dbuildtype=release).