GNU Astronomy Utilities Crop known issues

When running Crop, you may encounter strange errors and bugs. In these cases, please report a bug and we will try to fix it as soon as possible, see Report a bug. However, some things are beyond our control, or may take too long to fix directly. In this section we list such known issues that may occur in known cases and suggest the hack (or work-around) to fix the problem:

Crash with ‘Killed’ when cropping catalog from .fits.gz

This happens because CFISTIO (that reads and writes FITS files) will internally decompress the file in a temporary place (possibly in the RAM), then start reading from it. On the other hand, by default when given a catalog (with many crops) and not specifying --numthreads, Crop will use the maximum number of threads available on your system to do each crop faster. On an normal (not compressed) file, parallel access will not cause a problem, however, when attempting parallel access with the maximum number of threads on a compressed file, CFITSIO crashes with Killed. Therefore the following solutions can be used to fix this crash:

  • Decrease the number of threads (at the minimum, set --numthreads=1). Since this solution does not attempt to change any of your previous Crop command components or does not change your local file structure, it is the preferred way.
  • Decompress the file (with the command below) and feed the .fits file into Crop without changing the number of threads.
    $ gunzip -k image.fits.gz