sbmlteam / libsbml

The following program segfault when fed the following uncompressed file

#include <stdio.h>
#include <sbml/SBMLTypes.h>
#include "util.h"

int main (int argc, char *argv[])
{
  if (argc != 2)
  {
    printf("Usage: readSBML filename\n");
    return 2;
  }

  const char * filename = argv[1];
  SBMLDocument_t *d = readSBML(filename);

  int success = SBMLDocument_setLevelAndVersion(d, 3, 2);
  printf("Success: %d\n", success);

  ConversionProperties_t* props;

  props = ConversionProperties_create();
  ConversionOption_t * expandFuncDefOpt = ConversionOption_create("expandFunctionDefinitions");
  ConversionProperties_addOption(props, expandFuncDefOpt);
  SBMLDocument_convert(d, props);
  ConversionOption_free(expandFuncDefOpt);
  ConversionProperties_free(props);

  props = ConversionProperties_create();
  ConversionOption_t * inferUnitsOpt = ConversionOption_create("inferUnits");
  ConversionProperties_addOption(props, inferUnitsOpt);
  SBMLDocument_convert(d, props);
  ConversionOption_free(inferUnitsOpt);
  ConversionProperties_free(props);

  SBMLDocument_free(d);
}

From what I gathered, it is because tempUD1 is set to NULL here:

libsbml/src/sbml/units/UnitFormulaFormatter.cpp

Line 2635 in 49ce5b4

UnitDefinition * tempUD1 = inverseFunctionOnUnits(tempUD, child1,

The reason for that is that inverseFunctionOnUnits calls UnitDefinition::divide on two UnitDefinitions having different level and version (L2V4 like the original doc and L3V2 like the converted one), so we are falling in the following branch:

libsbml/src/sbml/UnitDefinition.cpp

Line 1467 in 49ce5b4

else if ( (ud1->getLevel() != ud2->getLevel()) ||

I found two ways to avoid the crash:

move the level/version conversion after function expansion and unit inference
keep level/version conversion first but group function expansion and unit inference into one convert call like this:

  props = ConversionProperties_create();
  ConversionOption_t * expandFuncDefOpt = ConversionOption_create("expandFunctionDefinitions");
  ConversionProperties_addOption(props, expandFuncDefOpt);
  ConversionOption_t * inferUnitsOpt = ConversionOption_create("inferUnits");
  ConversionProperties_addOption(props, inferUnitsOpt);
  SBMLDocument_convert(d, props);
  ConversionOption_free(expandFuncDefOpt);
  ConversionOption_free(inferUnitsOpt);
  ConversionProperties_free(props);

Having level/version conversion in between function expansion and unit inference also segfault.

Thanks very much for this. As far as I know you are the first person to have used the UnitInference since I wrote it some years ago and there may well be undiscovered issues. But thank you for the detailed report this is very helpful

Segmentation fault when doing function expansion and unit inference after conversion to L3V2