Segmentation faults frequently occur while mrs is indexing the pubmed databank, using the raw xml files from ftp://ftp.ncbi.nih.gov/pub/pmc/articles*.tar.gz as input. The location of the segfaults vary, but they always co-occur with an allocation or deallocation. Inspection of some of the deallocation segfaults at https://github.com/cmbi/mrs/blob/master/src/M6Lexicon.cpp#L213 shows that the involved pointers are valid.
Facts about the update process:
MRS always reports invalid checksums for the pumbed tars, though they are readable by commandline tar.
pubmed updating occurs in multiple threads. One thread per archive.
MRS uses a custom XML parser for pubmed
The pubmed xml files are much larger than the average pdb file.
Segmentation faults frequently occur while mrs is indexing the pubmed databank, using the raw xml files from ftp://ftp.ncbi.nih.gov/pub/pmc/articles*.tar.gz as input. The location of the segfaults vary, but they always co-occur with an allocation or deallocation. Inspection of some of the deallocation segfaults at https://github.com/cmbi/mrs/blob/master/src/M6Lexicon.cpp#L213 shows that the involved pointers are valid.
Facts about the update process: