score_jd2.mpi.linuxgccrelease failed

It looks like your job distribution system or kernel is killing your jobs because they are exhausting your available memory. As a rough rule of thumb, each Rosetta process needs about 1 GB of memory in the default state. (This depends highly on which protocol you're running, how big your proteins are, etc. - just scoring is going to be less memory intensive than other protocols, but I'd estimate at least 0.75 GB per process.) So if you're running MPI on one node with 12 processor, you're looking at around 12 GB of memory usage. If that node only has, say, 8 GB of memory, you'll run out of memory and you may get the jobs killed.

There's several ways of reducing memory usage. Probably the easiest is to disable patches you're probably not using. Adding "--chemical:exclude_patches LowerDNA UpperDNA Cterm_amidation SpecialRotamer VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylatedcys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm" to your commandline or flags file will save you about 200-250 MB (edit as appropriate if you need hydroxylated proline, say). If you want to go further, in the main/database/chemical/residue_type_sets/fa_standard/residue_types/ directory there's "*.slim" versions of residue_types.txt and patches.txt, which, if used to replace the non-slim versions, will likely net you another ~200 MB memory savings - you'll then only be able to deal with simple protein-only structures, though. You'll still need somewhere around 500 MB of memory for each process even with those changes.

The easiest way to fix things, though, is to simply run fewer processes on the node, so you limit the number of processors based on available memory, rather than available processors, and potentially spread your MPI runs out across more nodes, if available.