I'm running Rosetta single state design (though I imagine my question applies to MSD as well), which works great on a single core or my local machine. I'm using rosetta_scripts.mpi.linuxgccrelease as my package. It is compiled by my HPC administrator to function with the cluster.
I'm running this script on a single node, with 28 processors per node. I am generating 100 models for the time being, but when I view the design.fasc file after the design is completed, there are 28*100 = 2800 entries. However, there are only 100 PDBs produced as a result of the design. I believe that 2800 models were indeed designed, but the models are being overwritten by the last core to complete that particular numbered model (since they all have the same filename, i.e. pdbID_design_0001.pdb).
Why are my files getting overwritten by cores, and how do I make each core output a unique name for the design.fasc row entry and the .pdb output file?