I am preparing the pdbs from pdb.org for scaffold. About more than 6000 pdbs were downloaded and have been preparing. However, the memory leak was encountered. I have try to use -linmem_ig 10 and -jd2:delete_old_poses to resolve the problem. But the memory leak is still there.
Could you help me to solve this problem?
Thanks a lot.
The workstation we are using has 48 cores and 128GB memory, the rosetta version is 2019.1460699. I have also tried to run in another verision of rosetta (2018.48.60516), the memory leak also can be found.
mpirun -np 45 rosetta_scripts.mpi.linuxgccrelease -s scaffold/*.pdb.atoms @prepare.option > ppk_min.log &
<Rmsd name="rmsd" threshold="1.5" superimpose="1"/>
<Prepack name="ppk" jump_number="0"/>
<MinMover name="sc_bb_min" bb="1" chi="1"/>