sequence_tolerance is very slow when -ms:num_packs > 1

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    • August 25, 2016 at 8:17 pm #2495
      Anonymous

        Hi,

        here is the command I used. When I set num_packs to 1 which is the default value, the program runs pretty fast, when I set it to other values, the program is stuck there. The version is rosetta 3.6.

         

        sequence_tolerance.default.linuxgccrelease

            -in:file:s test.pdb

            -packing:resfile resfile -ex1 -ex2 -ex1aro -ex2aro

            -ms:pop_size 100 -ms:generations 100

            -ms:checkpoint:interval 1

            -ms:checkpoint:prefix startcheckpoint

            -ms:numresults 10

            -ms:mutate_rate 0.3

            -ms:fraction_by_recombination 0.5

            -ms:num_packs 2

            -seq_tol:fitness_master_weights 1 1 1 1 1 1 1

            -score:weights talaris2014

        Since there is no output after

        Score Type                  Other        A        B        C      A-B      A-C      B-C    Total

        fa_atr                      0.000 -453.511 -512.269-1143.447  -58.445  -30.394   -7.535-2205.601

        fa_rep                      0.000   57.574  175.912  133.226    7.056    2.837    1.549  378.154

        fa_sol                      0.000  249.464  295.335  650.335   27.090   18.049    5.384 1245.656

        fa_intra_rep                0.000    1.065    1.177    2.441    0.000    0.000    0.000    4.682

        fa_elec                     0.000  -50.126  -56.237 -107.023   -4.919   -3.522   -0.434 -222.261

        pro_close                   0.000    4.056    4.296    7.143    0.000    0.000    0.000   15.495

        hbond_sr_bb               -40.173    0.000    0.000    0.000    0.000    0.000    0.000  -40.173

        hbond_lr_bb              -148.777    0.000    0.000    0.000    0.000    0.000    0.000 -148.777

        hbond_bb_sc                 0.000   -6.987  -13.222  -43.142   -3.199   -2.022   -0.537  -69.110

        hbond_sc                    0.000   -7.488   -8.867  -17.966   -3.191    0.000    0.000  -37.511

        dslf_fa13                   0.000    2.973   -0.947   -3.452    0.000    0.000    0.000   -1.426

        rama                        0.000   -3.463   -9.752  -10.991    0.000    0.000    0.000  -24.205

        omega                       0.000   23.100   25.336   49.735    0.000    0.000    0.000   98.171

        fa_dun                      0.000  178.956  172.310  449.423    0.000    0.000    0.000  800.689

        p_aa_pp                     0.000  -14.153  -19.297  -32.825    0.000    0.000    0.000  -66.275

        yhh_planarity               0.000    0.857    0.664    1.164    0.000    0.000    0.000    2.686

        ref                         0.000   15.174   13.270  -15.349    0.000    0.000    0.000   13.095

        Total                    -188.949   -2.509   67.709  -80.727  -35.609  -15.053   -1.573 -256.711

        core.pack.pack_rotamers: built 18608 rotamers at 43 positions.

        core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph

        core.pack.interaction_graph.interaction_graph_factory: IG: 251642404 bytes

        app.sequence_tolerance: There are 1 positive states and 0 negative states

        protocols.multistate_design.MultiStatePacker: Best single-state design score:  -272.42

        I do not know what is the problem. Thank you very much for help.

        Best wishes,

        Ting

         

      • August 25, 2016 at 9:25 pm #11818
        Anonymous

          I don’t see anything obviously wrong with the for loop controlled by that variable.  I’ll let the authors know there’s a potential bug.

           

          You can try turning up the verbosity (I think it’s out:level 500) to see if whatever infinite loop it’s stuck in has some output to clue us in.

        • August 26, 2016 at 6:33 am #11819
          Anonymous

            Hi,

             

            here are the information given by ” out:level 500 “.

             

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 57: -62.7396 77.9973 0  Bump energy: 325.837 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 58: -62.7396 77.9973 180  Bump energy: 426.887 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 59: -62.7396 64.5831 0  Bump energy: 464.677 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 60: -62.7396 64.5831 180  Bump energy: 535.242 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 61: -53.8351 71.2902 0  Bump energy: 464.465 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 62: -53.8351 71.2902 180  Bump energy: 604.308 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 63: -53.8351 77.9973 0  Bump energy: 395.141 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 64: -53.8351 77.9973 180  Bump energy: 558.033 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 65: -53.8351 64.5831 0  Bump energy: 537.635 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 66: -53.8351 64.5831 180  Bump energy: 650.518 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 67: -71.6441 71.2902 0  Bump energy: 300.03 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 68: -71.6441 71.2902 180  Bump energy: 302.649 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 69: -71.6441 77.9973 0  Bump energy: 237.579 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 70: -71.6441 77.9973 180  Bump energy: 242.288 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 71: -71.6441 64.5831 0  Bump energy: 350.537 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 72: -71.6441 64.5831 180  Bump energy: 351.994 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 73: 179.006 102.599 0  Bump energy: -5.23143 … added

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 74: 179.006 102.599 180  Bump energy: -6.31903 … added

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 75: 179.006 110.198 0  Bump energy: -4.83757 … added

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 76: 179.006 110.198 180  Bump energy: -5.74812 … added

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 77: 179.006 95.0006 0  Bump energy: -5.15214 … added

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 78: 179.006 95.0006 180  Bump energy: -6.43787 … added

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 79: 188.894 102.599 0  Bump energy: 10.1128 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 80: 188.894 102.599 180  Bump energy: -6.64886 … added

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 81: 188.894 110.198 0  Bump energy: 5.55907 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 82: 188.894 110.198 180  Bump energy: -6.33822 … added

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 83: 188.894 95.0006 0  Bump energy: 13.1436 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 84: 188.894 95.0006 180  Bump energy: -6.6831 … added

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 85: 169.118 102.599 0  Bump energy: 28.3006 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 86: 169.118 102.599 180  Bump energy: 35.5096 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 87: 169.118 110.198 0  Bump energy: 16.2895 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 88: 169.118 110.198 180  Bump energy: 23.4577 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 89: 169.118 95.0006 0  Bump energy: 34.2241 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 90: 169.118 95.0006 180  Bump energy: 40.4823 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 91: -62.7396 119.418 0  Bump energy: 134.544 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 92: -62.7396 119.418 180  Bump energy: 304.247 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 93: -62.7396 127.127 0  Bump energy: 119.262 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 94: -62.7396 127.127 180  Bump energy: 289.339 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 95: -62.7396 111.708 0  Bump energy: 142.722 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 96: -62.7396 111.708 180  Bump energy: 307.642 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 97: -53.8351 119.418 0  Bump energy: 322.247 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 98: -53.8351 119.418 180  Bump energy: 496.793 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 99: -53.8351 127.127 0  Bump energy: 307.937 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 100: -53.8351 127.127 180  Bump energy: 480.624 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 101: -53.8351 111.708 0  Bump energy: 327.012 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 102: -53.8351 111.708 180  Bump energy: 510.315 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 103: -71.6441 119.418 0  Bump energy: 12.6719 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 104: -71.6441 119.418 180  Bump energy: 77.9712 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 105: -71.6441 127.127 0  Bump energy: 8.87936 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 106: -71.6441 127.127 180  Bump energy: 79.6865 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 107: -71.6441 111.708 0  Bump energy: 17.8848 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  Suggested rotamer 108: -71.6441 111.708 180  Bump energy: 73.2633 … deleted

            core.pack.rotamers.SingleResidueRotamerLibrary:  N rotamers before: 108 after: 19

            core.pack.pack_rotamers: built 18608 rotamers at 43 positions.

            core.pack.interaction_graph.interaction_graph_factory: Instantiating PDInteractionGraph

            core.pack.interaction_graph.interaction_graph_factory: IG: 251642404 bytes

            app.sequence_tolerance: There are 1 positive states and 0 negative states

            core.pack.annealer.AnnealerFactory: Creating FixbbSimAnnealer

            protocols.multistate_design.MultiStatePacker: Best single-state design score:  -272.56

            Thank you and best wishe,

            Ting

          • August 26, 2016 at 7:01 am #11820
            Anonymous

              Hi,

              I think I find the reason. If there are old checkpoint files in the folder, the calculation will be stuck. It is not relate to -ms:num_packs.

              Best wishes,

              Ting

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