[Dock-fans] failure on dock.mpi

Scott Brozell sbrozell at scripps.edu
Mon Jul 9 14:22:03 PDT 2007


Hi,

On Mon, 9 Jul 2007, Alessandro Nascimento wrote:

> I'm new to dock and also to molecular docking...
> I took a look at the tutorials, and I am trying to do my first dock
> using a database (zinc).
> When running dock in a single processor, my job works fine. When I try
> it in parallel (5 processors, mpich2), i get the following error
>
> [cli_1]: rank 0 in job 8  ruska_37276   caused collective abort of all ranks
>   exit status of rank 0: killed by signal 11
>
> I pasted my dock input file below. Any clue to this problem?

The error above is a generic one from MPI.
Did you look for clues in the dock output ?
What happens with 1, 2, or 3 numbers of processors ?

Did the dock6/install/test/mpi quality control regression test pass ?
Retry it:
cd dock6/install/test/mpi
make clean
make

Can you run other MPI programs ?

Scott

> ligand_atom_file                                             zinc.mol2
> limit_max_ligands                                            yes
> max_ligands                                                  100
> skip_molecule                                                no
> read_mol_solvation                                           no
> calculate_rmsd                                               no
> orient_ligand                                                yes
> automated_matching                                           yes
> receptor_site_file                                           rec.sph
> max_orientations                                             120000
> critical_points                                              yes
> chemical_matching                                            yes
> chem_match_tbl
> /home/apps/dock/dock6/parameters/chem_match.tbl
> use_ligand_spheres                                           no
> flexible_ligand                                              no
> bump_filter                                                  no
> score_molecules                                              yes
> contact_score_primary                                        no
> contact_score_secondary                                      no
> grid_score_primary                                           yes
> grid_score_secondary                                         no
> grid_score_rep_rad_scale                                     1
> grid_score_vdw_scale                                         1
> grid_score_es_scale                                          1
> grid_score_grid_prefix                                       grid
> dock3.5_score_secondary                                      no
> continuous_score_secondary                                   yes
> cont_score_rec_filename                                      rec_charged.mol2
> cont_score_att_exp                                           6
> cont_score_rep_exp                                           12
> cont_score_rep_rad_scale                                     1
> cont_score_dielectric                                        4.0
> cont_score_vdw_scale                                         1
> cont_score_es_scale                                          1
> minimize_ligand                                              yes
> simplex_max_iterations                                       1000
> simplex_max_cycles                                           1
> simplex_score_converge                                       0.1
> simplex_cycle_converge                                       1.0
> simplex_trans_step                                           1.0
> simplex_rot_step                                             0.1
> simplex_tors_step                                            10.0
> simplex_final_min                                            no
> simplex_secondary_minimize_pose                              yes
> use_advanced_secondary_simplex_parameters                    no
> simplex_secondary_max_iterations                             100
> simplex_secondary_min_add_internal                           no
> simplex_random_seed                                          0
> atom_model                                                   all
> vdw_defn_file
> /home/apps/dock/dock6/parameters/vdw_AMBER_parm99.defn
> flex_defn_file
> /home/apps/dock/dock6/parameters/flex.defn
> flex_drive_file
> /home/apps/dock/dock6/parameters/flex_drive.tbl
> chem_defn_file
> /home/apps/dock/dock6/parameters/chem.defn
> ligand_outfile_prefix                                        flex
> write_orientations                                           no
> num_primary_scored_conformers_rescored                       4
> cluster_primary_conformations                                yes
> cluster_rmsd_threshold                                       2.0
> num_clusterheads_for_rescore                                 5
> num_secondary_scored_conformers_written                      4
> rank_primary_ligands                                         no
> max_primary_ranked                                           10
> rank_secondary_ligands                                       no
> max_secondary_ranked                                         10


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