[Dock-fans] vm_allocate error when loading grid nrg on Intel Mac

Scott Brozell sbrozell at scripps.edu
Tue Sep 4 11:00:07 PDT 2007


Hi,

On Mon, 3 Sep 2007, Francis E Reyes wrote:

> I seem to have trouble running dock specifically having trouble
> loading my grid nrg file about 26 mb. This is on a Intel Quad Core
> Mac with 2 GB of ram. Funny thing is this nrg file works perfectly
> well on a PPC build, 1GB of ram.
>
> mercury 154% cat error.out
>
> --------------------------------------
> DOCK v6.1
>
> Released December 2006
> Copyright UCSF
> --------------------------------------
>
>
> Molecule Library Input Parameters
> ------------------------------------------------------------------------
> ------------------
> ligand_atom_file                                             /private/
> var/automount/home/reyesf/dock_TTH_trimer/bin2.mol2
> limit_max_ligands                                            no
> skip_molecule                                                yes
> initial_skip                                                 139
> read_mol_solvation                                           no
> calculate_rmsd                                               no
>
> Orient Ligand Parameters
> ------------------------------------------------------------------------
> ------------------
> orient_ligand                                                yes
> automated_matching                                           yes
> receptor_site_file                                           /private/
> var/automount/home/reyesf/dock_TTH_trimer/selected_spheres.sph
> max_orientations                                             100
> critical_points                                              no
> chemical_matching                                            no
> use_ligand_spheres                                           no
>
> Flexible Ligand Parameters
> ------------------------------------------------------------------------
> ------------------
> flexible_ligand                                              yes
> min_anchor_size                                              40
> pruning_use_clustering                                       yes
> pruning_max_orients                                          100
> pruning_clustering_cutoff                                    100
> use_internal_energy                                          yes
> internal_energy_att_exp                                      6
> internal_energy_rep_exp                                      12
> internal_energy_dielectric                                   4.0
> use_clash_overlap                                            no
>
> Bump Filter Parameters
> ------------------------------------------------------------------------
> ------------------
> bump_filter                                                  yes
> bump_grid_prefix                                             /private/
> var/automount/home/reyesf/dock_TTH_trimer/grid
> max_bumps_anchor                                             2
> max_bumps_growth                                             2
>
> Master Score Parameters
> ------------------------------------------------------------------------
> ------------------
> score_molecules                                              yes
>
> Contact Score Paramters
> ------------------------------------------------------------------------
> ------------------
> contact_score_primary                                        no
> contact_score_secondary                                      no
>
> Grid Score Parameters
> ------------------------------------------------------------------------
> ------------------
> 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                                       /private/
> var/automount/home/reyesf/dock_TTH_trimer/grid
>
> Dock3.5 Score Parameters
> ------------------------------------------------------------------------
> ------------------
> dock3.5_score_secondary                                      no
>
> Continuous Energy Score Parameters
> ------------------------------------------------------------------------
> ------------------
> continuous_score_secondary                                   no
>
> Zou GB/SA Score Parameters
> ------------------------------------------------------------------------
> ------------------
> gbsa_zou_score_secondary                                     no
>
> Hawkins GB/SA Score Parameters
> ------------------------------------------------------------------------
> ------------------
> gbsa_hawkins_score_secondary                                 no
>
> Amber Score Parameters
> ------------------------------------------------------------------------
> ------------------
> amber_score_secondary                                        no
>
> Warning:  No secondary scoring function selected.
>
>
> Simplex Minimization Parameters
> ------------------------------------------------------------------------
> ------------------
> minimize_ligand                                              yes
> minimize_anchor                                              yes
> minimize_flexible_growth                                     yes
> use_advanced_simplex_parameters                              no
> 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_anchor_max_iterations                                500
> simplex_grow_max_iterations                                  500
> simplex_final_min                                            no
> simplex_random_seed                                          0
>
> Atom Typing Parameters
> ------------------------------------------------------------------------
> ------------------
> atom_model                                                   all
> vdw_defn_file                                                /private/
> var/automount/home/reyesf/dock6/parameters/vdw_AMBER_parm99.defn
> flex_defn_file                                               /private/
> var/automount/home/reyesf/dock6/parameters/flex.defn
> flex_drive_file                                              /private/
> var/automount/home/reyesf/dock6/parameters/flex_drive.tbl
>
> Molecule Library Output Parameters
> ------------------------------------------------------------------------
> ------------------
> ligand_outfile_prefix                                        flex
> write_orientations                                           no
> num_scored_conformers_written                                10
> cluster_conformations                                        yes
> cluster_rmsd_threshold                                       2
> rank_ligands                                                 yes
> max_ranked_ligands                                           500
> ------------------------------------------------------------------------
> ------------------
>
> Initializing Library File Routines...
> Skipped 139 ligands
>
> Initializing Orienting Routines...
> Initializing Conformer Generator Routines...
> Initializing Bump Filter Routines...
> Reading the bump grid from /private/var/automount/home/reyesf/
> dock_TTH_trimer/grid.bmp
> Initializing Grid Score Routines...
> Reading the energy grid from /private/var/automount/home/reyesf/
> dock_TTH_trimer/grid.nrg
> Error: memory exhausted!
>    For Unix platforms increase the datasize, stacksize, and
>    memoryuse using the limit, ulimit, or unlimit commands.
> mercury 145% dock6 -i anchor_and_grow.in > error.out
> dock6(200) malloc: *** vm_allocate(size=2719518720) failed (error
> code=3)
> dock6(200) malloc: *** error: can't allocate region
> dock6(200) malloc: *** set a breakpoint in szone_error to debug
> terminate called after throwing an instance of 'std::bad_alloc'
>    what():  St9bad_alloc
> Abort
> mercury 146%

2719518720 = 2.5GB
Are you sure of the details ?

How were the grid file(s) generated ?
Note that transferring grid files across machines may fail:
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Grid

Are both machines 32 bit ?
Dock does not fully support 64 bit, but grid has worked for me on 64 bit:
http://dock.compbio.ucsf.edu/DOCK_6/faq.htm

Scott



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