[Dock-fans] Fwd: Large ligand on Large grid Kill mpirun

Scott Brozell sbrozell at scripps.edu
Sun Nov 18 00:04:36 PST 2007


Hi,

The failure occurs in Orient::match_ligand.
This is the focal point of much memory consumption.
The simplest patch would be additional hardware memory.

Scott

On Fri, 16 Nov 2007, Francesco Pietra wrote:

> I forgot an important observation: docking procedures went on regularly even
> for the largest (155 and 165 atoms) ligands when, on previous runs, the spheres
> covered ca 1/4 of the protein.
>
> --- Francesco Pietra <chiendarret at yahoo.com> wrote:
>
> > Date: Fri, 16 Nov 2007 02:11:22 -0800 (PST)
> > From: Francesco Pietra <chiendarret at yahoo.com>
> > Subject: Large ligand on Large grid Kill mpirun
> > To: dock-fans <dock-fans at docking.org>
> >
> > Following careful comparative runs I arrived at the conclusion that too large
> > ligands on large grids kill mpirun.
> >
> > With grid files and selected_spheres.sph (10,536,750 grid points), for
> > ligands
> > of 118 atoms, or less, docking and amber rescore procedures went to
> > completion
> > OK. Selected spheres was centered (Magis' sphere_select) symmetrically in the
> > protein for a 25A radius, whereby the spheres covered most of the protein.
> >
> > mpirun failure occurred with two ligands of much similar shape as above
> > though
> > larger (155 atoms and 165 atoms)
> >
> >
> > How mpirun was killed shortly after launching the rigid score procedure, is
> > shown by outputting the screen events following "mpirun -np 4 -i rigid.in -o
> > rigid.out 2>&1 | tee screen.out":
> >
> > Initializing MPI Routines...
> > Initializing MPI Routines...
> > Initializing MPI Routines...
> > Initializing MPI Routines...
> > terminate called after throwing an instance of 'std::bad_alloc'
> >   what():  St9bad_alloc
> > [deb64:03725] *** Process received signal ***
> > [deb64:03725] Signal: Aborted (6)
> > [deb64:03725] Signal code:  (-6)
> > [deb64:03725] [ 0] /lib/libpthread.so.0 [0x2b21e08e0410]
> > [deb64:03725] [ 1] /lib/libc.so.6(gsignal+0x3b) [0x2b21e0a1807b]
> > [deb64:03725] [ 2] /lib/libc.so.6(abort+0x10e) [0x2b21e0a1984e]
> > [deb64:03725] [ 3]
> > /usr/lib/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x114)
> > [0x2b21e0583424]
> > [deb64:03725] [ 4] /usr/lib/libstdc++.so.6 [0x2b21e05815a6]
> > [deb64:03725] [ 5] /usr/lib/libstdc++.so.6 [0x2b21e05815d3]
> > [deb64:03725] [ 6] /usr/lib/libstdc++.so.6 [0x2b21e05816ba]
> > [deb64:03725] [ 7] dock6.mpi(main+0) [0x42c180]
> > [deb64:03725] [ 8] /usr/lib/libstdc++.so.6(_Znwm+0x34) [0x2b21e0581954]
> > [deb64:03725] [ 9] /usr/lib/libstdc++.so.6(_Znam+0x9) [0x2b21e0581a49]
> > [deb64:03725] [10] dock6.mpi(_ZN6Orient12match_ligandER7DOCKMol+0x375)
> > [0x447a85]
> > [deb64:03725] [11] dock6.mpi(main+0xaf5) [0x42cc75]
> > [deb64:03725] [12] /lib/libc.so.6(__libc_start_main+0xda) [0x2b21e0a054ca]
> > [deb64:03725] [13] dock6.mpi(__gxx_personality_v0+0xc2) [0x41b4ea]
> > [deb64:03725] *** End of error message ***
> > mpirun noticed that job rank 0 with PID 3724 on node deb64 exited on signal
> > 15
> > (Terminated).
> > 3 additional processes aborted (not shown).
> >
> > File rigid.out showed correct reading of grid.nrg.
> >
> > _______
> > The procedure failed also on serial run with
> >
> > dock6 -i rigid.in -o rigid.out 2>&1 screen_serial.out
> >
> > screen_serial.out:
> >
> > terminate called after throwing an instance of 'std::bad_alloc'
> > waht(): St9bad_alloc
> >
> >
> > i.e, as it was already clear from the above, not a problem of mpi.
> >
> > ______
> >
> > I understand to be largely out of the main stream of docking procedures (and
> > probably scope). Nonetheless, I am interested in how these large ligands
> > behave. Therefore, how could I manage to compare the above ligands of various
> > size?. I am wondering about changing the grid space and see if docking with
> > the
> > smaller ligands changes much or not. If OK I could try the larger ligands
> > with
> > the new grid. Any better idea? I am not considering to work without a grid
> > because I want to compare several molecules. So far I used defaults from
> > tutorials, i.e. for grid.in:
> >
> > compute_grids                  yes
> > grid_spacing                   0.3
> > output_molecule                no
> > contact_score                  no
> > energy_score                   yes
> > energy_cutoff_distance         9999
> > atom_model                     a
> > attractive_exponent            6
> > repulsive_exponent             12
> > distance_dielectric            yes
> > dielectric_factor              4
> > bump_filter                    yes
> > bump_overlap                   0.75
> > receptor_file    /home/francesco/dockwork/grid/myprotein.mol2
> > box_file            /home/francesco/dockwork/grid/rec_box.pdb
> > vdw_definition_file /usr/local/dock6/parameters/vdw_AMBER_parm99.defn
> > score_grid_prefix              grid
> >
> >
> > All that was carried out using A. Magis' sphgen_cpp and sphere_select.
> >
> > Thanks
> >
> > francesco pietra


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