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

Scott Brozell sbrozell at scripps.edu
Sun Nov 18 10:58:03 PST 2007


Hi,

Check the memory availability with the limit command.
And change values with the limit, ulimit, or unlimit commands.

Scott

On Sun, 18 Nov 2007, Francesco Pietra wrote:

> There are 4GB ram (in 2GB slots Kingston ecc 400MHz) per processor (for a total
> of 16GB ram) and Linux is set to let all that be used. Perhaps you may suggest
> how to set the configuration better in order that all ram is used by DOCK.
>
> With the slightly smaller ligands, where DOCK run correctly, I detected through
> "top -i" a max of 24% memory used by one of the two processors in use. All four
> processors were only used during amber rescore, and only for the initial half
> reriod of the procedure. Then, the number dropped to two even for amber
> rescore.
> Thanks
> francesco
>
> --- Scott Brozell <sbrozell at scripps.edu> wrote:
>
> > 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
> >
>
>
>
>       ____________________________________________________________________________________
> Be a better sports nut!  Let your teams follow you
> with Yahoo Mobile. Try it now.  http://mobile.yahoo.com/sports;_ylt=At9_qDKvtAbMuh1G1SQtBI7ntAcJ
>



More information about the Dock-fans mailing list