[Dock-fans] Fw: Re: Fwd: Re: Ligand Docking with DOCK6

Scott Brozell sbrozell at scripps.edu
Thu Apr 17 23:53:35 PDT 2008


Hi,

On Thu, 17 Apr 2008, Francesco Pietra wrote:

> Hi:
> To remove any doubt (below) about the importance of max_orientations size, this was increased from 1000 to 10000. Same error message and behavior of CPU/MEM on "top -i" for command dock6 (serial flex run).
> 

Ok.

> Is previous suggestion:
> 
> "Some remaining possibilities are a too big selected_spheres.sph
> and a bug.  Please determine the size of the sphere file
> that does run with dock6 (and report the memory usage using
> top by systematically reducing selected_spheres.sph"
> 
> still valid in this form? If so, I'll follow these indications. There must be a way out of this issue, unless the memory request is highly exponential. The size of the ligand has increased by a tiny margin.
> 

Yes, definitely.  This is the prime candidate.

Scott

> Thanks
> francesco pietra
> 
> 
> --- On Wed, 4/16/08, Scott Brozell <sbrozell at scripps.edu> wrote:
> 
> > From: Scott Brozell <sbrozell at scripps.edu>
> > Subject: Re: Fw: Re: Fwd: Re: [Dock-fans] Ligand Docking with DOCK6
> > To: "Francesco Pietra" <chiendarret at yahoo.com>
> > Cc: "dock-fans" <dock-fans at docking.org>
> > Date: Wednesday, April 16, 2008, 11:11 PM
> > Hi,
> > 
> > On Wed, 16 Apr 2008, Francesco Pietra wrote:
> > 
> > > I got another message from the debian web list:
> > > 
> > > >>The std:: would to me make me think C++
> > namespace 'std' function
> > > >>'bad_alloc'.  So probably a bad_alloc
> > function exists in C++ and is
> > > >>returning an error.
> > > 
> > > >It is a standard exception thrown when the new()
> > operator fails.
> > > >Your running out of RAM, perhaps.
> > 
> > Yes.
> > 
> > 
> > > >Do you build this program yourself from source?
> > > 
> > > Yes, it passed OK all tests, both serial and parallel
> > and it works fine with smaller ligands.
> > > 
> > > francesco
> > > 
> > > --- On Wed, 4/16/08, Francesco Pietra
> > <chiendarret at yahoo.com> wrote:
> > > 
> > > > From: Francesco Pietra
> > <chiendarret at yahoo.com>
> > > > Subject: Re: Fwd: Re: [Dock-fans] Ligand Docking
> > with DOCK6
> > > > To: "Scott Brozell"
> > <sbrozell at scripps.edu>
> > > > Cc: "dock-fans"
> > <dock-fans at docking.org>
> > > > Date: Wednesday, April 16, 2008, 2:25 PM
> > > > Hi:
> > > > Having completed the new machine with 8 logical
> > 875
> > > > opterons and 24GB memory,  using the same two
> > raid1 HDD
> > > > (with few adjustments, such as shmmax to 24GB and
> > stack
> > > > size unlimited) of previous machine, I tried
> > again the flex
> > > > below. Quickly same error (St9bad_alloc) with
> > (top -i) CPU
> > > > starting at  100%% and MEM% 0 throughout.
> > > > 
> > > > I posted that error message to the debian web
> > list getting
> > > > a partial answer, that is reported here
> > unabridged:
> > > > 
> > > > The std:: would to me make me think C++ namespace
> > > > 'std' function
> > > > 'bad_alloc'.  So probably a bad_alloc
> > function
> > > > exists in C++ and is
> > > > returning an error.
> > > > I personally try to avoid dealing with C++ code
> > anymore. 
> > > > It is get
> > > > ting
> > > > too ugly after the STL stuff went in.
> > > > Try a search for 'C++ bad_alloc' and you
> > will find
> > > > lots of stuff on
> > > > bad_alloc in the C++ std library.  About 45000
> > hits in
> > > > google.
> > > > 
> > > > Is that suggesting anything before I go to
> > investigate
> > > > systematically the mem% vs. sphere_select
> > dimensions?
> > 
> > No.
> > 
> > 
> > > > I recall that with smaller selected_spheres the
> > error
> > > > message was: Could not complete growth; confirm
> > grid box is
> > > > large enough   to contain ligand and try
> > increasing
> > > > max_orients.
> > 
> > With continuous score the grid box does not exist;
> > it is still possible that max_orientations is too small,
> > but the value of 1000 makes it very unlikely.
> > 
> > Scott



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