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

Francesco Pietra chiendarret at yahoo.com
Wed Apr 16 15:37:50 PDT 2008


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.

>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?
> 
> 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.
> 
> Thanks
> francesco
> 
> 
> 
> 
> --- On Tue, 4/8/08, Scott Brozell
> <sbrozell at scripps.edu> wrote:
> 
> > From: Scott Brozell <sbrozell at scripps.edu>
> > Subject: 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: Tuesday, April 8, 2008, 2:49 PM
> > Hi,
> > 
> > On Tue, 8 Apr 2008, Francesco Pietra wrote:
> > 
> > > $ ulimit -s unlimited only changed in
> "ulimit
> > -a" output:
> > > stack size (k bytes, -s) unlimited
> > > 
> > > Under these new conditions, command:
> > > $ dock6 -i anchor_and_grow_nogrid.in -o
> > anchor_and_grow_nogrid.out
> > > resulted in a few seconds in:
> > > 
> > > terminate called after throwing and instance of
> > 'std::bad_alloc'
> > >    what (): St9bad_alloc
> > > Aborted
> > > 
> > > During this procedure
> > > 
> > > USER        PR  NI  VIRT    RES  
> > SHR    S   CPU   MEM   COMMAND
> > > francesco  20   0   42048  7476  1448  
> > R    100    0    dock6
> > 
> > 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.
> > I ran the continuous score tests using valgrind; there
> were
> > no memory problems detected.  A little gooogggling of 
> > debian std::bad_alloc 
> > didn't find much.  Naturally you should verify
> that all
> > the
> > debian/glib/gcc patches have been applied.
> > 
> > > actually CPU started at 73%, incresed to 100%,
> then
> > died. I am not sure I understand
> > > "memory exhausion", though I am sure
> that
> > during this procedure, memory for dock6
> > > command did not move from zero.
> > 
> > I assume that the dock output file still contained the
> > memory
> > exhausted error message.
> > 
> > Scott
> > 
> > 
> > > RAM on this machine is large because recently I
> used
> > to carry out DFT procedures
> > > with large molecules, recent functionals, and
> > relatively high basis sets.
> > > 
> > > The in file was as before:
> > > 
> > >
> > ligand_atom_file                                      
>      
> > > /home/francesco/dockwork/ligand.mol2
> > >
> > limit_max_ligands                                     
>      
> > no
> > >
> > skip_molecule                                         
>      
> > no
> > >
> > read_mol_solvation                                    
>      
> > no
> > >
> > calculate_rmsd                                        
>      
> > no
> > >
> > orient_ligand                                         
>      
> > yes
> > >
> > automated_matching                                    
>      
> > yes
> > >
> > receptor_site_file                                    
>      
> > > /home/francesco/dockwork/selected_spheres.sph
> > >
> > max_orientations                                      
>      
> > 1000
> > >
> > critical_points                                       
>      
> > no
> > >
> > chemical_matching                                     
>      
> > no
> > >
> > use_ligand_spheres                                    
>      
> > no
> > >
> > 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                                           
>      
> > no
> > >
> > score_molecules                                       
>      
> > yes
> > >
> > contact_score_primary                                 
>      
> > no
> > >
> > contact_score_secondary                               
>      
> > no
> > >
> > grid_score_primary                                    
>      
> > no
> > >
> > grid_score_secondary                                  
>      
> > no
> > >
> > dock3.5_score_primary                                 
>      
> > no
> > >
> > dock3.5_score_secondary                               
>      
> > no
> > >
> > continuous_score_primary                              
>      
> > yes
> > >
> > continuous_score_secondary                            
>      
> > no
> > >
> > cont_score_rec_filename                               
>      
> > > /home/francesco/dockwork/protein.mol2
> > >
> > cont_score_att_exp                                    
>      
> > 6
> > >
> > cont_score_rep_exp                                    
>      
> > 12
> > >
> > cont_score_rep_rad_scale                              
>      
> > 1
> > >
> > cont_score_use_dist_dep_dielectric                    
>      
> > yes
> > >
> > cont_score_dielectric                                 
>      
> > 4.0
> > >
> > cont_score_vdw_scale                                  
>      
> > 1
> > >
> > cont_score_es_scale                                   
>      
> > 1
> > >
> > gbsa_zou_score_secondary                              
>      
> > no
> > >
> > gbsa_hawkins_score_secondary                          
>      
> > no
> > >
> > amber_score_secondary                                 
>      
> > no
> > >
> > 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_model                                            
>      
> > all
> > >
> > vdw_defn_file                                         
>      
> > > /usr/local/dock6/parameters/vdw_AMBER_parm99.defn
> > >
> > flex_defn_file                                        
>      
> > > /usr/local/dock6/parameters/flex.defn
> > >
> > flex_drive_file                                       
>      
> > > /usr/local/dock6/parameters/flex_drive.tbl
> > >
> > ligand_outfile_prefix                                 
>      
> > flex
> > >
> > write_orientations                                    
>      
> > no
> > >
> > num_scored_conformers                                 
>      
> > 1
> > >
> > rank_ligands                                          
>      
> > no
> > > 
> > > Now, with memory slots and HDs from  this
> machine,
> > and second hand additional
> > > material, I am trying to assemble an 8 CPUs
> shared
> > memory (total 24GB). If lucky,
> > > I'll also have to reinstall the OS and
> > applications. All that in spare time.
> > > Nevertheless,  succeeding with Dock/Amber with
> the
> > above large ligands is my primary
> > > interest at this time.
> 
> 
>      
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