[Dock-fans] parallel input script

parinay parinay at gmail.com
Mon Jul 25 23:54:55 PDT 2005


Hi,
I am running Dock5 with MPICH.
Right now with one processors run , the dock5, binary is not doing any
molecule processing.

The default run also does not process any molecules.
e.g. ../../bin/dock5 -i dock.in -o /home/parinay/dock5.log 
                gives '0 molecules processed.'

mpirun -np 1  ../../bin/dock5 -i dock.in -o /home/parinay/dock5.log
                gives the same

mpirun -np 1  ../../bin/dock5.mpi  -i dock.in -o /home/parinay/dock5.log
                also gives the same.

I tried compiling MPICH and thus in turn dock5 with ch_p4 as well as ch_shmem.

For more than one processors run (2,4,8) I have the results and the
dock5 log shows that it has processed 30 molecules(this is what my
molecule file says to do in dock.in )

I have to profile the scaling of dock5 with increasing number of
processors. I have the numbers for 2, 4 8 processors .But for a single
processor run, the dock5 log says '0 Molecules processed'.

Is this expected ?? Is there something significant that I am missing ?
Let me also know if any input is required from my side.Any help on
this is appreciated.

thanks & reagrds,
parinay

On 7/19/05, Terry Lang <terry at cgl.ucsf.edu> wrote:
> Dear Nancy,
> 
> In order to run dock using multiple processors, you need to use the
> following commands:
> 
>  % set path = ( $path /usr/local/mpi/bin )
> 
>  % mpirun -np 8 dock5.mpi -i dock.in -o dock.out
> 
> 
> This should take care of your mpi problem. However, if mpi was the
> problem for your run, you would get different output. Try running the
> multi-ligand mol2 file again without mpi to see if there is something
> additionally wrong.
> 
> Good luck,
> Terry
> 
> 
> Nancy Deng wrote:
> 
> > Dear All,
> >
> > I am seeking help from you about running dock on multiprocessors. I
> > have no problem now to let the database docking by 5.2 version on
> > single node, (linux cluster).
> >
> > The "dock.in" file was directly copied from the demo folder which is
> > available in the 5.2 package. So, I added two lines to make it as the
> > input for the parrallel script ( I also paste the dock.in below for
> > your reference):
> > parallel_jobs yes
> > multipleligands yes
> >
> > The problem is that after i lauched "dock5.mpi -i dock.in -o
> > dock.out", the job was killed silently without any verbose complain.
> > From the bottom of dock.out file, it shows
> > " 0 Molecules Processed
> > Elapsed time: 0.09 seconds"
> >
> >
> > I am just wondering whether anyone would suggest me how to solve the
> > problem, and i'm very grateful to your any input!!!
> >
> > nancy
> >
> > **************below paste the input for your references********
> > ligand_atom_file ./Peakdale.mol2
> > ligand_outfile_prefix lig
> > limit_max_ligands no
> > write_orientations yes
> > write_conformations no
> > initial_skip 0
> > calculate_rmsd yes
> > use_rmsd_reference_mol no
> > rank_ligands no
> > num_scored_poses_written 1
> > orient_ligand yes
> > automated_matching yes
> > receptor_site_file ./selected_spheres.sph
> > max_orientations 500
> > critical_points no
> > chemical_matching no
> > use_ligand_spheres no
> > flexible_ligand yes
> > ag_conf_search yes
> > min_anchor_size 50
> > num_anchor_poses 50
> > number_confs_per_cycle 50
> > 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 yes
> > bump_grid_prefix ../3_grid/grid
> > max_bumps 3
> > score_molecules yes
> > energy_score_primary yes
> > energy_score_secondary yes
> > vdw_scale 1
> > es_scale 1
> > nrg_grid_prefix ../3_grid/grid
> > minimize_ligand yes
> > minimize_anchor yes
> > minimize_flexible_growth yes
> > minimize_final_pose 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_min_max_iterations 50
> > simplex_flex_min_max_iterations 10
> > simplex_final_min_max_iterations 100
> > simplex_random_seed 0
> > atom_model all
> > vdw_defn_file /usr/usc/dock/5.2.0/parameters/vdw_AMBER_parm96.defn
> > flex_defn_file /usr/usc/dock/5.2.0/parameters/flex.defn
> > flex_drive_file /usr/usc/dock/5.2.0/parameters/flex_drive.tbl
> > chem_defn_file /usr/usc/dock/5.2.0/parameters/chem.defn
> > contact_score no
> > parallel_jobs yes
> > multiple_ligands yes
> > ***********end of dock.in attachment************
> >
> >
> >
> >
> >
> > ----- Original Message ----- From: "Sheng-Hung Wang"
> > <gentamicin5 at yahoo.com.tw>
> > To: <dock-fans at docking.org>
> > Sent: Thursday, July 07, 2005 9:54 AM
> > Subject: Re: [Dock-fans] UCSF DOCK
> >
> >
> >> Try PMOL2Q, it's free.
> >> http://home.pchome.com.tw/team/gentamicin/mol/mol.htm
> >>
> >>
> >> --- Shmuel Elmakies <shmulik at bioinfo.tau.ac.il>
> >>
> >>>
> >>> Dear Sir/madam
> >>>
> >>> I am new to DOCK 5. Reviewing the tutorial I noticed that the DOCK
> >>> procedure requires sybyl. This one is not mentioned in the
> >>> installation
> >>> section in the manual, and I was wondering whether it is mandatory or
> >>> can
> >>> be substituted by another package. how can I get it? Is it freeware?
> >>>
> >>> Best Regards,
> >>>
> >>> Shmuel Elmakies
> >>> System Administrator
> >>> Bioinformatics Unit
> >>> G.S. Wise faculty of Life Science
> >>> Tel Aviv University
> >>> Phone 972-3-6405099
> >>> _______________________________________________
> >>> Dock-fans mailing list
> >>> Dock-fans at docking.org
> >>> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >>>
> >>
> >>
> >> __________________________________________________
> >> ·Q§Y®É¦¬¨ì·s«H³qª¾¡H
> >> °¨¤W¤U¸üYahoo!©_¼¯§Y®É³q°T
> >> http://messenger.yahoo.com.tw/
> >> _______________________________________________
> >> Dock-fans mailing list
> >> Dock-fans at docking.org
> >> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >
> >
> > _______________________________________________
> > Dock-fans mailing list
> > Dock-fans at docking.org
> > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> 
> 
> --
> P. Therese Lang
> Kuntz and James Labs
> UCSF--Chemistry and Chemical Biology
> Phone: (415)476-3986
> 
> 
> 
> 
> _______________________________________________
> Dock-fans mailing list
> Dock-fans at docking.org
> http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> 


-- 
easy is right
begin right and you're easy
continue easy and you're right
the right way to go easy is to forget the right way
and forget that the going is easy....



More information about the Dock-fans mailing list