[Dock-fans] Fwd: Re: Ligand Docking with DOCK6
Scott Brozell
sbrozell at scripps.edu
Mon Apr 7 21:42:49 PDT 2008
Hi,
On Fri, 4 Apr 2008, Francesco Pietra wrote:
> Collected here are answers to the questions posed below. Additional info is provided
> about kernel code, heap, and mem. On a separate mail I reported failure to batch
> run: it was caused by running sysstat. OK when sysstat was stopped.
Ok, probably command line syntax for -o. Maybe this would work:
sysstat ( dock6 -i foo -o bar )
> $ ulimit -a:
>
> core file size (blocks, -c) 0
> data seg size (kbytes, -d) unlimited
> max nice (-e) 0
> file size (blocks, -f) unlimited
> pending signals (-i) unlimited
> max locked memory (kbytes, -l) unlimited
> max memory size (kbytes, -m) unlimited
> open files (-n) 1024
> pipe size (512 bytes, -p) 8
> POSIX message queues (bytes, -q) unlimited
> max rt priority (-r) 0
> stack size (kbytes, -s) 8192
> cpu time (seconds, -t) unlimited
> max user processes (-u) unlimited
> virtual memory (kbytes, -v) unlimited
> file locks (-x) unlimited
The item that is suspiciously small is the stack size.
Did you try to increase it already ?
$ ulimit -s unlimited
> ls -ls:
>
> 123608 -rw-r--r-- 1 francesco francesco 126441016 2008-04-02 grid.nrg
> 10308 -rw-r--r-- 1 francesco francesco 10536782 2008-04-02 grid.bmp
> 40 -rw-r--r-- 1 francesco francesco 37088 2008-04-02 selected_spheres.sph
These grids are not big.
But the sphere file is not small.
> During the few seconds that the procedure was active
So I gather that dock6 terminated with a memory exhausion as you
have indicated previously ?
> PID USER PR NI VIRT RES SHR S %CPU %MEM COMMND
> 3643 francesco 15 0 10596 7484 960 R 73 0.0 top
The command is top; you need to report this line for command dock6!
Your machine has lots of memory. So the memory exhausion is curious.
Scott
> $ kernel:
> 91:Memory: 16432744k/17825792k available (1929k kernel code, 343044k
> reserved, 864k data, 176k init) 309:Freeing unused kernel memory: 176k freed
>
> $ cat /proc/self/maps
> 00400000-00405000 r-xp 00000000 09:02 1700624 /bin/cat
> 00504000-00505000 rw-p 00004000 09:02 1700624 /bin/cat
> 00505000-00526000 rw-p 00505000 00:00 0 [heap]
> 2b7bdc138000-2b7bdc14f000 r-xp 00000000 09:02 1471913
> /lib/ld-2.3.6.so
> 2b7bdc14f000-2b7bdc151000 rw-p 2b7bdc14f000 00:00 0
> 2b7bdc24e000-2b7bdc250000 rw-p 00016000 09:02 1471913
> /lib/ld-2.3.6.so
> 2b7bdc250000-2b7bdc371000 r-xp 00000000 09:02 1471926
> /lib/libc-2.3.6.so
> 2b7bdc371000-2b7bdc471000 ---p 00121000 09:02 1471926
> /lib/libc-2.3.6.so
> 2b7bdc471000-2b7bdc486000 r--p 00121000 09:02 1471926
> /lib/libc-2.3.6.so
> 2b7bdc486000-2b7bdc489000 rw-p 00136000 09:02 1471926
> /lib/libc-2.3.6.so
> 2b7bdc489000-2b7bdc48f000 rw-p 2b7bdc489000 00:00 0
> 2b7bdc48f000-2b7bdc5b7000 r--p 00000000 09:03 948498
> /usr/lib/locale/locale-archive
> 7fffce95c000-7fffce972000 rw-p 7fffce95c000 00:00 0 [stack]
> ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0 [vdso]
>
> $ cat /proc/meminfo:
> MemTotal: 16438048 kB
> MemFree: 16335060 kB
> Buffers: 4816 kB
> Cached: 37892 kB
> SwapCached: 0 kB
> Active: 42756 kB
> Inactive: 17764 kB
> HighTotal: 0 kB
> HighFree: 0 kB
> LowTotal: 16438048 kB
> LowFree: 16335060 kB
> SwapTotal: 6835576 kB
> SwapFree: 6835576 kB
> Dirty: 0 kB
> Writeback: 0 kB
> AnonPages: 17672 kB
> Mapped: 7112 kB
> Slab: 19932 kB
> PageTables: 1316 kB
> NFS_Unstable: 0 kB
> Bounce: 0 kB
> CommitLimit: 15054600 kB
> Committed_AS: 40972 kB
> VmallocTotal: 34359738367 kB
> VmallocUsed: 3932 kB
> VmallocChunk: 34359734427 kB
>
> Hope this suffices.
> Thanks
> francesco
>
>
>
>
> --- On Thu, 4/3/08, 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: Thursday, April 3, 2008, 2:23 PM
>
> Hi,
> On Wed, 2 Apr 2008, Francesco Pietra wrote:
> > With Dock v. 6.2, I run serial interactive
> > $ dock6 -i rigid_nogrid.in
> > where the in file was added of
> > cont_score_rep_rad_scale 1
> > cont_score_use_dist_dep_dielectric
> yes
> > as printed below:
> >
> > ligand_atom_file /home/francesco/dockwork/ctx3c_dock62/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/ctx3c_dock62/selected_spheres.sph
> > max_orientations 1000
> > critical_points no
> > chemical_matching no
> > use_ligand_spheres no
> > flexible_ligand no
> > bump_filter no
> > score_molecules yes
> > contact_score_primary no
> > contact_score_secondary no
> > grid_score_primary no
> > grid_score_secondary no
> > grid_score_rep_rad_scale no
> > grid_score_vdw_scale no
> > grid_score_es_scale no
> > grid_score_grid_prefix no
> > dock3.5_score_secondary no
> > continuous_score_primary yes
> > continuous_score_secondary no
> >
> cont_score_rec_filename /home/francesco/dockwork/ctx3c_dock62/protein.mol2
> > cont_score_rep_rad_scale 1
> > cont_score_use_dist_dep_dielectric yes
> > cont_score_att_exp 6
> > cont_score_rep_ex 12
> > 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_primary no
> > amber_score_secondary no
> > minimize_ligand yes
> > simplex_max_iterations 1000
> > 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_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 rigid_nogrid
> > write_orientations no
> > num_scored_conformers_written 1
> > rank_ligands no
> >
> > accepting defaults. A statement was also presented which was not in the in
> file:
> >
> > num_scored_conformers [1]
> Yes num_scored_conformers replaced num_scored_conformers_written in 6.2.
> It is useful to first try old inputs interactively when the DOCK version
> has been updated to underscore input changes.
> > I accepted the [1] default..
> >
> > It run out of memory:
> >
> > Initialing Library File Routines ...
> > Initializing Orienting Routines...
> > Error: memory exhausted!
> > If this occurs during grid reading then a likely cause is a
> grid that is
> too large.
> > Some machines have a very restrictive policy on allocating available
> resources: For
> > Unix platforms increase the datasize, stacksize, and memoryuse using the
> limit,
> > ulimit, or unlimit commands; use trial and error to find the apt one of
> the
> > commands.
> >
> > terminate called after throwing an instance of 'std::bad_alloc'
> > what(): St9bad_alloc
> > Aborted
> > _______-
> > It was not reading grid. I use Debian Linux amd64. The memory is set with
> shmmax and
> > when computing with nwchem all 16GB available are used.
> >
> > Command
> > ulit
> > repots
> > unlimited
> Huh, what is the complete output of the limit command ?
> What are the sizes of your grid and sphere files; use ls -ls
> Run dock6 and send the top output for that process; see below.
> > I did nothing recently about "datasize" "stacksize".
> Should I
> investigate about
> > these?
> Definitely, isn't that clear from the error message ?
> This error message seems clear to me, and I wonder why it is ignored:
> http://blur.compbio.ucsf.edu/pipermail/dock-fans/2008-March/001468.html
> I have confirmed that continuous score will substitute for grid score
> in flexible docking. Here are some memory highlights:
> cd dock6/install/test/grid_score
> ../../../bin/dock6 -i grid2.dockin -o grid2.dockout
> top shows
> PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
> 23224 srb 17 0 43464 3352 1652 R 99 0.0 0:01.35 dock6
> with the verbatim dock6/install/test/grid_generation
> grid_spacing 0.5
> 356 -rw-r--r-- 1 srb appl 359152 Apr 3 15:55 grid.nrg
> Radically increasing the size of the grid:
> 4031 sb 18 0 337m 298m 1652 R 80 3.7 0:01.18 dock6
> grid_spacing 0.05
> 302848 -rw-r--r-- 1 309805888 Apr 3 15:41
> grid.nrg
> For continuous score
> 22689 srb 25 0 44848 4808 1696 R 100 0.1 0:06.96 dock6
> grid2.dockin input files diff
> 24c24
> < grid_score_primary yes
> ---
> > grid_score_primary no
> 26,29c26
> < grid_score_rep_rad_scale 1
> < grid_score_vdw_scale 1
> < grid_score_es_scale 1
> < grid_score_grid_prefix
> ../grid_generation/grid
> ---
> > dock3.5_score_primary no
> 30a28
> > continuous_score_primary yes
> 31a30,37
> > cont_score_rec_filename rec.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
> Scott
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