Re: [gmx-users] the mdrun choked or maybe braked.

[Justin A. Lemkul]

#ZHAO LINA# wrote:
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Friday, August 13, 2010 7:06 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the mdrun choked or maybe braked.

#ZHAO LINA# wrote:
 Hi,

The problem just like this, in md.log
\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\
There are: 130889 Atoms
splitting topology...
Walking down the molecule graph to make constraint-blocks
There are 43925 charge group borders and 43271 shake borders
There are 43271 total borders
Division over nodes in atoms:
    9348    9348    9348    9351    9348    9351    9348    9351
9348    9351
    9348    9351    9348    9350
Walking down the molecule graph to make constraint-blocks
CPU=  0, lastcg= 3245, targetcg=25208, myshift=    8
CPU=  1, lastcg= 6361, targetcg=28324, myshift=    8
CPU=  2, lastcg= 9477, targetcg=31440, myshift=    8
CPU=  3, lastcg=12594, targetcg=34557, myshift=    8
CPU=  4, lastcg=15710, targetcg=37673, myshift=    8
CPU=  5, lastcg=18827, targetcg=40790, myshift=    8
CPU=  6, lastcg=21943, targetcg=43906, myshift=    7
CPU=  7, lastcg=25060, targetcg= 3098, myshift=    7
CPU=  8, lastcg=28176, targetcg= 6214, myshift=    7
CPU=  9, lastcg=31293, targetcg= 9331, myshift=    7
CPU= 10, lastcg=34409, targetcg=12447, myshift=    7
CPU= 11, lastcg=37526, targetcg=15564, myshift=    7
CPU= 12, lastcg=40642, targetcg=18680, myshift=    7
CPU= 13, lastcg=43924, targetcg=21962, myshift=    8
pd->shift =   8, pd->bshift=  0
Division of bonded forces over processors
CPU              0     1     2     3     4     5     6     7     8
9    10
  11    12    13
G96ANGLES     2376     0     0     0     0     0     0     0     0
0     0
   0     0     0
PDIHS          774     0     0     0     0     0     0     0     0
0     0
   0     0     0
IDIHS          852     0     0     0     0     0     0     0     0
0     0
   0     0     0
LJ14          2436     0     0     0     0     0     0     0     0
0     0
   0     0     0
CONSTR        1614     0     0     0     0     0     0     0     0
0     0
   0     0     0
SETTLE        2586  3116  3116  3117  3116  3117  3116  3117  3116
3117  3116
3117  3116  3034
Workload division
nnodes:          14
pd->shift:        8
pd->bshift:       0
Nodeid   atom0   #atom     cg0       #cg
     0       0    9348       0      3246
     1    9348    9348    3246      3116
     2   18696    9348    6362      3116
     3   28044    9351    9478      3117
     4   37395    9348   12595      3116
     5   46743    9351   15711      3117
     6   56094    9348   18828      3116
     7   65442    9351   21944      3117
     8   74793    9348   25061      3116
     9   84141    9351   28177      3117
    10   93492    9348   31294      3116
    11  102840    9351   34410      3117
    12  112191    9348   37527      3116
    13  121539    9350   40643      3282

Max number of connections per atom is 27
Total number of connections is 32076
Max number of graph edges per atom is 4
Total number of graph edges is 13572
Initial temperature: 303.113 K

Started mdrun on node 0 Fri Aug 13 14:38:46 2010

           Step           Time         Lambda
              0        0.00000        0.00000

Grid: 10 x 45 x 10 cells
   Energies (kJ/mol)
       G96Angle    Proper Dih.  Improper Dih.          LJ-14     Coulomb-14
    2.96784e+03    1.16372e+03    9.89996e+02   -1.07478e+01    2.63019e+04
        LJ (SR)        LJ (LR)   Coulomb (SR)   Coulomb (LR)       RF excl.
    3.11913e+05   -8.40005e+03   -2.19295e+06   -1.39523e+04   -3.36479e+04
      Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
   -1.90563e+06    3.31599e+05   -1.57403e+06    3.04444e+02    1.07070e+01
  Cons. rmsd ()
    2.63140e-05
\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\

Nothing more at the end,
I changed the 16 cores to 14 cores, still has the same problem. And when
I checked the status, it showed me it's finished.


Please provide more information.  It mdrun stopped, it must have had a reason.
Please provide your .mdp file, description of the system, and what you did as
far as energy minimization and/or equilibration prior to whatever this run was
doing.  If mdrun fails, there's always a reason, and it would be very odd if
Gromacs simply stopped without providing some kind of indicative output.

-Justin



Can you tell me the possible reasons? Mainly which part I need to check?


Based on what you posted before, there is no possible way to tell you what's 
wrong, and hence why I asked for more information.  Check all output - stdout, 
stderr, log files, whatever other files your queuing system (if applicable) 
might give you.  There are numerous reasons for mdrun to stop, but very odd that 
no error messages would be produced.  Without more information, it's just idle 
guesswork.

-Justin

--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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