[CP2K:8808] very long calculation time

Amin amin.jaf... at gmail.com
Mon Mar 13 15:10:02 CET 2017


Dear Marcella,

Your guess is very likely to be correct. because just a couple of minutes 
ago an other job that I had submitted before (same structure without co2 
molecule) stopped (because of wall-time) after a week of calculation and as 
I checked the output file for last modification time, I strangely found out 
that the last modification time was about yesterday!! That says there has 
been nothing written since yesterday on the output file while the program 
just stopped right now! 
Apparently, I need to contact technical staff.

Thank you very much. 

Regards,

Amin 


On Monday, March 13, 2017 at 2:35:47 PM UTC+1, Marcella Iannuzzi wrote:
>
> Dear Amin,
>
> if this is your whole output, only 18 steps of the geometry optimisation 
> have been performed, 
> each taking between 40 and 100 seconds. The SCF cycle requires actually a 
> small number of iterations, each taking few seconds.
> From these information, one can only conclude that  your job was hanging 
> for a week, after the calculation of these 18 steps.
> Did you check when the output file has been modified for the last time? 
> Did you check every time to time ow the calculation was going on during 
> that week?
> Anyway, I would guess that the problem is related to the machine where the 
> job is running.
> regards
> Marcella
>
> On Monday, March 13, 2017 at 1:43:10 PM UTC+1, Amin wrote:
>>
>> I couldn't be able to attach the output file here.
>> I need LSD, because the calculation done by VASP was spin polarized.
>> Here are the information about the last step of optimization- after that 
>> calculations reached wall-time and stopped:
>>
>>  --------  Informations at step =    18 ------------
>>   Optimization Method        =                 BFGS
>>   Total Energy               =     -5827.0471607579
>>   Real energy change         =         0.0858127047
>>   Predicted change in energy =       -14.5174588205
>>   Scaling factor             =         0.0077495614
>>   Step size                  =         0.4724315332
>>   Trust radius               =         0.4724315332
>>   Decrease in energy         =                   NO
>>   Used time                  =               93.234
>>
>>   Convergence check :
>>   Max. step size             =         0.4724315332
>>   Conv. limit for step size  =         0.0030000000
>>   Convergence in step size   =                   NO
>>   RMS step size              =         0.0495642754
>>   Conv. limit for RMS step   =         0.0015000000
>>   Convergence in RMS step    =                   NO
>>   Max. gradient              =         0.1337540443
>>   Conv. limit for gradients  =         0.0004500000
>>   Conv. for gradients        =                   NO
>>   RMS gradient               =         0.0130474061
>>   Conv. limit for RMS grad.  =         0.0003000000
>>   Conv. for gradients        =                   NO
>>  ---------------------------------------------------
>>
>>   ----------------------------------- OT 
>> ---------------------------------------
>>   Minimizer      : CG                  : conjugate gradient
>>   Preconditioner : FULL_ALL            : diagonalization, state selective
>>   Precond_solver : DEFAULT
>>   Line search    : 2PNT                : 2 energies, one gradient
>>   stepsize       :    0.15000000                  energy_gap     :   
>>  0.08000000
>>   eps_taylor     :   0.10000E-15                  max_taylor     :       
>>       4
>>   ----------------------------------- OT 
>> ---------------------------------------
>>
>>   Step     Update method      Time    Convergence         Total energy   
>>  Change
>>   
>> ------------------------------------------------------------------------------
>>      1 OT CG       0.15E+00    8.8     0.00180844     -5825.0697567570 
>> -5.83E+03
>>
>>
>> On Monday, March 13, 2017 at 12:11:02 PM UTC+1, jgh wrote:
>>>
>>> Hi 
>>>
>>> you still didn't answer my question: 
>>>
>>> is your 'long' simulation time caused by: 
>>>
>>> - slow convergence of geometry optimization 
>>>      ==> Numbers please. 
>>> - slow convergence of SCF 
>>>      ==> How many iterations? Did it converge at all? 
>>> - high CPU time per SCF cycle? 
>>>      ==> Give us some numbers. It is impossible to say something 
>>>          without having any information. 
>>>
>>> Do you really need LSD? 
>>>
>>> regards 
>>>
>>> -------------------------------------------------------------- 
>>> Juerg Hutter                         Phone : ++41 44 635 4491 
>>> Institut für Chemie C                FAX   : ++41 44 635 6838 
>>> Universität Zürich                   E-mail: hut... at chem.uzh.ch 
>>> Winterthurerstrasse 190 
>>> CH-8057 Zürich, Switzerland 
>>> --------------------------------------------------------------- 
>>>
>>> -----cp... at googlegroups.com wrote: -----To: cp2k <cp... at googlegroups.com> 
>>>
>>> From: Amin 
>>> Sent by: cp... at googlegroups.com 
>>> Date: 03/13/2017 12:07PM 
>>> Subject: Re: [CP2K:8808] very long calculation time 
>>>
>>> To add up some thing: I think that is because of the slow convergence of 
>>> the SCF.The interesting point is that with 48 atoms in my supercell, SCF 
>>> converged in less than one hour! but now with 192 atoms, it takes more than 
>>> a week (even more!, because it hasn't converged yet!) 
>>>
>>> On Monday, March 13, 2017 at 11:57:14 AM UTC+1, Amin wrote:Thank you 
>>> very much for your swift reply.I am replicating a calculation that has been 
>>> done previously by VASP. at first I tried to calculate adsorption energy 
>>> with 48 atoms in my supercell, but there was a major difference between my 
>>> results and the previous one. Then I modified my structure to include more 
>>> atoms. I'll try to apply your suggestions but I also attach my complete 
>>> input file in case that it might help to give a better 
>>> perspective. -Because of this point that calculation stopped after reaching 
>>> the wall-time, I set the new input file to use the Restart wave-function. 
>>> But I'm not sure that it's been done correctly! Sorry if my questions are 
>>> so rudimentary!  
>>> I sincerely appreciate your time and considerations. 
>>>
>>> &GLOBAL  PROJECT  Chemisorption-newconf  RUN_TYPE GEO_OPT  PRINT_LEVEL 
>>> LOW  EXTENDED_FFT_LENGTHS&END GLOBAL 
>>> &FORCE_EVAL  METHOD Quickstep               &DFT    
>>> WFN_RESTART_FILE_NAME Chemisorption-newconf-RESTART.wfn     
>>> BASIS_SET_FILE_NAME  BASIS_MOLOPT    POTENTIAL_FILE_NAME  GTH_POTENTIALS    
>>> LSD    CHARGE 0    MULTIPLICITY 1    &MGRID        CUTOFF 800       
>>>  REL_CUTOFF 60    &END MGRID    &QS        METHOD GPW        EPS_DEFAULT 
>>> 1.0E-12    &END QS    &POISSON        PERIODIC XYZ    &END POISSON    &SCF 
>>>                              SCF_GUESS RESTART      EPS_SCF 1.0E-6      
>>> MAX_SCF 100      &OT        PRECONDITIONER FULL_ALL        MINIMIZER CG    
>>>   &END OT      &OUTER_SCF        MAX_SCF 20        EPS_SCF 1.0E-6      &END 
>>> OUTER_SCF    &END SCF    &XC                             &XC_FUNCTIONAL 
>>> PBE      &END XC_FUNCTIONAL      &VDW_POTENTIAL       
>>>  DISPERSION_FUNCTIONAL PAIR_POTENTIAL        &PAIR_POTENTIAL               
>>>  TYPE DFTD3(BJ)                REFERENCE_FUNCTIONAL PBE               
>>>  CALCULATE_C9_TERM .FALSE.                PARAMETER_FILE_NAME dftd3.dat     
>>>            R_CUTOFF 15.0        &END PAIR_POTENTIAL      &END 
>>> VDW_POTENTIAL    &END XC  &END DFT 
>>>   &SUBSYS    &CELL      ABC 15.138 15.138 30.0000      PERIODIC XYZ     
>>> &END CELL    &TOPOLOGY      COORD_FILE_FORMAT XYZ      COORD_FILE_NAME 
>>>  ./Anatase001-192.xyz    &END    &KIND C      ELEMENT C      BASIS_SET 
>>> DZVP-MOLOPT-SR-GTH      POTENTIAL GTH-PBE-q4    &END KIND     &KIND Ti      
>>> ELEMENT Ti      BASIS_SET DZVP-MOLOPT-SR-GTH      POTENTIAL GTH-PBE-q12    
>>> &END KIND    &KIND O      ELEMENT O      BASIS_SET DZVP-MOLOPT-SR-GTH      
>>> POTENTIAL GTH-PBE-q6    &END KIND  &END SUBSYS  &PRINT       
>>>  &TOTAL_NUMBERS ON        &END TOTAL_NUMBERS  &END PRINT&END 
>>> FORCE_EVAL&MOTION        &GEO_OPT          OPTIMIZER BFGS         
>>>  MAX_FORCE 4.50000000E-004        &END        &CONSTRAINT         
>>>  &FIXED_ATOMS                LIST 0..95          &END FIXED_ATOMS       
>>>  &END CONSTRAINT&END MOTION 
>>> On Monday, March 13, 2017 at 11:35:58 AM UTC+1, jgh wrote:Hi 
>>>
>>>
>>>
>>> is your 'long' simulation time caused by: 
>>>
>>>
>>>
>>> - slow convergence of geometry optimization 
>>>
>>> - slow convergence of SCF 
>>>
>>> - high CPU time per SCF cycle? 
>>>
>>>
>>>
>>> To improve CPU time per SCF I would suggest (guessing without 
>>>
>>> knowing your full input) 
>>>
>>> - use only MOLOPT-SR basis sets 
>>>
>>> - reduce EPS_DEFAULT to 1.e-10 
>>>
>>> - Preconditioner -> FULL_SINGLE_INVERSE 
>>>
>>>
>>>
>>> Do you really need LSD? 
>>>
>>>
>>>
>>> regards 
>>>
>>>
>>>
>>> Juerg Hutter 
>>>
>>> -------------------------------------------------------------- 
>>>
>>> Juerg Hutter                         Phone : ++41 44 635 4491 
>>>
>>> Institut für Chemie C                FAX   : ++41 44 635 6838 
>>>
>>> Universität Zürich                   E-mail: hut... at chem.uzh.ch 
>>>
>>> Winterthurerstrasse 190 
>>>
>>> CH-8057 Zürich, Switzerland 
>>>
>>> --------------------------------------------------------------- 
>>>
>>>
>>>
>>> -----cp... at googlegroups.com wrote: -----To: cp2k <cp... at googlegroups.com> 
>>>
>>>
>>> From: Amin 
>>>
>>> Sent by: cp... at googlegroups.com 
>>>
>>> Date: 03/13/2017 10:28AM 
>>>
>>> Subject: [CP2K:8806] very long calculation time 
>>>
>>>
>>>
>>> Hi all,I am trying to calculate the adsorption energy of co2 on Tio2 
>>> surface (with 192 atoms in my supercell). but the problem is that it takes 
>>> too long time to be calculated. I'm using 80 processors (2.8 GHz - each) 
>>> but as I set the wall time for 7 days, it reached that wall time and 
>>> calculations stopped. I have done similar calculations for fewer atoms 
>>> (48,98) in super cell but in those cases (even with fewer CPUs) it takes at 
>>> most 1 day to calculate everything. Because I'm a beginner in CP2K, I don't 
>>> have any idea weather this amount of time for calculation is reasonable. I 
>>> have attached critical parts of my input file. I will be grateful if 
>>> someone gives a comment regarding my question.- Any suggestion for 
>>> decreasing the calculation time with the same number of atoms is warmly 
>>> appreciated.. :) 
>>>
>>> &GLOBAL  PROJECT  Ch  RUN_TYPE GEO_OPT  PRINT_LEVEL LOW  
>>> EXTENDED_FFT_LENGTHS&END GLOBAL 
>>>
>>> &FORCE_EVAL  METHOD Quickstep       &DFT    BASIS_SET_FILE_NAME 
>>>  BASIS_MOLOPT    POTENTIAL_FILE_NAME  GTH_POTENTIALS    LSD    CHARGE 0    
>>> MULTIPLICITY 1    &MGRID        CUTOFF 800        REL_CUTOFF 60    &END 
>>> MGRID    &QS        METHOD GPW        EPS_DEFAULT 1.0E-12    &END QS    
>>> &POISSON        PERIODIC XYZ    &END POISSON    &SCF                        
>>>     SCF_GUESS ATOMIC      EPS_SCF 1.0E-6      MAX_SCF 100      &OT       
>>>  PRECONDITIONER FULL_ALL        MINIMIZER CG      &END OT      &OUTER_SCF   
>>>      MAX_SCF 20        EPS_SCF 1.0E-6      &END OUTER_SCF    &END SCF    
>>> &XC                  &XC_FUNCTIONAL PBE      &END XC_FUNCTIONAL      
>>> &VDW_POTENTIAL        DISPERSION_FUNCTIONAL PAIR_POTENTIAL       
>>>  &PAIR_POTENTIAL                TYPE DFTD3(BJ)               
>>>  REFERENCE_FUNCTIONAL PBE                CALCULATE_C9_TERM .FALSE.         
>>>        PARAMETER_FILE_NAME dftd3.dat                R_CUTOFF 15.0       
>>>  &END PAIR_POTENTIAL      &END VDW_POTENTIAL    &END XC  &END DFT 
>>>
>>>   &SUBSYS    &CELL      ABC 15.138 15.138 30.0000      PERIODIC XYZ     
>>> &END CELL    &TOPOLOGY      COORD_FILE_FORMAT XYZ      COORD_FILE_NAME 
>>>  ./Anatase001-192.xyz    &END 
>>>
>>> &END FORCE_EVAL&MOTION        &GEO_OPT          OPTIMIZER BFGS         
>>>  MAX_FORCE 4.50000000E-004        &END        &CONSTRAINT         
>>>  &FIXED_ATOMS                LIST 0..95          &END FIXED_ATOMS       
>>>  &END CONSTRAINT&END MOTION 
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
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>>>
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