very long calculation time

Stefan Becuwe stefan... at gmail.com
Thu Mar 23 11:02:42 CET 2017


I further investigated Amin's case on the cluster he's using and on another 
cluster too. The difference between 2.6 and 3.0 he noticed, is related to 
dependencies. Both versions are installed correctly, as far as we can see. 
It turns out that the computation does finish when I use CP2K without any 
dependencies (both 2.6 and 3.0). However, when Libint (1.1.4) and/or libxc 
(2.2.3) are dependencies, the computation seems to hang after 10 minutes, 
meaning no output is being written any longer (tested with CP2K 2.7, 3.0 
and 4.1). Are any issues known with Libint or libxc?

Regards,
Stefan

Op dinsdag 21 maart 2017 13:52:24 UTC+1 schreef Amin:
>
> To close this thread, I want to mention that as I changed the version of 
> CP2K from 3.0 to 2.6 the problem solved! I did it after changing every 
> single parameter with my input file and structure. I have no idea that was 
> a problem with CP2K itself or just the version 3.0 package was not 
> installed correctly on our machine. 
>
> On Thursday, March 16, 2017 at 10:38:19 AM UTC+1, Amin wrote:
>>
>> Hi,
>> I noticed that the main problem for me is that in some cases CP2K stops 
>> updating the output file after a few minutes from the beginning of the 
>> calculation. 
>> For example: I put 2 jobs in the cluster (one for Slab + Co2 and the 
>> other was just Tio2 Slab), after almost 20 minutes the calculation for slab 
>> completed very nicely, but for slab + co2 it's still running (after several 
>> hours!) and there is no update on the output file! 
>> It also happened for me during an other calculation. in both cases, 
>> program stops to write on the output file and it continues to be in this 
>> situation until the wall-time is reached! and then job is being killed by 
>> the machine.
>> Now here is the question: what can cause this problem? to gain some 
>> straight, what kind of errors in input file, structure,... can stop the 
>> program from generating the output file?? And why isn't there any error in 
>> the output file? 
>> Once that I found out that the reason can not be about the input file or 
>> structure then I can be sure that it is some kind of technical problem with 
>> the machine that I'm using. 
>> I wound be very grateful if someone shares her/his experiences with me in 
>> this case.
>>
>> On Monday, March 13, 2017 at 10:28:21 AM UTC+1, Amin wrote:
>>>
>>> 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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