[CP2K-user] [CP2K:14265] Re: Hybrid functional calculation problem

fa...@gmail.com fabia... at gmail.com
Sun Nov 22 16:42:47 UTC 2020


Can cp2k access all the memory on the cluster? On linux you can use 
ulimit -s unlimited
to remove any limit on the amount of memory a process can use.

I usually use SCREEN_ON_INITIAL_P. I found that for large systems it is 
faster to run two energy minimizations with the key word enabled (such that 
the second restarts from a converged PBE0 wfn) than running a single 
minimization without SCREEN_ON_INITIAL_P. But that probably depends on the 
system you simulate.

You should converge the cutoff with respect to the properties that you are 
interested in. Run a test system with increasing cutoff and look at, e.g. 
the energy, pdos, etc.

Number of sph. ERI's calculated on the fly:        4763533420139 
This number should always be 0. If it is larger, increase the memory cp2k 
has available.

Fabian
On Sunday, 22 November 2020 at 17:24:13 UTC+1 Lucas Lodeiro wrote:

> Dear Fabian,
>
> Thanks for your advise. I forgot to clarify the time ejecution... my 
> mistake. 
> The calculation runs for 5 or 7 minutes, and stops... the walltime for the 
> calculation was set as 72hrs, then I do not believe this is the problem. 
> Now I am running the same input in a littler cluster (different form the 
> problematic crash) with 64 proc and 250GB RAM, and the calculation works 
> fine (so so slow, 9 hr per scf step, but runs... the total RAM assigned for 
> the ERI's is not sufficient but the problem is not appear)... It is no 
> practical to use this little cluster, then I need to fix the problem in the 
> big one, to use more RAM and more processors (more than 220 it is 
> possible), but as the program does not show what is happening, I cannot 
> tell anything to the cluster admin to recompile or fix the problem. :(
>
> This is the output in the little cluster:
>
>   Step     Update method      Time    Convergence         Total energy   
>  Change
>   
> ------------------------------------------------------------------------------
>
>   HFX_MEM_INFO| Est. max. program size before HFX [MiB]:                   
>  1371
>
>  *** WARNING in hfx_energy_potential.F:605 :: The Kohn Sham matrix is not 
>  ***
>
>  *** 100% occupied. This may result in incorrect Hartree-Fock results. Try 
> ***
>  *** to decrease EPS_PGF_ORB and EPS_FILTER_MATRIX in the QS section. For 
>  ***
>  *** more information see FAQ: https://www.cp2k.org/faq:hfx_eps_warning   
>  ***
>
>   HFX_MEM_INFO| Number of cart. primitive ERI's calculated:       
> 27043173676632
>   HFX_MEM_INFO| Number of sph. ERI's calculated:                   
> 4879985997918
>   HFX_MEM_INFO| Number of sph. ERI's stored in-core:               
>  116452577779
>   HFX_MEM_INFO| Number of sph. ERI's stored on disk:                       
>     0
>   HFX_MEM_INFO| Number of sph. ERI's calculated on the fly:       
>  4763533420139
>   HFX_MEM_INFO| Total memory consumption ERI's RAM [MiB]:                 
> 143042
>   HFX_MEM_INFO| Whereof max-vals [MiB]:                                   
>   1380
>   HFX_MEM_INFO| Total compression factor ERI's RAM:                       
>   6.21
>   HFX_MEM_INFO| Total memory consumption ERI's disk [MiB]:                 
>     0
>   HFX_MEM_INFO| Total compression factor ERI's disk:                       
>  0.00
>   HFX_MEM_INFO| Size of density/Fock matrix [MiB]:                         
>   266
>   HFX_MEM_INFO| Size of buffers [MiB]:                                     
>    98
>   HFX_MEM_INFO| Number of periodic image cells considered:                 
>     5
>   HFX_MEM_INFO| Est. max. program size after HFX  [MiB]:                   
>  3834
>
>      1 NoMix/Diag. 0.40E+00 ******     5.46488333    -20625.2826573514 
> -2.06E+04
>
> About the SCREEN_ON_INITIAL_P, I read that to use it, you need a very good 
> guess (more than de GGA converged one) as for example the last step or 
> frame from a GEO_OPT or MD... Is it really useful when the guess is the GGA 
> wavefunction?
> About the CUTOFF_RADIUS, I read that 6 or 7 it is a good compromise, and 
> as my cell is approximately twice, I use the minimal image convention to 
> decide the 8.62 number which is near the recomended (6 or 7). If I reduce 
> it, does the computational cost diminish considerably?
>
> Regards - Lucas
>
> El dom, 22 nov 2020 a las 12:53, fa... at gmail.com (<fa... at gmail.com>) 
> escribió:
>
>> Dear Lucas,
>>
>> cp2k was computes the four-center integrals during (or prior) to the 
>> first SCF cycle. I assume the job ran out of time during this task  For a 
>> system with more than 1000 atoms this takes a lot of time. With only 220 
>> CPUs this could take several hours in fact.
>>
>> To speed up the calculation you should use SCREEN_ON_INITIAL_P T and 
>> restart using a well converged PBE wfn. Other than that, there is little 
>> you can do other than assign the job more time and/or CPUs. (Of course, 
>> reducing CUTOFF_RADIUS        8.62 would help too but could negatively 
>> affect the result).
>>
>> Cheers,
>> Fabian
>>
>> On Sunday, 22 November 2020 at 01:21:05 UTC+1 Lucas Lodeiro wrote:
>>
>>> Hi all, 
>>> I need to perform a hybrid calculation with CP2K7.1, over a big system 
>>> (+1000 atoms). I study the manual, the tutorials and some videos of CP2K 
>>> developers to improve my input. But the program exits the calculation when 
>>> the HF part is running... I see the memory usage on the fly, and there is 
>>> no peak which explains the fail (I used 4000Mb with 220 processors).
>>> The output does not show some explanation... Thinking in the memory, I 
>>> try with a largemem node at our cluster, using 15000Mb with 220 processors, 
>>> but the program exists at the same point without message, just killing the 
>>> process. 
>>> The output shows a warning:
>>>
>>>  *** WARNING in hfx_energy_potential.F:591 :: The Kohn Sham matrix is 
>>> not  ***
>>>  *** 100% occupied. This may result in incorrect Hartree-Fock results. 
>>> Try ***
>>>  *** to decrease EPS_PGF_ORB and EPS_FILTER_MATRIX in the QS section. 
>>> For  ***
>>>  *** more information see FAQ: https://www.cp2k.org/faq:hfx_eps_warning 
>>>    ***
>>>
>>> but I read this is not a very complicated issue, and the calculation has 
>>> to continue and not crash
>>> Also I decrease the EPS__PGF_ORB, but the warning and the problem 
>>> persist. 
>>>
>>> I do not know if the problem could be located in other parts of my 
>>> input... for example I use the PBE0-T_C-LR (I use PBC for XY), and ADMM. In 
>>> the ADMM options, I use ADMM_PURIFICATION_METHOD = NONE, due to I read that 
>>> ADMM1 is the only one useful for smearing calculations. 
>>>
>>> I run this system with PBE (for the first guess of PBE0), and there is 
>>> no problem in that case.
>>> Moreover, I try with other CP2K versions (7.0, 6.1 and 5.1) compiled 
>>> into the cluster with (libint_max_am=6), and the calculation crash, but 
>>> show this problem:
>>>
>>>
>>>  *******************************************************************************
>>>  *   ___                                                                 
>>>       *
>>>  *  /   \                                                               
>>>        *
>>>  * [ABORT]                                                               
>>>       *
>>>  *  \___/       CP2K and libint were compiled with different 
>>> LIBINT_MAX_AM.    *
>>>  *    |                                                                 
>>>        *
>>>  *  O/|                                                                 
>>>        *
>>>  * /| |                                                                 
>>>        *
>>>  * / \                                               
>>>  hfx_libint_wrapper.F:134 *
>>>
>>>  *******************************************************************************
>>>
>>>
>>>  ===== Routine Calling Stack ===== 
>>>
>>>             2 hfx_create
>>>             1 CP2K
>>>
>>> It seems like this problem is not present in the 7.1 version, as the 
>>> program does not show it, and the compilation information does not 
>>> show LIBINT_MAX_AM value...
>>>
>>> If somebody could give me some advice, I will appreciate it. :)
>>> I attach the input file, and the output file for 7.1 version.
>>>
>>> Regards - Lucas Lodeiro
>>>
>>> -- 
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>
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