[CP2K:2146] Re: Cell size problem

Teodoro Laino teodor... at gmail.com
Fri Jun 26 09:44:30 CEST 2009


Yep.. it is an allocation error.. you are running out of memory..
You can:
1) run with a larger number of procs. Did you try it?
2) Alternatively you can try to decrease the memory requested for the MT 
adding
 &MT
    REL_CUTOFF 1.0
&END
 in the POISSON section.

Teo

robertom wrote:
> Running on 16CPU the locallog files generated are only 10
> (p2,p3,p4,p6,p7,p8,p9,p12,p13,p14)
> p2 file follow
>
>  **** Local logger file of mpi task       2 in communicator       0
>  **** pid=   23562
> host=node1001
>  **** file created by ****
>
>  ===== Routine Calling Stack =====
>
>            10 fft_wrap_pw1pw2_280
>             9 fft_wrap_pw1pw2
>             8 MTin_create_screen_fn
>             7 pw_poisson_solve
>             6 qs_ks_build_kohn_sham_matrix
>             5 qs_ks_update_qs_env
>             4 init_scf_loop
>             3 scf_env_do_scf
>             2 qs_energies
>             1 CP2K
>  **** file created by ****
>  *
>  *** 22:24:34 ERRORL2 in pw_zero processor      2  err=-300
> condition  ***
>  *** FAILED at line
> 1472                                                ***
>  *
>
>  ===== Routine Calling Stack =====
>
>            10 fft_wrap_pw1pw2_280
>             9 fft_wrap_pw1pw2
>             8 MTin_create_screen_fn
>             7 pw_poisson_solve
>             6 qs_ks_build_kohn_sham_matrix
>             5 qs_ks_update_qs_env
>             4 init_scf_loop
>             3 scf_env_do_scf
>             2 qs_energies
>             1 CP2K
>  **** Local logger file of mpi task       2 in communicator       0
>  **** pid=   13961
> host=node0790
>  **** file created by ****
>
>  ===== Routine Calling Stack =====
>
>            10 fft_wrap_pw1pw2_280
>             9 fft_wrap_pw1pw2
>             8 MTin_create_screen_fn
>             7 pw_poisson_solve
>             6 qs_ks_build_kohn_sham_matrix
>             5 qs_ks_update_qs_env
>             4 init_scf_loop
>             3 scf_env_do_scf
>             2 qs_energies
>             1 CP2K
>  **** file created by ****
>  *
>  *** 22:40:10 ERRORL2 in pw_zero processor      2  err=-300
> condition  ***
>  *** FAILED at line
> 1472                                                ***
>  *
>
>  ===== Routine Calling Stack =====
>
>            10 fft_wrap_pw1pw2_280
>             9 fft_wrap_pw1pw2
>             8 MTin_create_screen_fn
>             7 pw_poisson_solve
>             6 qs_ks_build_kohn_sham_matrix
>             5 qs_ks_update_qs_env
>             4 init_scf_loop
>             3 scf_env_do_scf
>             2 qs_energies
>             1 CP2K
>  **** Local logger file of mpi task       2 in communicator       0
>  **** pid=   15664
> host=node0959
>  **** file created by ****
>
>  ===== Routine Calling Stack =====
>
>            10 fft_wrap_pw1pw2_280
>             9 fft_wrap_pw1pw2
>             8 MTin_create_screen_fn
>             7 pw_poisson_solve
>             6 qs_ks_build_kohn_sham_matrix
>             5 qs_ks_update_qs_env
>             4 init_scf_loop
>             3 scf_env_do_scf
>             2 qs_energies
>             1 CP2K
>  **** file created by ****
>  *
>  *** 09:26:42 ERRORL2 in pw_zero processor      2  err=-300
> condition  ***
>  *** FAILED at line
> 1472                                                ***
>  *
>
>  ===== Routine Calling Stack =====
>
>            10 fft_wrap_pw1pw2_280
>             9 fft_wrap_pw1pw2
>             8 MTin_create_screen_fn
>             7 pw_poisson_solve
>             6 qs_ks_build_kohn_sham_matrix
>             5 qs_ks_update_qs_env
>             4 init_scf_loop
>             3 scf_env_do_scf
>             2 qs_energies
>             1 CP2K
>
>
> On Jun 25, 11:25 pm, Laino Teodoro <teodor... at gmail.com> wrote:
>   
>> Very probably it is an allocation problem (running out of memory).
>> To be sure you should post more info. For example, in the working  
>> directory there should be
>> several *localLog* files. The content of one of them would be helpful..
>>
>> Teo
>>
>> On 25 Jun 2009, at 22:49, roberto wrote:
>>
>>
>>
>>
>>
>>     
>>> I have perfomed a WF optimization of a little peptide in vacuo without
>>> problem.
>>> If I try to increase the size of the cell (from 35x35x35 to 40x40x40),
>>> the simulation fail.
>>> I post the inputfile and follow the output error message.
>>>       
>>> Thanks for any suggestion.
>>>       
>>> ## INPUT ##
>>> &FORCE_EVAL
>>>   METHOD Quickstep
>>>   &DFT
>>>     &POISSON
>>>       PERIODIC NONE
>>>       POISSON_SOLVER MT
>>>     &END POISSON
>>>     CHARGE +1
>>>     &MGRID
>>>       CUTOFF 280
>>>     &END MGRID
>>>     &QS
>>>       EPS_DEFAULT 1.0E-8
>>>     &END QS
>>>     &SCF
>>>       &OT
>>>         PRECONDITIONER FULL_SINGLE_INVERSE
>>>       &END OT
>>>       MAX_SCF 40
>>>       &OUTER_SCF
>>>         MAX_SCF 5
>>>       &END OUTER_SCF
>>>   &END SCF
>>>     &XC
>>>       &XC_FUNCTIONAL BLYP
>>>       &END XC_FUNCTIONAL
>>>     &END XC
>>>   &END DFT
>>>   &SUBSYS
>>>     &CELL
>>>       PERIODIC NONE
>>>       ABC 40.0 40.0 40.0
>>>       UNIT ANGSTROM
>>>     &END CELL
>>>     &COORD
>>>   N        11.4324736309       -6.1371572063       10.1357218931
>>>   H        11.1948075937       -6.8906101345       10.7821924672
>>>   H        10.9381862969       -6.3405541515        9.2632495044
>>>   C        10.9499715702       -4.8402675750       10.6521973274
>>>   H        11.3386245365       -4.7296425589       11.6677585473
>>>   C        11.4913131810       -3.6752836914        9.7832152944
>>>   H        11.2516744925       -3.8960378486        8.7344971467
>>>   H        10.9285010983       -2.7702123308       10.0417793494
>>>   C        12.9962124352       -3.4081941284        9.9438576821
>>>   H        13.2545611858       -3.3414422460       11.0083607468
>>>   H        13.5793843176       -4.2349628942        9.5244606629
>>>   C        13.4276150724       -2.0986464686        9.2465939026
>>>   H        14.5097616796       -1.9519749811        9.3487493765
>>>   H        13.1879571320       -2.1284201500        8.1783151066
>>>   N        12.7146699325       -0.9515928240        9.8558121776
>>>   H        12.5828552979       -1.0107633654       10.8919178425
>>>   C        12.1135559906        0.0441274020        9.2139901029
>>>   N        12.4394518112        0.3403191250        7.9167217260
>>>   H        13.4354822732        0.3681036873        7.7191911152
>>>   H        11.9329746051        1.1211570509        7.5131991344
>>>   N        11.1218376294        0.7371180721        9.8136134969
>>>   H        10.8845997299        0.4742930918       10.7753580754
>>>   H        11.0626157210        1.7370925590        9.6197738858
>>>   C         9.4085853225       -4.6963484515       10.6225043190
>>>   O         8.7929578553       -4.9975325132        9.5903800315
>>>   N         8.7856778560       -4.1441412798       11.7203597433
>>>   C         7.3486285567       -3.8102551517       11.7099480717
>>>   H         6.8197192907       -4.5278210668       11.0766326891
>>>   C         6.9582417964       -3.9259460918       13.2069269204
>>>   H         6.0748168733       -3.3358993177       13.4681026699
>>>   H         6.7441098192       -4.9759288944       13.4343207792
>>>   C         8.2282987207       -3.4419031893       13.9424055935
>>>   H         8.2310874957       -2.3492127686       13.9975911707
>>>   H         8.2955580201       -3.8288025246       14.9625954573
>>>   C         9.4034512549       -3.9235517293       13.0609426956
>>>   H        10.2003124860       -3.1759063533       13.0064126519
>>>   H         9.8280374116       -4.8622782613       13.4349980596
>>>   C         7.1101286450       -2.3801594356       11.1412507028
>>>   O         8.0203520380       -1.5310504742       11.0477720011
>>>   N         5.8392674941       -2.0823894794       10.7205335448
>>>   C         5.6355139703       -0.8941970496        9.8616586631
>>>   H         6.4068582242       -0.9016299355        9.0817309576
>>>   C         4.2200778144       -1.1170421588        9.2549104403
>>>   H         3.7003760394       -0.1719620880        9.0653987172
>>>   H         4.3221404500       -1.6430084891        8.2982109770
>>>   C         3.4941370231       -2.0064473870       10.2877472021
>>>   H         3.0786537890       -1.3852707278       11.0878641139
>>>   H         2.6836333737       -2.5921705326        9.8413944307
>>>   C         4.6079587796       -2.9171615522       10.8501847587
>>>   H         4.4363094156       -3.1758339663       11.8977183292
>>>   H         4.7026866900       -3.8463230114       10.2747817658
>>>   C         5.7458899497        0.4525397791       10.6137692543
>>>   O         5.2154503855        0.7039309036       11.7192531172
>>>   N         6.4344225918        1.3948594344        9.9368461571
>>>   H         6.9322429528        1.1986520759        9.0691552019
>>>   C         6.5700409770        2.7589843070       10.4088570300
>>>   H         5.5947332208        3.1651635665       10.6980024914
>>>   H         7.2187935767        2.8031426981       11.2970319085
>>>   C         7.2295977003        3.5687623281        9.2776439289
>>>   O         7.7340229907        2.9845949290        8.3112331112
>>>   N         7.2238485090        4.9191972013        9.5096174983
>>>   H         6.6972441974        5.2437226270       10.3188538415
>>>   C         7.9461520189        5.9673404267        8.7653679704
>>>   H         8.0948922681        5.6108506893        7.7422282223
>>>   C         7.1259847303        7.2983111829        8.7421278471
>>>   H         7.7166350535        8.0185624933        8.1702963661
>>>   H         6.1954232051        7.1154799216        8.1942654314
>>>   C         6.8262531031        7.8236225973       10.1409243252
>>>   C         7.8009125294        8.5254653877       10.8745041594
>>>   H         8.7512326191        8.7682386096       10.4069719956
>>>   C         5.5931262870        7.5527765173       10.7617727760
>>>   H         4.7994354740        7.0694296050       10.1946741872
>>>   C         7.5588299749        8.9164837495       12.1941172113
>>>   H         8.3165010987        9.4774015857       12.7357860474
>>>   C         5.3567146254        7.9306360270       12.0896783873
>>>   H         4.3996280301        7.7066013719       12.5536143802
>>>   C         6.3440138894        8.6051885011       12.8127723611
>>>   H         6.1632870999        8.8990656943       13.8430462390
>>>   C         9.3571813479        6.2746847214        9.3428304585
>>>   O        10.0791474867        7.1283336115        8.8105336198
>>>   N         9.6823888175        5.6087213903       10.4868666966
>>>   H         9.1151350681        4.8239948493       10.7846719438
>>>   C        11.0098655520        5.6810980820       11.0893328531
>>>   H        11.3426585696        6.7203820495       11.0590121012
>>>   C        10.9201366090        5.2066006718       12.5630668632
>>>   H        11.9200185517        5.1756653398       13.0151902147
>>>   H        10.3015773371        5.9179548033       13.1188135468
>>>   O        10.2584835828        3.9285493471       12.6795126544
>>>   H        10.8564137049        3.2408538678       12.3296344025
>>>   C        11.9591884550        4.7647976442       10.3069677329
>>>   O        11.6296147202        3.5817188030       10.0708465781
>>>   N        13.1788137378        5.2443511260        9.9396802843
>>>   C        14.0563338490        4.4032200505        9.0829530013
>>>   H        13.4719025368        4.0064794776        8.2494747614
>>>   C        15.1397054888        5.3960392482        8.5730358684
>>>   H        16.1203110935        4.9234846486        8.4844687895
>>>   H        14.8553721417        5.7493278524        7.5765557887
>>>   C        15.1264756032        6.5643344145        9.5850212352
>>>   H        15.7735259998        6.3373775806       10.4394603902
>>>   H        15.4728307826        7.5034783310        9.1434240480
>>>   C        13.6595469021        6.6572283699       10.0451222428
>>>   H        13.5728058669        7.0165901585       11.0727973352
>>>   H        13.0585342596        7.3015141176        9.3943770370
>>>   C        14.6014154503        3.1332153934        9.7817732244
>>>   O        14.7387246309        2.1025043414        9.1057259732
>>>   N        14.9321391220        3.2469089599       11.1089829812
>>>   H        14.5620137473        4.0402574483       11.6282916218
>>>   C        15.3192535703        2.1011402694       11.9474204093
>>>   H        15.0780360517        1.2020681276       11.3732515255
>>>   C        16.8585665040        2.0994231406       12.2382822730
>>>   H        17.3539614068        2.1958403990       11.2643638601
>>>   H        17.1082296466        2.9955427380       12.8181669038
>>>   C        17.3697857804        0.8568138702       12.9524885282
>>>   C        17.3797137994       -0.3930013796       12.3059460314
>>>   H        17.0418999476       -0.4717813269       11.2744331783
>>>   C        17.8502344440        0.9299228647       14.2688436131
>>>   H        17.8584539601        1.8877312361       14.7838482599
>>>   C        17.8431707860       -1.5357637564       12.9659077610
>>>   H        17.8448134688       -2.4938071540       12.4526028964
>>>   C        18.3280162135       -0.2086287981       14.9255393119
>>>   H        18.7080035730       -0.1258151027       15.9403383929
>>>   C        18.3199824362       -1.4468283157       14.2780028322
>>>   H        18.6875105233       -2.3333511257       14.7873511883
>>>   C        14.4291885252        2.1139040343       13.2372349862
>>>   O        13.8712375863        3.1460055627       13.6428990047
>>>   N        14.3252227703        0.8875480108       13.8432137400
>>>   H        14.8187807167        0.1440451701       13.3544501520
>>>   C        13.0771550709        0.3363039184       14.4658453947
>>>   H        13.4083046903      
>>>       
>> ...
>>
>> read more ยป
>>     
> >
>   




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