[Pw_forum] no scf started for huge system

Thu Jul 9 15:29:16 CEST 2015

Hi,  in order to run on a parallel machine please have a look at
http://www.quantum-espresso.org/wp-content/uploads/Doc/user_guide/node15.html
Whick version of mpi are you using?

2015-07-09 15:25 GMT+02:00 Ludwig, Stephan <
stephan.ludwig at pi1.physik.uni-stuttgart.de>:

>  Hello,
>
> Of course you are right, but this is not the reason why the my calculation
> does not start..
>
>
> Thanks and Regards
>
>
> Stephan
>
> -----Original message-----
> *From:* Gabriel Greene <gabriel.greene at tyndall.ie>
> *Sent:* Thursday 9th July 2015 12:58
> *To:* PWSCF Forum <pw_forum at pwscf.org>
> *Subject:* Re: [Pw_forum] no scf started for huge system
>
>
> Also, since you are using ultrasoft pseudopotentials you will need to set
> the charge density cutoff, and shouldnt rely on the default value.
>
> ecutrho should be 8-12 X ecutwfc, see the input file description
> http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#idp119152
>
>
> Gabriel Greene
> Tyndall National Institute
> University College Cork
> Ireland
>
>  ------------------------------
> *From:* pw_forum-bounces at pwscf.org [pw_forum-bounces at pwscf.org] on behalf
> of Ludwig, Stephan [stephan.ludwig at pi1.physik.uni-stuttgart.de]
> *Sent:* Thursday, July 09, 2015 11:48 AM
> *To:* PWSCF Forum
> *Subject:* Re: [Pw_forum] no scf started for huge system
>
>   Hello,
>
> I tried found out that when I increase ecutwfc to 400 I receive an error
> message:
>
>
>  Initial potential from superposition of free atoms
>
> starting charge 875.99411, renormalised to 876.00000
>
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Error in routine diropn (3):
> wrong record length
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> stopping ...
> --------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> ------------------------------------------------------------
>
> 
>
> Does anybody know what this means?
>
>
>  Thanks and Regards
>
>
>  Stephan
>
>
>  -----Original message-----
> *From:* Ludwig, Stephan <stephan.ludwig at pi1.physik.uni-stuttgart.de>
> *Sent:* Thursday 9th July 2015 12:42
> *To:* Forum, PWSCF (pw_forum at pwscf.org) <pw_forum at pwscf.org>
> *Subject:* [Pw_forum] no scf started for huge system
>
>  Hello
>
> I try to do scf calculation for an organic salt with 236 atoms in a unit
> cell.
>
> I'm working on a cluster using 45 procs for the calculation.
>
> Within the allowed time span (2 days) these procs do not even start the
> scf cycles.
>
> The last part of the output data is:
>
>
>  Largest allocated arrays est. size (Mb) dimensions
> Kohn-Sham Wavefunctions 7508.34 Mb ( 935488, 526)
> NL pseudopotentials 20098.38 Mb ( 935488, 1408)
> Each V/rho on FFT grid 243.00 Mb (15925248)
> Each G-vector array 57.08 Mb ( 7481721)
> G-vector shells 14.43 Mb ( 1891088)
> Largest temporary arrays est. size (Mb) dimensions
> Auxiliary wavefunctions 30033.37 Mb ( 935488, 2104)
> Each subspace H/S matrix 67.55 Mb ( 2104, 2104)
> Each <psi_i|beta_j> matrix 11.30 Mb ( 1408, 526)
> Arrays for rho mixing 1944.00 Mb (15925248, 8)
>
> Check: negative/imaginary core charge= -0.000001 0.000000
>
> Initial potential from superposition of free atoms
>
> 
>
> starting charge 875.99411, renormalised to 876.00000
> Starting wfc are 704 randomized atomic wfcs
>
> 
>
> Then the job cancels due to time limit.
>
> I want to be sure that this happens just because of the fact that the
> system is too huge and not because I made some bad mistake.
>
> My input file looks like this:
>
>
>  &CONTROL
> title = 'etot_vs_ecutwfc' ,
> calculation = 'scf' ,
> wf_collect = .FALSE.,
> outdir = './' ,
> wfcdir = './' ,
> pseudo_dir = '/home/st/st_st/st_phy72394/pseudo/' ,
> prefix = 'MeDH-TTPetot_vs_ecutwfc' ,
> /
> &SYSTEM
> ibrav = -12,
> A = 32.783 ,
> B = 7.995 ,
> C = 11.170 ,
> cosAB = 0 ,
> cosAC = -0.132602381688 ,
> cosBC = 0 ,
> nat = 236,
> ntyp = 5,
> ecutwfc = 200,
> occupations = 'smearing' ,
> degauss = 0.02 ,
> smearing = 'gaussian' ,
> exxdiv_treatment = 'gygi-baldereschi' ,
> /
> &ELECTRONS
> conv_thr = 1.0D-8
> /
> ATOMIC_SPECIES
> H 1.00790 H.pz-rrkjus_psl.0.1.UPF
> C 12.01100 C.pz-n-rrkjus_psl.0.1.UPF
> F 18.98800 F.pz-n-rrkjus_psl.0.1.UPF
> S 32.06500 S.pz-n-rrkjus_psl.0.1.UPF
> As 74.92200 As.pz-n-rrkjus_psl.0.2.UPF
> ATOMIC_POSITIONS angstroms
> S 5.52835 0.29521 2.16999
> S 21.91985 4.29246 2.16999
> S 4.78777 7.69929 7.70567
> S 21.17927 3.70204 7.70567
> S 8.91117 6.37745 3.91040
> S 25.30267 2.38020 3.91040
> S 8.17058 1.61705 9.44608
> S 24.56208 5.61430 9.44608
> S 8.53628 0.30838 1.68728
> S 24.92778 4.30563 1.68728
> S 7.79569 7.68612 7.22296
> S 24.18719 3.68887 7.22296
> S 5.91488 6.35256 4.41083
> S 22.30638 2.35531 4.41083
> S 5.17429 1.64194 9.94651
> S 21.56579 5.63919 9.94651
> As 31.25307 7.42312 4.40640
> As 14.86156 3.42587 4.40640
> As 30.51248 0.57138 9.94208
> As 14.12098 4.56863 9.94208
> S 22.77175 0.24544 7.42335
> S 6.38025 4.24269 7.42335
> S 23.51233 7.74906 1.88767
> S 7.12083 3.75181 1.88767
> S 22.41272 6.31548 5.17143
> S 6.02122 2.31823 5.17143
> S 21.67213 1.67902 10.70711
> S 5.28063 5.67627 10.70711
> S 19.75130 0.27959 7.86510
> S 3.35980 4.27684 7.86510
> S 20.49188 7.71491 2.32941
> S 4.10038 3.71766 2.32941
> S 19.39879 6.33792 5.62425
> S 3.00729 2.34067 5.62425
> S 20.13937 1.65658 0.08857
> S 3.74787 5.65383 0.08857
> S 25.96310 0.08881 6.99046
> S 9.57160 4.08606 6.99046
> S 26.70368 7.90569 1.45478
> S 10.31218 3.90844 1.45478
> S 25.56056 6.28376 4.68983
> S 9.16906 2.28651 4.68983
> S 24.81997 1.71074 10.22551
> S 8.42848 5.70799 10.22551
> S 12.08748 6.57702 3.54505
> S 28.47898 2.57977 3.54505
> S 11.34689 1.41748 9.08073
> S 27.73839 5.41473 9.08073
> S 11.74373 0.68898 1.53781
> S 28.13523 4.68623 1.53781
> S 11.00315 7.30552 7.07349
> S 27.39465 3.30827 7.07349
> C 2.50124 7.97352 2.72134
> C 18.89274 3.97627 2.72134
> C 1.76066 0.02098 8.25702
> C 18.15215 4.01823 8.25702
> H 2.98979 0.63970 2.22534
> H 19.38129 4.63695 2.22534
> H 2.24920 7.35480 7.76102
> H 18.64071 3.35755 7.76102
> H 1.85588 0.41427 3.28266
> H 18.24738 4.41152 3.28266
> H 1.11530 7.58023 8.81834
> H 17.50680 3.58298 8.81834
> H 2.05231 7.38359 2.11352
> H 18.44381 3.38634 2.11352
> H 1.31173 0.61091 7.64920
> H 17.70323 4.60816 7.64920
> F 32.09159 6.20228 3.55280
> F 15.70009 2.20503 3.55280
> F 31.35101 1.79222 9.08848
> F 14.95951 5.78947 9.08848
> F 31.99917 0.61481 3.45094
> F 15.60767 4.61206 3.45094
> F 31.25859 7.37969 8.98662
> F 14.86709 3.38244 8.98662
> F 30.39326 0.65482 5.22458
> F 14.00176 4.65207 5.22458
> F 29.65268 7.33968 10.76026
> F 13.26118 3.34243 10.76026
> F 30.47339 6.23106 5.35854
> F 14.08189 2.23381 5.35854
> F 29.73280 1.76344 10.89422
> F 13.34130 5.76069 10.89422
> F 29.96030 7.30601 3.28598
> F 13.56880 3.30876 3.28598
> F 29.21972 0.68849 8.82166
> F 12.82821 4.68574 8.82166
> F -0.26088 7.52461 5.52461
> F 16.13062 3.52736 5.52461
> F -1.00147 0.46989 11.06029
> F 15.39003 4.46714 11.06029
> C 4.77264 7.25965 3.40666
> C 21.16414 3.26240 3.40666
> C 4.03205 0.73485 8.94234
> C 20.42355 4.73210 8.94234
> C 7.12868 7.79932 2.56191
> C 23.52018 3.80207 2.56191
> C 6.38809 0.19518 8.09759
> C 22.77959 4.19243 8.09759
> C 24.86295 7.22306 5.97079
> C 8.47145 3.22581 5.97079
> C 25.60353 0.77144 0.43510
> C 9.21203 4.76869 0.43510
> C 18.61690 7.45190 6.77235
> C 2.22540 3.45465 6.77235
> C 19.35749 0.54260 1.23667
> C 2.96599 4.53985 1.23667
> C 11.00638 7.55584 2.60731
> C 27.39788 3.55859 2.60731
> C 10.26580 0.43866 8.14299
> C 26.65730 4.43591 8.14299
> C 9.65436 7.44215 2.72245
> C 26.04587 3.44490 2.72245
> C 8.91378 0.55235 8.25813
> C 25.30528 4.54960 8.25813
> C 16.66566 0.56358 7.82192
> C 0.27416 4.56083 7.82192
> C 17.40624 7.43092 2.28624
> C 1.01474 3.43367 2.28624
> H 17.33387 0.90270 8.42088
> H 0.94237 4.89995 8.42088
> H 18.07446 7.09180 2.88520
> H 1.68295 3.09455 2.88520
> H 15.99844 0.08734 8.32234
> H -0.39307 4.08459 8.32234
> H 16.73902 7.90716 2.78666
> H 0.34752 3.90991 2.78666
> H 16.25380 1.29452 7.35581
> H -0.13770 5.29177 7.35581
> H 16.99438 6.69998 1.82013
> H 0.60288 2.70273 1.82013
> C 2.84149 6.31548 4.62008
> C 19.23299 2.31823 4.62008
> C 2.10091 1.67902 10.15576
> C 18.49241 5.67627 10.15576
> H 3.50975 5.72019 4.96440
> H 19.90125 1.72294 4.96440
> H 2.76917 2.27431 10.50008
> H 19.16067 6.27156 10.50008
> H 2.12009 5.80314 4.23922
> H 18.51159 1.80589 4.23922
> H 1.37951 2.19136 9.77491
> H 17.77101 6.18861 9.77491
> H 2.49999 6.86149 5.33308
> H 18.89149 2.86424 5.33308
> H 1.75941 1.13301 10.86876
> H 18.15091 5.13026 10.86876
> C 16.35379 6.90785 5.93536
> C -0.03771 2.91060 5.93536
> C 17.09438 1.08665 0.39968
> C 0.70288 5.08390 0.39968
> H 16.84589 6.32182 5.35300
> H 0.45439 2.32457 5.35300
> H 16.10531 1.67268 10.88868
> H -0.28619 5.66993 10.88868
> H 15.86389 7.54510 5.40947
> H -0.52761 3.54785 5.40947
> H 15.12331 0.44940 10.94515
> H -1.26819 4.44665 10.94515
> H 15.74245 6.39404 6.46678
> H -0.64905 2.39679 6.46678
> H 16.48303 1.60046 0.93110
> H 0.09153 5.59771 0.93110
> C 17.30660 7.62854 6.82992
> C 0.91510 3.63129 6.82992
> C 18.04719 0.36596 1.29424
> C 1.65569 4.36321 1.29424
> C 3.44486 7.19037 3.56498
> C 19.83636 3.19312 3.56498
> C 2.70427 0.80413 9.10066
> C 19.09577 4.80138 9.10066
> C 7.30907 6.93029 3.56166
> C 23.70057 2.93304 3.56166
> C 6.56849 1.06421 9.09734
> C 22.95999 5.06146 9.09734
> C 23.51465 7.25282 6.17782
> C 7.12315 3.25557 6.17782
> C 24.25523 0.74168 0.64214
> C 7.86373 4.73893 0.64214
> C 21.16001 7.74028 6.99710
> C 4.76851 3.74303 6.99710
> C 21.90060 0.25422 1.46142
> C 5.50910 4.25147 1.46142
> C 21.00252 6.87857 5.99071
> C 4.61102 2.88132 5.99071
> C 21.74310 1.11593 0.45503
> C 5.35160 5.11318 0.45503
> C 27.41664 7.76370 5.98186
> C 11.02514 3.76645 5.98186
> C 28.15722 0.23080 0.44618
> C 11.76572 4.22805 0.44618
> H 27.59489 0.54455 5.42718
> H 11.20339 4.54180 5.42718
> H 26.85431 7.44995 10.96286
> H 10.46280 3.45270 10.96286
> H 28.18126 7.63147 6.56310
> H 11.78976 3.63422 6.56310
> H 28.92184 0.36303 1.02742
> H 12.53034 4.36028 1.02742
> C 27.26323 6.60922 5.13933
> C 10.87173 2.61197 5.13933
> C 26.52265 1.38528 10.67501
> C 10.13115 5.38253 10.67501
> H 27.61795 5.83339 5.59879
> H 11.22645 1.83614 5.59879
> H 28.35854 2.16111 0.06311
> H 11.96704 6.15836 0.06311
> H 27.78169 6.73853 4.33001
> H 11.39019 2.74128 4.33001
> H 27.04111 1.25597 9.86569
> H 10.64961 5.25322 9.86569
> C 13.44202 0.18298 1.85556
> C 29.83352 4.18023 1.85556
> C 12.70144 7.81152 7.39124
> C 29.09294 3.81427 7.39124
> H 13.72839 7.55876 1.16581
> H 30.11989 3.56151 1.16581
> H 12.98780 0.43574 6.70150
> H 29.37930 4.43299 6.70150
> H 14.02273 0.95930 1.82235
> H 30.41423 4.95655 1.82235
> H 13.28214 7.03520 7.35803
> H 29.67364 3.03795 7.35803
> C 13.55775 7.53144 3.17416
> C 29.94925 3.53419 3.17416
> C 12.81716 0.46306 8.70984
> C 29.20866 4.46031 8.70984
> H 13.68661 0.21518 3.85616
> H 30.07811 4.21243 3.85616
> H 12.94602 7.77932 9.39184
> H 29.33752 3.78207 9.39184
> H 14.33307 6.94883 3.18191
> H 30.72457 2.95158 3.18191
> H 13.59248 1.04567 8.71759
> H 29.98398 5.04292 8.71759
> K_POINTS automatic
> 1 2 2 0 0 0
>
>
>  Has anybody made similar experiences? Any ideas how to come at least to
> a scf calculation?
>
> Does anybody know any tricks and hints for huge systems?
>
>
>  Thanks and regards
>
>
>  Stephan
>
>
>  _______________________________________________
>
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> Pw_forum at pwscf.org
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>
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>
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>
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