[Pw_forum] Problem
Chao Cao
cao at qtp.ufl.edu
Wed Dec 8 18:38:36 CET 2004
Hi,
I guess what you mean is the program just got stalled, without any error,
output whatsoever, am I right?
Actually I got the same problem when I do vc-relax. In my case, it runs
well for the first two steps, and then no output, no error any more until
it's killed.
It seems that this problem is actually related with MPI, and, somehow with
the library you used. I tried to use a serial version of pw, and it runs
OK. Furthurmore, if I abandom MKL, it also runs without stalled. Did you
use MKL to compile this code?
Best wishes,
Chao Cao
-------------------------------------------------------------------------
QTP, University of Florida
NPB 2331, Gainesville, Florida, U.S.A. 32611
On Tue, 7 Dec 2004, Sergey Lisenkov wrote:
> Dear Kostya,
>
> you know, I got the same "frozen situation", when I try to do variable-cell dynamics. But I used NFS disk and PWscf is frozen again after 2 steps:
>
> Program PWSCF v.2.1.1 starts ...
> Today is 7Dec2004 at 19:43:51
>
> Parallel version (MPI)
>
> Number of processors in use: 18
> R & G space division: nprocp = 18
>
> Ultrasoft (Vanderbilt) Pseudopotentials
>
> Current dimensions of program pwscf are:
> ntypx =10 npk =40000 lmax = 3
> nchix = 6 ndmx = 2000 nbrx =14 nqfx = 8
>
> Planes per process (thick) : nr3 = 80 npp = 5 ncplane = 2640
>
> Planes per process (smooth): nr3s= 72 npps= 4 ncplanes= 2376
>
> Proc/ planes cols G planes cols G columns G
> Pool (dense grid) (smooth grid) (wavefct grid)
> 1 5 98 4730 4 94 4480 26 656
> 2 5 98 4730 4 94 4478 27 655
> 3 5 98 4730 4 94 4480 27 655
> 4 5 98 4730 4 94 4486 26 654
> 5 5 98 4730 4 94 4480 26 656
> 6 5 98 4730 4 95 4489 26 656
> 7 5 98 4730 4 95 4485 26 654
> 8 5 98 4730 4 95 4485 26 654
> 9 4 98 4730 4 95 4487 26 654
> 10 4 98 4730 4 95 4483 26 654
> 11 4 98 4730 4 94 4480 26 654
> 12 4 98 4730 4 94 4482 26 654
> 13 4 98 4728 4 94 4480 26 654
> 14 4 98 4724 4 94 4476 26 654
> 15 4 98 4724 4 94 4472 27 655
> 16 4 98 4724 4 94 4474 28 654
> 17 4 98 4724 4 94 4472 26 654
> 18 4 97 4723 4 94 4478 26 654
> 0 80 1763 85107 72 1697 80647 473 11781
>
> bravais-lattice index = 8
> lattice parameter (a_0) = 8.0748 a.u.
> unit-cell volume = 2883.5668 (a.u.)^3
> number of atoms/cell = 16
> number of atomic types = 2
> kinetic-energy cutoff = 35.0000 Ry
> charge density cutoff = 145.0000 Ry
> convergence threshold = 1.0E-06
> beta = 0.1500
> number of iterations used = 7 plain mixing
> Exchange-correlation = SLA PW PBE PBE (1434)
> iswitch = 3 nstep = ****
>
> celldm(1)= 8.074803 celldm(2)= 2.340276 celldm(3)= 2.340276
> celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000
>
> crystal axes: (cart. coord. in units of a_0)
> a(1) = ( 1.000000 0.000000 0.000000 )
> a(2) = ( 0.000000 2.340276 0.000000 )
> a(3) = ( 0.000000 0.000000 2.340276 )
>
> reciprocal axes: (cart. coord. in units 2 pi/a_0)
> b(1) = ( 1.000000 0.000000 0.000000 )
> b(2) = ( 0.000000 0.427300 0.000000 )
> b(3) = ( 0.000000 0.000000 0.427300 )
>
>
> PSEUDO 1 is B (US) zval = 3.0 lmax= 1 lloc= 0
> Version 0 0 0 of US pseudo code
> Using log mesh of 781 points
> The pseudopotential has 4 beta functions with:
> l(1) = 0
> l(2) = 0
> l(3) = 1
> l(4) = 1
> Q(r) pseudized with 8 coefficients, rinner = 1.100 1.100 1.100
>
>
> PSEUDO 2 is N (US) zval = 5.0 lmax= 1 lloc= 0
> Version 0 0 0 of US pseudo code
> Using log mesh of 729 points
> The pseudopotential has 4 beta functions with:
> l(1) = 0
> l(2) = 0
> l(3) = 1
> l(4) = 1
> Q(r) pseudized with 8 coefficients, rinner = 0.800 0.800 0.800
>
>
> atomic species valence mass pseudopotential
> B 3.00 10.81110 B ( 1.00)
> N 5.00 14.00674 N ( 1.00)
>
> cell mass = 15.08744 UMA
>
> No symmetry!
>
> Cartesian axes
>
> site n. atom positions (a_0 units)
> 1 N tau( 1) = ( 0.4993804 -0.1221248 0.2955561 )
> 2 B tau( 2) = ( 0.1642459 -0.0857586 0.2955638 )
> 3 B tau( 3) = ( -0.3356975 0.0260137 0.5652328 )
> 4 N tau( 4) = ( -0.0006116 0.0002668 0.5910044 )
> 5 B tau( 5) = ( 0.1642593 0.2957787 0.6767961 )
> 6 N tau( 6) = ( 0.4993832 0.2957965 0.7132159 )
> 7 B tau( 7) = ( -0.3357281 0.0257259 0.0257129 )
> 8 B tau( 8) = ( -0.3357254 0.5654183 0.5649323 )
> 9 N tau( 9) = ( -0.0006333 0.5911870 0.5906732 )
> 10 N tau( 10) = ( 0.4993471 0.7132579 0.2950897 )
> 11 B tau( 11) = ( 0.1642120 0.6768934 0.2951413 )
> 12 B tau( 12) = ( -0.3357535 0.5651029 0.0254115 )
> 13 N tau( 13) = ( -0.0006388 -0.0000407 0.0000457 )
> 14 N tau( 14) = ( -0.0006613 0.5908415 -0.0002828 )
> 15 N tau( 15) = ( 0.4993523 0.2953286 -0.1226120 )
> 16 B tau( 16) = ( 0.1642320 0.2953550 -0.0861093 )
>
> number of k points= 3
> cart. coord. in units 2pi/a_0
> k( 1) = ( 0.0833333 0.0000000 0.0000000), wk = 0.6666667
> k( 2) = ( 0.2500000 0.0000000 0.0000000), wk = 0.6666667
> k( 3) = ( 0.4166667 0.0000000 0.0000000), wk = 0.6666667
>
> G cutoff = 239.4816 ( 85107 G-vectors) FFT grid: ( 32, 80, 80)
> G cutoff = 231.2236 ( 80647 G-vectors) smooth grid: ( 32, 72, 72)
>
> nbndx = 128 nbnd = 32 natomwfc = 64 npwx = 574
> nelec = 64.00 nkb = 128 ngl = 4730
>
> Initial potential from superposition of free atoms
> Starting wfc are atomic
>
> total cpu time spent up to now is 4.79 secs
>
> Self-consistent Calculation
>
> iteration # 1 ecut= 35.00 ryd beta=0.15
> Davidson diagonalization (with overlap)
> ethr = 1.00E-02, avg # of iterations = 2.0
>
> total cpu time spent up to now is 7.02 secs
>
> total energy = -208.10720991 ryd
> estimated scf accuracy < 3.25606013 ryd
>
> iteration # 2 ecut= 35.00 ryd beta=0.15
> Davidson diagonalization (with overlap)
> ethr = 5.09E-03, avg # of iterations = 1.3
>
> total cpu time spent up to now is 8.79 secs
>
> total energy = -208.82465604 ryd
> estimated scf accuracy < 1.56463136 ryd
>
> iteration # 3 ecut= 35.00 ryd beta=0.15
> Davidson diagonalization (with overlap)
> ethr = 2.44E-03, avg # of iterations = 2.3
>
> total cpu time spent up to now is 10.89 secs
> total energy = -209.44549531 ryd
> estimated scf accuracy < 0.16948246 ryd
>
> iteration # 4 ecut= 35.00 ryd beta=0.15
> Davidson diagonalization (with overlap)
> ethr = 2.65E-04, avg # of iterations = 2.3
>
> total cpu time spent up to now is 12.98 secs
>
> total energy = -209.47783435 ryd
> estimated scf accuracy < 0.10070496 ryd
>
> iteration # 5 ecut= 35.00 ryd beta=0.15
> Davidson diagonalization (with overlap)
> ethr = 1.57E-04, avg # of iterations = 2.3
>
> total cpu time spent up to now is 15.45 secs
>
> total energy = -209.48609317 ryd
> estimated scf accuracy < 0.02032163 ryd
>
> iteration # 6 ecut= 35.00 ryd beta=0.15
> Davidson diagonalization (with overlap)
> ethr = 3.18E-05, avg # of iterations = 2.7
>
> total cpu time spent up to now is 17.24 secs
>
> total energy = -209.48646142 ryd
> estimated scf accuracy < 0.01660795 ryd
>
> iteration # 7 ecut= 35.00 ryd beta=0.15
> Davidson diagonalization (with overlap)
> ethr = 2.59E-05, avg # of iterations = 2.0
>
> total cpu time spent up to now is 19.01 secs
>
> total energy = -209.49166262 ryd
> estimated scf accuracy < 0.00417486 ryd
>
> iteration # 8 ecut= 35.00 ryd beta=0.15
> Davidson diagonalization (with overlap)
> ethr = 6.52E-06, avg # of iterations = 2.7
> total cpu time spent up to now is 21.11 secs
>
> total energy = -209.49352509 ryd
> estimated scf accuracy < 0.00117656 ryd
>
> iteration # 9 ecut= 35.00 ryd beta=0.15
> Davidson diagonalization (with overlap)
> ethr = 1.84E-06, avg # of iterations = 2.3
>
> total cpu time spent up to now is 23.08 secs
>
> total energy = -209.49335203 ryd
> estimated scf accuracy < 0.00183403 ryd
>
> iteration # 10 ecut= 35.00 ryd beta=0.15
> Davidson diagonalization (with overlap)
> ethr = 1.84E-06, avg # of iterations = 2.7
>
> total cpu time spent up to now is 25.19 secs
>
> total energy = -209.49404888 ryd
> estimated scf accuracy < 0.00014904 ryd
>
> iteration # 11 ecut= 35.00 ryd beta=0.15
> Davidson diagonalization (with overlap)
> ethr = 2.33E-07, avg # of iterations = 3.7
>
> total cpu time spent up to now is 27.54 secs
>
> total energy = -209.49413146 ryd
> estimated scf accuracy < 0.00000388 ryd
>
> iteration # 12 ecut= 35.00 ryd beta=0.15
> Davidson diagonalization (with overlap)
> ethr = 6.07E-09, avg # of iterations = 4.3
>
> total cpu time spent up to now is 30.11 secs
>
> total energy = -209.49413365 ryd
> estimated scf accuracy < 0.00000433 ryd
>
>
> total cpu time spent up to now is 32.20 secs
>
> End of self-consistent calculation
>
> ! total energy = -209.49413488 ryd
> estimated scf accuracy < 0.00000065 ryd
>
> convergence has been achieved
>
> Forces acting on atoms (Ry/au):
>
> atom 1 type 2 force = -0.00001007 0.00016467 -0.00001999
> atom 2 type 1 force = -0.00001424 0.00001237 0.00003827
> atom 3 type 1 force = -0.00004530 0.00010475 -0.00005932
> atom 4 type 2 force = 0.00003382 0.00014103 -0.00018160
> atom 5 type 1 force = -0.00003876 0.00003243 -0.00013273
> atom 6 type 2 force = -0.00003223 -0.00000721 -0.00017324
> atom 7 type 1 force = -0.00004009 0.00007679 0.00013730
> atom 8 type 1 force = -0.00000606 -0.00004819 -0.00006458
> atom 9 type 2 force = -0.00001970 -0.00014764 -0.00014193
> atom 10 type 2 force = 0.00002075 -0.00018103 0.00001522
> atom 11 type 1 force = 0.00002795 -0.00008695 -0.00000023
> atom 12 type 1 force = 0.00001893 -0.00002804 0.00014747
> atom 13 type 2 force = 0.00004076 0.00010451 0.00006335
> atom 14 type 2 force = 0.00007473 -0.00016426 0.00006457
> atom 15 type 2 force = 0.00000220 -0.00002651 0.00026057
> atom 16 type 1 force = -0.00001268 0.00005328 0.00004687
>
> Total force = 0.000647 Total SCF correction = 0.001402
>
>
> entering subroutine stress ...
>
> total stress (ryd/bohr**3) (kbar) P= -1.94
> -0.00001858 0.00000014 -0.00000017 -2.73 0.02 -0.03
> 0.00000014 -0.00001029 -0.00000002 0.02 -1.51 0.00
> -0.00000017 -0.00000002 -0.00001067 -0.03 0.00 -1.57
>
>
> Parrinello-Rahman Damped Cell-Dynamics Minimization
> convergence thresholds: EPSE = 0.10E-03 EPSF = 0.40E-03 EPSP = 0.50E+00
>
> Entering Dynamics; it = 1 time = 0.00000 pico-seconds
>
> new lattice vectors (alat unit) :
> 0.999999960 0.000000000 0.000000000
> 0.000000000 2.340276143 0.000000000
> -0.000000001 0.000000000 2.340276143
> new unit-cell volume = 2883.5666 (a.u.)^3
> new positions in cryst coord
> N 0.499380448 -0.052183941 0.126291113
> B 0.164245854 -0.036644631 0.126294431
> B -0.335697516 0.011115641 0.241523960
> N -0.000611582 0.000114005 0.252536172
> B 0.164259343 0.126386219 0.289194955
> N 0.499383204 0.126393838 0.304757172
> B -0.335728076 0.010992689 0.010987113
> B -0.335725411 0.241603240 0.241395573
> N -0.000633330 0.252614195 0.252394656
> N 0.499347077 0.304775112 0.126091828
> B 0.164211956 0.289236550 0.126113890
> B -0.335753463 0.241468487 0.010858335
> N -0.000638785 -0.000017395 0.000019527
> N -0.000661288 0.252466555 -0.000120820
> N 0.499352259 0.126193896 -0.052392090
> B 0.164231976 0.126205211 -0.036794508
> new positions in cart coord (alat unit)
> N 0.499380428 -0.122124831 0.295556079
> B 0.164245847 -0.085758556 0.295563844
> B -0.335697502 0.026013669 0.565232761
> N -0.000611582 0.000266803 0.591004378
> B 0.164259337 0.295778652 0.676796053
> N 0.499383184 0.295796484 0.713215939
> B -0.335728063 0.025725927 0.025712879
> B -0.335725397 0.565418298 0.564932301
> N -0.000633330 0.591186974 0.590673191
> N 0.499347057 0.713257923 0.295089698
> B 0.164211950 0.676893397 0.295141328
> B -0.335753450 0.565102940 0.025411502
> N -0.000638785 -0.000040709 0.000045699
> N -0.000661288 0.590841456 -0.000282752
> N 0.499352239 0.295328564 -0.122611959
> B 0.164231970 0.295355045 -0.086109309
>
> Ekin = 0.00000000 Ryd T = 0.0 K Etot = -209.49413488
>
> NEW-OLD atomic charge density approx. for the potential
> NEW K-POINTS
> 0.0833333 0.0000000 0.0000000 0.6666667
> 0.2500000 0.0000000 0.0000000 0.6666667
> 0.4166667 0.0000000 0.0000000 0.6666667
>
> total cpu time spent up to now is 41.82 secs
>
> Self-consistent Calculation
>
> iteration # 1 ecut= 35.00 ryd beta=0.15
> Davidson diagonalization (with overlap)
> ethr = 1.00E-05, avg # of iterations = 2.0
>
> Threshold (ethr) on eigenvalues was too large:
> Diagonalizing with lowered threshold
>
> Davidson diagonalization (with overlap)
> ethr = 9.68E-09, avg # of iterations = 1.0
>
> total cpu time spent up to now is 44.79 secs
>
> End of self-consistent calculation
>
> ! total energy = -209.49415398 ryd
> estimated scf accuracy < 0.00000068 ryd
>
> convergence has been achieved
>
> Forces acting on atoms (Ry/au):
>
> atom 1 type 2 force = -0.00002733 -0.00001631 0.00000017
> atom 2 type 1 force = -0.00004559 0.00001704 0.00002749
> atom 3 type 1 force = -0.00004336 0.00011056 -0.00002767
> atom 4 type 2 force = -0.00000177 0.00002277 -0.00011466
> atom 5 type 1 force = -0.00002565 0.00004549 -0.00012336
> atom 6 type 2 force = -0.00000297 -0.00002501 -0.00003472
> atom 7 type 1 force = -0.00000558 0.00008407 0.00010816
> atom 8 type 1 force = 0.00002779 -0.00005580 -0.00003582
> atom 9 type 2 force = -0.00001384 -0.00007975 -0.00010757
> atom 10 type 2 force = 0.00000353 -0.00000007 -0.00000444
> atom 11 type 1 force = -0.00000348 -0.00009170 0.00000976
> atom 12 type 1 force = 0.00002145 -0.00003381 0.00011541
> atom 13 type 2 force = 0.00004664 0.00003672 0.00002990
> atom 14 type 2 force = 0.00003904 -0.00004607 -0.00000093
> atom 15 type 2 force = 0.00003154 -0.00000831 0.00012058
> atom 16 type 1 force = -0.00000043 0.00004016 0.00003770
>
> Total force = 0.000380 Total SCF correction = 0.002323
>
>
> entering subroutine stress ...
>
> total stress (ryd/bohr**3) (kbar) P= -2.11
> -0.00001899 0.00000014 -0.00000017 -2.79 0.02 -0.03
> 0.00000014 -0.00001184 0.00000000 0.02 -1.74 0.00
> -0.00000017 0.00000000 -0.00001211 -0.03 0.00 -1.78
>
>
> Entering Dynamics; it = 2 time = 0.00005 pico-seconds
>
> new lattice vectors (alat unit) :
> 0.999999859 0.000000001 -0.000000001
> 0.000000001 2.340276117 0.000000000
> -0.000000002 0.000000000 2.340276116
> new unit-cell volume = 2883.5663 (a.u.)^3
> new positions in cryst coord
> N 0.499380447 -0.052183941 0.126291113
> B 0.164245853 -0.036644631 0.126294431
> B -0.335697516 0.011115641 0.241523960
> N -0.000611582 0.000114005 0.252536171
> B 0.164259343 0.126386219 0.289194954
> N 0.499383204 0.126393838 0.304757172
> B -0.335728076 0.010992690 0.010987114
> B -0.335725411 0.241603239 0.241395573
> N -0.000633330 0.252614194 0.252394655
> N 0.499347077 0.304775112 0.126091828
> B 0.164211956 0.289236549 0.126113890
> B -0.335753462 0.241468487 0.010858336
> N -0.000638785 -0.000017395 0.000019527
> N -0.000661288 0.252466555 -0.000120820
> N 0.499352260 0.126193896 -0.052392089
> B 0.164231976 0.126205211 -0.036794508
> new positions in cart coord (alat unit)
> N 0.499380377 -0.122124830 0.295556075
> B 0.164245830 -0.085758555 0.295563841
> B -0.335697469 0.026013669 0.565232755
> N -0.000611582 0.000266803 0.591004369
> B 0.164259319 0.295778650 0.676796043
> N 0.499383134 0.295796481 0.713215931
> B -0.335728029 0.025725929 0.025712882
> B -0.335725363 0.565418291 0.564932295
> N -0.000633330 0.591186966 0.590673183
> N 0.499347007 0.713257916 0.295089694
> B 0.164211933 0.676893389 0.295141325
> B -0.335753415 0.565102933 0.025411504
> N -0.000638785 -0.000040709 0.000045699
> N -0.000661287 0.590841450 -0.000282753
> N 0.499352190 0.295328561 -0.122611955
> B 0.164231953 0.295355042 -0.086109308
>
> Ekin = 0.00000000 Ryd T = 0.0 K Etot = -209.49415398
>
> NEW-OLD atomic charge density approx. for the potential
>
>
> I guess there are some hidden problems in the code. Did you have the same problem?
>
> Best wishes,
> Sergey
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