[Pw_forum] parallelization issue
Giacomo Saielli
giacomo.saielli at unipd.it
Fri Oct 15 10:50:40 CEST 2004
Dear developers,
I wonder if the comments of paragraph 7.4 of espresso manual v 2.1,
parallelization issue of pw.x, apply also for the cp.x module.
This is because I found the md simulations of my system with cp.x to be
not as fast as I need it.
I have a system made of 242 atoms, 137 of which are protons, the rest
C, N, O. This is the relevant input section (I use Vanderbilt PPs):
&system
ibrav = 14,
celldm(1) = 27.5945666,
celldm(2) = 1.0,
celldm(3) = 1.0,
celldm(4) = 0.0,
celldm(5) = 0.0,
celldm(6) = 0.0,
nat = 242,
ntyp = 4,
nbnd = 316,
nelec = 632,
ecutwfc = 30.0,
ecutrho = 180.0,
nr1b= 10, nr2b = 10, nr3b = 10,
xc_type = 'PBE',
/
&electrons
emass = 400.d0,
emass_cutoff = 2.5d0,
orthogonalization = 'ortho',
ortho_eps = 5.d-8,
ortho_max = 15,
electron_dynamics = 'verlet',
! electron_damping = 0.4,
! electron_velocities = 'zero',
electron_temperature = 'not_controlled',
/
&ions
ion_dynamics = 'verlet',
! ion_velocities = 'zero',
ion_temperature = 'nose',
fnosep = 60.0,
tempw = 300.0,
/
A test CPMD run with cp.x takes about 50 hours of total cpu (16 procs on IBM SP4 at CINECA, all PE of the same node) for 100 steps, that is about 15 fs (dt is 6 a.u. about 0.145 fs). This makes inpossible to run the simulation for some tens of picoseconds as I would like, since it would take something of the order of 10^5 cpu hours.
The question is if this numbers sounds correct to you, for this system size, so that the only chance is to build a smaller system, or if there is space for improvement playing with the choice of kpoints grid and other grids as mentioned in the Espresso manual,concerning pw.x.
Here I attach the beginning of the output file
thank you very much
best wishes
Giacomo
************************************************************************
**** ****
**** CPV: variable-cell Car-Parrinello molecular dynamics ****
**** using ultrasoft Vanderbilt pseudopotentials - v.2.1 ****
**** ****
************************************************************************
Parallel version (MPI)
Number of processors in use: 16
Warning: card &CELL ignored
Warning: card CELL_DYNAMICS = 'NONE', ignored
Warning: card CELL_VELOCITIES = 'ZERO', ignored
Warning: card PRESS = 0.0D0, ignored
Warning: card WMASS = 70000.0D0 ignored
Warning: card / ignored
reading ppot for species # 1 from file /scratch/padpdb42/saielli/PWSCF/TMA/CP/O.pbe-van_bm.UPF
reading ppot for species # 2 from file /scratch/padpdb42/saielli/PWSCF/TMA/CP/N.pbe-van_bm.UPF
reading ppot for species # 3 from file /scratch/padpdb42/saielli/PWSCF/TMA/CP/C.pbe-van_bm.UPF
reading ppot for species # 4 from file /scratch/padpdb42/saielli/PWSCF/TMA/CP/H.pbe-van_bm.UPF
wmass (calculated) = 233945.31
nbeg= 1 nomore= 100 iprint= 2
reads from 51 writes on 51
time step = 6.0000
parameters for electron dynamics:
emass= 400.00 emaec= 2.50ry
orthog. with lagrange multipliers: eps= 0.50E-07 max= 15
verlet algorithm for electron dynamics
with friction frice = 0.0000 , grease = 1.0000
ions are allowed to move
ion dynamics with fricp = 0.0000 and greasp = 1.0000
ion dynamics with nose` temp. control:
temperature required= 300.00000(kelvin) nose` mass = 16599.975
internal stress tensor calculated
cell parameters are not allowed to move
iprsta = 1
unit vectors of full simulation cell
in real space: in reciprocal space:
27.5946 0.0000 0.0000 1.0000 0.0000 0.0000
0.0000 27.5946 0.0000 0.0000 1.0000 0.0000
0.0000 0.0000 27.5946 0.0000 0.0000 1.0000
Proc planes cols G planes cols G columns G
(dense grid) (smooth grid) (wavefct grid)
1 8 680 53548 7 456 29172 114 3634
2 8 680 53548 7 456 29172 114 3634
3 8 680 53548 7 456 29172 114 3630
4 8 680 53548 7 456 29152 114 3630
5 8 681 53549 7 455 29151 113 3629
6 8 680 53548 7 456 29168 114 3630
7 8 682 53554 7 456 29132 114 3630
8 8 682 53554 7 456 29132 114 3630
9 7 682 53554 7 454 29126 112 3628
10 7 682 53554 7 454 29118 112 3628
11 7 682 53554 7 454 29126 112 3628
12 7 682 53550 7 456 29160 116 3632
13 7 682 53550 7 456 29148 112 3628
14 7 682 53550 7 456 29156 112 3628
15 7 682 53550 6 456 29168 112 3628
16 7 682 53550 6 456 29164 114 3630
0 120 10901 856809 110 7289 466417 1813 58077
ggen: # of g vectors < gcut ng= 26774
ggen: # of g vectors < gcuts ngs= 14586
ggen: # of g vectors < gcutw ngw= 1817
ggen: # of g shells < gcut ngl= 2655
unit vectors of box grid cell
in real space: in reciprocal space:
2.2995 0.0000 0.0000 1.0000 0.0000 0.0000
0.0000 2.2995 0.0000 0.0000 1.0000 0.0000
0.0000 0.0000 2.2995 0.0000 0.0000 1.0000
ggenb: # of gb vectors < gcutb ngb = 243
ggenb: # of gb shells < gcutb ngbl= 22
initialization
ibrav= 14 alat= 27.595 omega=21012.1616
gcut= 3471.84 gcuts= 2314.56 gcutw= 578.64
k-points: nkpt= 1
meshes:
dense grid: nr1 ,nr2, nr3 = 120 120 120 nr1x, nr2x, nr3x = 120 120 120
smooth grid: nr1s,nr2s,nr3s = 110 110 110 nr1sx,nr2sx,nr3sx= 110 110 110
box grid: nr1b,nr2b,nr3b = 10 10 10 nr1bx,nr2bx,nr3bx= 10 10 10
exchange-correlation potential: SLA PW PBE PBE
ecutw= 30.0 ryd ecuts= 120.0 ryd ecut= 180.0 ryd
# of electrons= 632 # of states= 316
nspin= 1
occupation numbers:
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0 2.0
# of atomic species 4
is= 1
na= 25 atomic mass= 16.00 gaussian rcmax= 0.50
atomic coordinates:
5.34 27.52 7.83
0.95 14.73 1.13
7.35 10.64 21.18
19.98 18.54 1.18
2.28 5.20 1.24
.....
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--
Giacomo Saielli
Istituto per la Tecnologia delle Membrane del CNR, Sezione di Padova;
Via Marzolo, 1 - 35131 Padova, Italy;
Tel: +39-049-8275279; Fax: -5239;
http://www.chfi.unipd.it/home/g.saielli/
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