[gpaw-users] BSSE parallel issue
Ask Hjorth Larsen
asklarsen at gmail.com
Sun Sep 1 15:35:27 CEST 2013
Hello
It works for me.
Note that 17 atoms is not enough for scalapack to be a good idea.
The first parameter in your mixer should be 0.04, not 0.4.
Best regards
Ask
2013/9/1 Glen Jenness <glenjenness at gmail.com>:
> Hi GPAW users!
> I ran into a curious problem when running GPAW in parallel while specifying
> ghost centers for a BSSE correction.
>
> I will be able to run my dimer system (in this case a CO molecule on a Rh
> (111) surface), but then when I specify calc.set(setups={'Rh': 'ghost"
> etc.), it'll enter the memory estimate part, and then freeze if I run over 1
> node.
>
> A colleague suggested setting the parallel option sl_auto to True, but doing
> so gives:
>
> ] [27] gpaw-python(PyObject_Call+0x5d) [0x49128d]
> [compute-0-6:29024] [28] gpaw-python(PyEval_EvalFrameEx+0x399d) [0x50dbfd]
> [compute-0-6:29024] [29] gpaw-python(PyEval_EvalCodeEx+0x89b) [0x511ffb]
> [compute-0-6:29024] *** End of error message ***
> [compute-0-9.local:17479] [0,0,0] ORTE_ERROR_LOG: Timeout in file
> base/pls_base_orted_cmds.c at line 275
> [compute-0-9.local:17479] [0,0,0] ORTE_ERROR_LOG: Timeout in file
> pls_tm_module.c at line 572
> [compute-0-9.local:17479] [0,0,0] ORTE_ERROR_LOG: Timeout in file
> errmgr_hnp.c at line 90
> mpirun noticed that job rank 0 with PID 17481 on node compute-0-9 exited on
> signal 11 (Segmentation fault).
> [compute-0-9.local:17479] [0,0,0] ORTE_ERROR_LOG: Timeout in file
> base/pls_base_orted_cmds.c at line 188
> [compute-0-9.local:17479] [0,0,0] ORTE_ERROR_LOG: Timeout in file
> pls_tm_module.c at line 603
>
>
> Any idea what could cause either issue?
>
> Thanks!
>
> My python input is:
>
> from ase.atoms import Atoms
> from ase.lattice.surface import fcc111, add_adsorbate
> from ase.constraints import FixAtoms
> from ase.optimize.lbfgs import LBFGS
> from ase.parallel import parprint
>
> from gpaw import GPAW, Mixer, FermiDirac
>
> PL = {'sl_auto': True}
>
> verb = False
> mix = Mixer(beta=0.40, nmaxold=45, weight=50.0)
> occ = FermiDirac(0.1)
>
> calc = GPAW(mode='lcao', basis='dzp', txt='rhodium.txt', kpts=(5,5,1),
> occupations=occ, xc='PBE', verbose=verb, mixer=mix, parallel=PL)
>
> rhodium = fcc111('Rh', (1,1,4), vacuum=8.0)
> constraint = FixAtoms([0, 1])
> rhodium.set_constraint(constraint)
> rhodium *= (2,2,1)
>
> co = Atoms('CO', positions=[(0,0,0), (0,0,1.14)])
> add_adsorbate(rhodium, co, 1.8, position='ontop')
>
> rhodium.set_calculator(calc)
>
> opt = LBFGS(rhodium, trajectory='co-rhodium.traj')
> opt.run(fmax=0.01)
> e_ads = rhodium.get_potential_energy()
> parprint('e_ads = %f' % e_ads)
>
> calc.set(setups={'Rh': 'ghost', 'C': 'paw', 'O': 'paw'})
> rhodium.set_calculator(calc)
> e_co = rhodium.get_potential_energy()
> parprint('e_co = %s' % e_co)
>
> calc.set(setups={'Rh': 'paw', 'C': 'ghost', 'O': 'ghost'})
> rhodium.set_calculator(calc)
> e_surf = rhodium.get_potential_energy()
> parprint('e_surf = %s' % e_surf)
>
> parprint('E_BE = %f' % ( e_ads - e_co - e_surf))
>
> --
> Dr. Glen Jenness
> Schmidt Group/Morgan Group
> Department of Chemistry/Materials Science and Engineering (MSAE)
> University of Wisconsin - Madison
>
> _______________________________________________
> gpaw-users mailing list
> gpaw-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users
-------------- next part --------------
___ ___ ___ _ _ _
| | |_ | | | |
| | | | | . | | | |
|__ | _|___|_____| 0.9.1.10645
|___|_|
User: askhl at surt.fysik.dtu.dk
Date: Sun Sep 1 15:32:37 2013
Arch: x86_64
Pid: 9092
Dir: /home/camp/askhl/src/gpaw/gpaw
ase: /home/camp/askhl/src/ase/ase (version 3.8.0)
numpy: /usr/lib64/python2.6/site-packages/numpy (version 1.4.1)
scipy: /home/opt/el6/common/scipy-0.7.2-5/lib64/python2.6/site-packages/scipy (version 0.7.2)
units: Angstrom and eV
cores: 8
Memory estimate
---------------
Process memory now: 40.88 MiB
Calculator 36.36 MiB
Density 6.68 MiB
Arrays 1.54 MiB
Localized functions 0.00 MiB
Mixer 5.14 MiB
Hamiltonian 2.16 MiB
Arrays 1.01 MiB
XC 0.00 MiB
Poisson 1.15 MiB
vbar 0.00 MiB
Wavefunctions 27.52 MiB
C [qnM] 0.54 MiB
S, T [2 x qmm] 23.69 MiB
P [aqMi] 0.00 MiB
TCI 0.00 MiB
BasisFunctions 3.29 MiB
Eigensolver 0.00 MiB
Positions:
0 Rh 0.0000 0.0000 8.0000
1 Rh 1.3435 0.7757 10.1939
2 Rh 0.0000 1.5513 12.3879
3 Rh 0.0000 0.0000 14.5818
4 Rh 1.3435 2.3270 8.0000
5 Rh 2.6870 3.1027 10.1939
6 Rh 1.3435 3.8784 12.3879
7 Rh 1.3435 2.3270 14.5818
8 Rh 2.6870 0.0000 8.0000
9 Rh 4.0305 0.7757 10.1939
10 Rh 2.6870 1.5513 12.3879
11 Rh 2.6870 0.0000 14.5818
12 Rh 4.0305 2.3270 8.0000
13 Rh 5.3740 3.1027 10.1939
14 Rh 4.0305 3.8784 12.3879
15 Rh 4.0305 2.3270 14.5818
16 C 0.0000 0.0000 16.3818
17 O 0.0000 0.0000 17.5218
O
C Rh Rh
Rh RRh Rh
Rh Rh
Rh Rh
Rh Rh
Rh Rh
Rh Rh
Unit Cell:
Periodic X Y Z Points Spacing
--------------------------------------------------------------------
1. axis: yes 5.374012 0.000000 0.000000 24 0.1939
2. axis: yes 2.687006 4.654031 0.000000 24 0.1939
3. axis: no 0.000000 0.000000 22.581793 112 0.2016
Ghost setup for Rh
LCAO basis set for Rh:
Name: dzp
Basis set was loaded from file /home/camp/askhl/src/setups-gpaw/gpaw-setups-0.9.9672/Rh.dzp.basis.gz
Number of radial functions: 7
Number of spherical harmonics: 23
l=0, rc=9.5469 Bohr: 5s-sz confined orbital
l=1, rc=3.6250 Bohr: 4p-sz confined orbital
l=2, rc=5.9844 Bohr: 4d-sz confined orbital
l=0, rc=5.7344 Bohr: 5s-dz split-valence wave
l=1, rc=2.4531 Bohr: 4p-dz split-valence wave
l=2, rc=3.5625 Bohr: 4d-dz split-valence wave
l=2, rc=3.6250 Bohr: d-type Gaussian polarization
Ghost setup for C
LCAO basis set for C:
Name: dzp
Basis set was loaded from file /home/camp/askhl/src/setups-gpaw/gpaw-setups-0.9.9672/C.dzp.basis.gz
Number of radial functions: 5
Number of spherical harmonics: 13
l=0, rc=5.5469 Bohr: 2s-sz confined orbital
l=1, rc=6.6719 Bohr: 2p-sz confined orbital
l=0, rc=3.0312 Bohr: 2s-dz split-valence wave
l=1, rc=3.7500 Bohr: 2p-dz split-valence wave
l=2, rc=6.6719 Bohr: d-type Gaussian polarization
Ghost setup for O
LCAO basis set for O:
Name: dzp
Basis set was loaded from file /home/camp/askhl/src/setups-gpaw/gpaw-setups-0.9.9672/O.dzp.basis.gz
Number of radial functions: 5
Number of spherical harmonics: 13
l=0, rc=4.3438 Bohr: 2s-sz confined orbital
l=1, rc=5.3906 Bohr: 2p-sz confined orbital
l=0, rc=2.2969 Bohr: 2s-dz split-valence wave
l=1, rc=2.8906 Bohr: 2p-dz split-valence wave
l=2, rc=5.3906 Bohr: d-type Gaussian polarization
Using the PBE Exchange-Correlation Functional.
Spin-Paired Calculation
Total Charge: 0.000000
Fermi Temperature: 0.100000
Wave functions: LCAO
Eigensolver: lcao (direct)
XC and Coulomb potentials evaluated on a 48*48*224 grid
Interpolation: tri-quintic (5. degree polynomial)
Poisson solver: Jacobi solver with 5 multi-grid levels
Stencil: 8*3+1=25 point O(h^6) finite-difference Laplacian
Reference Energy: 0.000000
Total number of cores used: 8
Domain Decomposition: 1 x 1 x 8
Diagonalizer layout: Serial LAPACK
Symmetries present: 6
25 k-points: 5 x 5 x 1 Monkhorst-Pack grid
5 k-points in the Irreducible Part of the Brillouin Zone
Linear Mixing Parameter: 0.4
Pulay Mixing with 45 Old Densities
Damping of Long Wave Oscillations: 50
Convergence Criteria:
Total Energy Change: 0.0005 eV / electron
Integral of Absolute Density Change: 0.0001 electrons
Integral of Absolute Eigenstate Change: 4e-08 eV^2
Number of Atoms: 18
Number of Atomic Orbitals: 394
Number of Bands in Calculation: 18
Bands to Converge: Occupied States Only
Number of Valence Electrons: 0
log10-error: Total Iterations:
Time WFS Density Energy Fermi Poisson
iter: 1 15:32:43 -0.000000 19 1
iter: 2 15:32:47 -0.000000 0 1
iter: 3 15:32:52 -0.000000 0 1
------------------------------------
Converged After 3 Iterations.
Energy Contributions Relative to Reference Atoms:(reference = 0.000000)
-------------------------
Kinetic: +0.000000
Potential: +0.000000
External: +0.000000
XC: -0.000000
Entropy (-ST): -0.000000
Local: +0.000000
-------------------------
Free Energy: -0.000000
Zero Kelvin: -0.000000
Fermi Level: -1.71636
Dipole Moment: [-0. -0. -0.]
Forces in eV/Ang:
0 Rh -0.00000 0.00000 -0.00000
1 Rh -0.00000 -0.00000 0.00000
2 Rh 0.00000 -0.00000 -0.00000
3 Rh 0.00000 0.00000 0.00000
4 Rh 0.00000 -0.00000 -0.00000
5 Rh 0.00000 0.00000 0.00000
6 Rh 0.00000 0.00000 -0.00000
7 Rh 0.00000 -0.00000 0.00000
8 Rh 0.00000 0.00000 -0.00000
9 Rh 0.00000 -0.00000 0.00000
10 Rh 0.00000 0.00000 -0.00000
11 Rh -0.00000 0.00000 0.00000
12 Rh -0.00000 -0.00000 -0.00000
13 Rh 0.00000 -0.00000 0.00000
14 Rh -0.00000 0.00000 -0.00000
15 Rh -0.00000 -0.00000 0.00000
16 C 0.00000 -0.00000 -0.00000
17 O 0.00000 -0.00000 -0.00000
Memory estimate
---------------
Process memory now: 189.95 MiB
Calculator 37.26 MiB
Density 6.83 MiB
Arrays 1.54 MiB
Localized functions 0.16 MiB
Mixer 5.14 MiB
Hamiltonian 2.17 MiB
Arrays 1.01 MiB
XC 0.00 MiB
Poisson 1.15 MiB
vbar 0.01 MiB
Wavefunctions 28.25 MiB
C [qnM] 1.26 MiB
S, T [2 x qmm] 23.69 MiB
P [aqMi] 0.01 MiB
TCI 0.00 MiB
BasisFunctions 3.29 MiB
Eigensolver 0.00 MiB
Positions:
0 Rh 0.0000 0.0000 8.0000
1 Rh 1.3435 0.7757 10.1939
2 Rh 0.0000 1.5513 12.3879
3 Rh 0.0000 0.0000 14.5818
4 Rh 1.3435 2.3270 8.0000
5 Rh 2.6870 3.1027 10.1939
6 Rh 1.3435 3.8784 12.3879
7 Rh 1.3435 2.3270 14.5818
8 Rh 2.6870 0.0000 8.0000
9 Rh 4.0305 0.7757 10.1939
10 Rh 2.6870 1.5513 12.3879
11 Rh 2.6870 0.0000 14.5818
12 Rh 4.0305 2.3270 8.0000
13 Rh 5.3740 3.1027 10.1939
14 Rh 4.0305 3.8784 12.3879
15 Rh 4.0305 2.3270 14.5818
16 C 0.0000 0.0000 16.3818
17 O 0.0000 0.0000 17.5218
O
C Rh Rh
Rh RRh Rh
Rh Rh
Rh Rh
Rh Rh
Rh Rh
Rh Rh
Unit Cell:
Periodic X Y Z Points Spacing
--------------------------------------------------------------------
1. axis: yes 5.374012 0.000000 0.000000 24 0.1939
2. axis: yes 2.687006 4.654031 0.000000 24 0.1939
3. axis: no 0.000000 0.000000 22.581793 112 0.2016
Ghost setup for Rh
LCAO basis set for Rh:
Name: dzp
Basis set was loaded from file /home/camp/askhl/src/setups-gpaw/gpaw-setups-0.9.9672/Rh.dzp.basis.gz
Number of radial functions: 7
Number of spherical harmonics: 23
l=0, rc=9.5469 Bohr: 5s-sz confined orbital
l=1, rc=3.6250 Bohr: 4p-sz confined orbital
l=2, rc=5.9844 Bohr: 4d-sz confined orbital
l=0, rc=5.7344 Bohr: 5s-dz split-valence wave
l=1, rc=2.4531 Bohr: 4p-dz split-valence wave
l=2, rc=3.5625 Bohr: 4d-dz split-valence wave
l=2, rc=3.6250 Bohr: d-type Gaussian polarization
C-setup:
name : Carbon
id : 4aa54d4b901d75f77cc0ea3eec22967b
Z : 6
valence: 4
core : 2
charge : 0.0
file : /home/camp/askhl/src/setups-gpaw/gpaw-setups-0.9.9672/C.PBE.gz
cutoffs: 0.64(comp), 1.14(filt), 1.14(core), lmax=2
valence states:
energy radius
2s(2) -13.751 0.635
2p(2) -5.284 0.635
*s 13.461 0.635
*p 21.927 0.635
*d 0.000 0.635
LCAO basis set for C:
Name: dzp
Basis set was loaded from file /home/camp/askhl/src/setups-gpaw/gpaw-setups-0.9.9672/C.dzp.basis.gz
Number of radial functions: 5
Number of spherical harmonics: 13
l=0, rc=5.5469 Bohr: 2s-sz confined orbital
l=1, rc=6.6719 Bohr: 2p-sz confined orbital
l=0, rc=3.0312 Bohr: 2s-dz split-valence wave
l=1, rc=3.7500 Bohr: 2p-dz split-valence wave
l=2, rc=6.6719 Bohr: d-type Gaussian polarization
O-setup:
name : Oxygen
id : 32ecd46bf208036f09c70b0ec9a88b78
Z : 8
valence: 6
core : 2
charge : 0.0
file : /home/camp/askhl/src/setups-gpaw/gpaw-setups-0.9.9672/O.PBE.gz
cutoffs: 0.67(comp), 1.17(filt), 0.83(core), lmax=2
valence states:
energy radius
2s(2) -23.961 0.688
2p(4) -9.029 0.598
*s 3.251 0.688
*p 18.182 0.598
*d 0.000 0.619
LCAO basis set for O:
Name: dzp
Basis set was loaded from file /home/camp/askhl/src/setups-gpaw/gpaw-setups-0.9.9672/O.dzp.basis.gz
Number of radial functions: 5
Number of spherical harmonics: 13
l=0, rc=4.3438 Bohr: 2s-sz confined orbital
l=1, rc=5.3906 Bohr: 2p-sz confined orbital
l=0, rc=2.2969 Bohr: 2s-dz split-valence wave
l=1, rc=2.8906 Bohr: 2p-dz split-valence wave
l=2, rc=5.3906 Bohr: d-type Gaussian polarization
Using the PBE Exchange-Correlation Functional.
Spin-Paired Calculation
Total Charge: 0.000000
Fermi Temperature: 0.100000
Wave functions: LCAO
Eigensolver: lcao (direct)
XC and Coulomb potentials evaluated on a 48*48*224 grid
Interpolation: tri-quintic (5. degree polynomial)
Poisson solver: Jacobi solver with 5 multi-grid levels
Stencil: 8*3+1=25 point O(h^6) finite-difference Laplacian
Reference Energy: -3068.481503
Total number of cores used: 8
Domain Decomposition: 1 x 1 x 8
Diagonalizer layout: Serial LAPACK
Symmetries present: 6
25 k-points: 5 x 5 x 1 Monkhorst-Pack grid
5 k-points in the Irreducible Part of the Brillouin Zone
Linear Mixing Parameter: 0.4
Pulay Mixing with 45 Old Densities
Damping of Long Wave Oscillations: 50
Convergence Criteria:
Total Energy Change: 0.0005 eV / electron
Integral of Absolute Density Change: 0.0001 electrons
Integral of Absolute Eigenstate Change: 4e-08 eV^2
Number of Atoms: 18
Number of Atomic Orbitals: 394
Number of Bands in Calculation: 42
Bands to Converge: Occupied States Only
Number of Valence Electrons: 10
log10-error: Total Iterations:
Time WFS Density Energy Fermi Poisson
iter: 1 15:33:15 -13.901408 27 31
iter: 2 15:33:19 -1.01 -13.752048 0 10
iter: 3 15:33:24 -1.28 -13.717216 0 26
iter: 4 15:33:29 -1.47 -13.681458 0 8
iter: 5 15:33:34 -2.31 -13.680771 0 6
iter: 6 15:33:38 -2.95 -13.680699 0 4
iter: 7 15:33:43 -3.25 -13.680743 0 3
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