[ase-users] MPI error in writing a trajectory file
Glen Jenness
glenjenness at gmail.com
Tue Jul 16 16:41:11 CEST 2024
Dear users,
I have been trying to get GPAW-24.6.0 and ASE-3.23.0 working on a new
system and whilst I have gotten several issues straightened out, I am
stumped on this last hurdle.
The error is:
rank=00 L00: Traceback (most recent call last):
rank=00 L01: File
"/p/home/gjenness/programs/gpaw-rebuild/build/lib.linux-x86_64-3.8/gpaw/__init__.py",
line 161, in main
rank=00 L02: runpy.run_path(gpaw_args.script, run_name='__main__')
rank=00 L03: File
"/p/app/projects/erdc-cct/programs/anaconda3.8/lib/python3.8/runpy.py",
line 265, in run_path
rank=00 L04: return _run_module_code(code, init_globals, run_name,
rank=00 L05: File
"/p/app/projects/erdc-cct/programs/anaconda3.8/lib/python3.8/runpy.py",
line 97, in _run_module_code
rank=00 L06: _run_code(code, mod_globals, init_globals,
rank=00 L07: File
"/p/app/projects/erdc-cct/programs/anaconda3.8/lib/python3.8/runpy.py",
line 87, in _run_code
rank=00 L08: exec(code, run_globals)
rank=00 L09: File "mwe.py", line 16, in <module>
rank=00 L10: opt.run(fmax=0.05)
rank=00 L11: File
"/p/app/projects/erdc-cct/programs/ase/3.23.0/ase/optimize/optimize.py",
line 430, in run
rank=00 L12: return Dynamics.run(self, steps=steps)
rank=00 L13: File
"/p/app/projects/erdc-cct/programs/ase/3.23.0/ase/optimize/optimize.py",
line 275, in run
rank=00 L14: for converged in Dynamics.irun(self, steps=steps):
rank=00 L15: File
"/p/app/projects/erdc-cct/programs/ase/3.23.0/ase/optimize/optimize.py",
line 236, in irun
rank=00 L16: elif len(self.trajectory) == 0:
rank=00 L17: File
"/p/app/projects/erdc-cct/programs/ase/3.23.0/ase/io/trajectory.py", line
225, in __len__
rank=00 L18: return self.comm.sum_scalar(len(self.backend))
rank=00 L19: AttributeError: 'MPI' object has no attribute 'sum_scalar'
Looking at the code, it should be pulling the MPI setup from the
gpaw-python interpreter; however I am not an MPI expert so I am not sure
what is going on.
GPAW is compiled with AMD's AOCC and openmp (which now runs fine).
I have attached a MWE that produces the problem. I have tried the optimizer
with both trajectory='initial2.traj' and calling the Trajectory class
directly, both with the same result (the MWE has the former).
Thank you for any assistance.
--
Dr. Glen Jenness
Environmental Lab
Engineering Research and Development Center (ERDC)
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___ ___ ___ _ _ _
| | |_ | | | |
| | | | | . | | | |
|__ | _|___|_____| 22.8.1b1
|___|_|
User: gjenness at r02u18n01.navydsrc.hpc.local
Date: Tue Jul 16 14:34:24 2024
Arch: x86_64
Pid: 241242
CWD: /p/work1/gjenness/climb_internals_test
Python: 3.8.5
gpaw: /p/home/gjenness/programs/gpaw-rebuild/build/lib.linux-x86_64-3.8/gpaw
_gpaw: /p/home/gjenness/programs/gpaw-rebuild/build/bin.linux-x86_64-3.8/
gpaw-python (79eb7a4772)
ase: /p/app/projects/erdc-cct/programs/ase/3.23.0/ase (version 3.23.0-73cecb28dd)
numpy: /p/app/projects/erdc-cct/programs/anaconda3.8/lib/python3.8/site-packages/numpy (version 1.19.2)
scipy: /p/app/projects/erdc-cct/programs/anaconda3.8/lib/python3.8/site-packages/scipy (version 1.5.2)
libxc: 6.2.2
units: Angstrom and eV
cores: 64
OpenMP: False
OMP_NUM_THREADS: 1
Input parameters:
basis: dzp
mode: lcao
System changes: positions, numbers, cell, pbc, initial_charges, initial_magmoms
Initialize ...
species:
Pt:
name: Platinum
id: 5a6399afde4becbffda6f57f3efd9534
Z: 78.0
valence: 16
core: 62
charge: 0.0
file: /p/app/projects/erdc-cct/programs/gpaw-data/gpaw-setups-0.9.20000/Pt.LDA.gz
compensation charges: {type: gauss,
rc: 0.41,
lmax: 2}
cutoffs: {filter: 2.26,
core: 2.26}
valence states:
# energy rcut
- 6s(1.00) -5.930 1.307
- 5p(6.00) -56.318 1.371
- 6p(0.00) -0.962 1.371
- 5d(9.00) -6.387 1.307
- s 21.281 1.307
- d 20.825 1.307
# LCAO basis set for Pt:
# Name: dzp
# File: /p/app/projects/erdc-cct/programs/gpaw-data/gpaw-setups-0.9.20000/Pt.dzp.basis.gz
# Number of radial functions: 9
# Number of spherical harmonics: 27
# l=0, rc=8.5938 Bohr: 6s-sz confined orbital
# l=1, rc=3.5781 Bohr: 5p-sz confined orbital
# l=1, rc=13.6250 Bohr: 6p-sz confined orbital
# l=2, rc=6.0938 Bohr: 5d-sz confined orbital
# l=0, rc=5.0625 Bohr: 6s-dz split-valence wave
# l=1, rc=2.4219 Bohr: 5p-dz split-valence wave
# l=1, rc=8.3281 Bohr: 6p-dz split-valence wave
# l=2, rc=3.6406 Bohr: 5d-dz split-valence wave
# l=1, rc=8.5938 Bohr: p-type Gaussian polarization
# Number of RI-basis functions 0
Reference energy: -8501644.730769 # eV
Spin-paired calculation
Convergence criteria:
Maximum [total energy] change in last 3 cyles: 0.0005 eV / electron
Maximum integral of absolute [dens]ity change: 0.0001 electrons / valence electron
Maximum integral of absolute [eigenst]ate change: 4e-08 eV^2 / valence electron
Maximum number of scf [iter]ations: 333
(Square brackets indicate name in SCF output, whereas a 'c' in
the SCF output indicates the quantity has converged.)
Symmetries present (total): 2
( 1 0 0) ( 0 1 0)
( 0 1 0) ( 1 0 0)
( 0 0 1) ( 0 0 1)
1 k-point (Gamma)
1 k-point in the irreducible part of the Brillouin zone
k-points in crystal coordinates weights
0: 0.00000000 0.00000000 0.00000000 1/1
Wave functions: LCAO
Diagonalizer: Serial LAPACK
Atomic Correction: dense with blas
Data-type: float
Occupation numbers: Fermi-Dirac:
width: 0.1000 # eV
Eigensolver
LCAO using direct dense diagonalizer
Densities:
Coarse grid: 28*28*128 grid
Fine grid: 56*56*256 grid
Total Charge: 0.000000
Density mixing:
Method: separate
Backend: pulay
Linear mixing parameter: 0.05
old densities: 5
Damping of long wavelength oscillations: 50
Hamiltonian:
XC and Coulomb potentials evaluated on a 56*56*256 grid
Using the LDA Exchange-Correlation functional
Interpolation: tri-quintic (5. degree polynomial)
Poisson solver: FastPoissonSolver using
Stencil: 6*3+1=19 point O(h^6) finite-difference Laplacian
FFT axes: [0, 1]
FST axes: [2]
Memory estimate:
Process memory now: 226.86 MiB
Calculator: 8.24 MiB
Density: 2.00 MiB
Arrays: 0.29 MiB
Localized functions: 1.60 MiB
Mixer: 0.10 MiB
Hamiltonian: 0.29 MiB
Arrays: 0.19 MiB
XC: 0.00 MiB
Poisson: 0.00 MiB
vbar: 0.10 MiB
Wavefunctions: 5.95 MiB
C [qnM]: 0.59 MiB
S, T [2 x qmm]: 3.21 MiB
P [aqMi]: 0.00 MiB
BasisFunctions: 2.15 MiB
Eigensolver: 0.00 MiB
Total number of cores used: 64
Domain decomposition: 2 x 2 x 16
Number of atoms: 17
Number of atomic orbitals: 459
Number of bands in calculation: 168
Number of valence electrons: 272
Bands to converge: occupied
... initialized
Initializing position-dependent things.
Density initialized from atomic densities
.-------------.
/| |
/ | |
* | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| |Pt |
|Pt| Pt |
Pt | Pt |
| | Pt Pt |
| |Pt Pt |
| | |
|Pt| Pt |
Pt | PPt Pt |
| | |
| |Pt Pt |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| .-------------.
| / /
|/ /
*-------------*
Positions:
0 Pt 1.385929 1.385929 10.000000 ( 0.0000, 0.0000, 0.0000)
1 Pt 4.157788 1.385929 10.000000 ( 0.0000, 0.0000, 0.0000)
2 Pt 1.385929 4.157788 10.000000 ( 0.0000, 0.0000, 0.0000)
3 Pt 4.157788 4.157788 10.000000 ( 0.0000, 0.0000, 0.0000)
4 Pt 0.000000 0.000000 11.960000 ( 0.0000, 0.0000, 0.0000)
5 Pt 2.771859 0.000000 11.960000 ( 0.0000, 0.0000, 0.0000)
6 Pt 0.000000 2.771859 11.960000 ( 0.0000, 0.0000, 0.0000)
7 Pt 2.771859 2.771859 11.960000 ( 0.0000, 0.0000, 0.0000)
8 Pt 1.385929 1.385929 13.920000 ( 0.0000, 0.0000, 0.0000)
9 Pt 4.157788 1.385929 13.920000 ( 0.0000, 0.0000, 0.0000)
10 Pt 1.385929 4.157788 13.920000 ( 0.0000, 0.0000, 0.0000)
11 Pt 4.157788 4.157788 13.920000 ( 0.0000, 0.0000, 0.0000)
12 Pt 0.000000 0.000000 15.880000 ( 0.0000, 0.0000, 0.0000)
13 Pt 2.771859 0.000000 15.880000 ( 0.0000, 0.0000, 0.0000)
14 Pt 0.000000 2.771859 15.880000 ( 0.0000, 0.0000, 0.0000)
15 Pt 2.771859 2.771859 15.880000 ( 0.0000, 0.0000, 0.0000)
16 Pt 1.385929 1.385929 17.491000 ( 0.0000, 0.0000, 0.0000)
Unit cell:
periodic x y z points spacing
1. axis: yes 5.543717 0.000000 0.000000 28 0.1980
2. axis: yes 0.000000 5.543717 0.000000 28 0.1980
3. axis: no 0.000000 0.000000 25.880000 128 0.2022
Lengths: 5.543717 5.543717 25.880000
Angles: 90.000000 90.000000 90.000000
Effective grid spacing dv^(1/3) = 0.1994
iter time total log10-change:
energy eigst dens
iter: 1 14:34:27 -108.010272 c
iter: 2 14:34:28 -102.864982 c -1.18
iter: 3 14:34:29 -99.914862 c -1.28
iter: 4 14:34:30 -98.247526 c -1.34
iter: 5 14:34:31 -96.131520 c -1.56
iter: 6 14:34:32 -95.038136 c -1.71
iter: 7 14:34:33 -93.813680 c -1.76
iter: 8 14:34:34 -93.730740 c -1.94
iter: 9 14:34:35 -93.598249 c -2.01
iter: 10 14:34:36 -93.272552 c -2.07
iter: 11 14:34:37 -93.201964 c -2.32
iter: 12 14:34:38 -93.170538c c -2.41
iter: 13 14:34:39 -93.192315c c -2.52
iter: 14 14:34:40 -93.135898c c -2.44
iter: 15 14:34:41 -93.116586c c -2.69
iter: 16 14:34:42 -93.113105c c -2.68
iter: 17 14:34:43 -93.114605c c -2.90
iter: 18 14:34:44 -93.115324c c -3.04
iter: 19 14:34:46 -93.120765c c -3.15
iter: 20 14:34:47 -93.117184c c -3.09
iter: 21 14:34:48 -93.115396c c -3.32
iter: 22 14:34:49 -93.115650c c -3.51
iter: 23 14:34:50 -93.113249c c -3.61
iter: 24 14:34:51 -93.113691c c -3.67
iter: 25 14:34:52 -93.113566c c -3.87
iter: 26 14:34:53 -93.113520c c -3.85
iter: 27 14:34:54 -93.113698c c -3.93
iter: 28 14:34:55 -93.113683c c -4.03c
Converged after 28 iterations.
Dipole moment: (-6.399275, -6.399275, 0.056909) |e|*Ang
Energy contributions relative to reference atoms: (reference = -8501644.730769)
Kinetic: +115.280615
Potential: -113.440948
External: +0.000000
XC: -94.643446
Entropy (-ST): -1.195455
Local: +0.287824
--------------------------
Free energy: -93.711410
Extrapolated: -93.113683
Band Eigenvalues Occupancy
0 -58.61462 2.00000
1 -58.61462 2.00000
2 -58.53997 2.00000
3 -58.48216 2.00000
4 -58.45808 2.00000
5 -58.45808 2.00000
6 -58.44469 2.00000
7 -58.43486 2.00000
8 -58.43486 2.00000
9 -58.40108 2.00000
10 -58.34265 2.00000
11 -58.34265 2.00000
12 -58.28446 2.00000
13 -58.28446 2.00000
14 -58.22181 2.00000
15 -58.22181 2.00000
16 -58.21742 2.00000
17 -58.20769 2.00000
18 -58.20769 2.00000
19 -58.19738 2.00000
20 -58.18624 2.00000
21 -58.18624 2.00000
22 -58.18236 2.00000
23 -58.13885 2.00000
24 -58.11746 2.00000
25 -58.10882 2.00000
26 -58.10882 2.00000
27 -58.06948 2.00000
28 -58.06948 2.00000
29 -58.05652 2.00000
30 -57.99932 2.00000
31 -57.98206 2.00000
32 -57.98206 2.00000
33 -57.97106 2.00000
34 -57.97106 2.00000
35 -57.96835 2.00000
36 -57.94478 2.00000
37 -57.94478 2.00000
38 -57.90514 2.00000
39 -57.90514 2.00000
40 -57.89320 2.00000
41 -57.85125 2.00000
42 -57.75776 2.00000
43 -57.73836 2.00000
44 -57.60515 2.00000
45 -57.52126 2.00000
46 -57.46086 2.00000
47 -57.45800 2.00000
48 -57.44127 2.00000
49 -57.44127 2.00000
50 -57.31372 2.00000
51 -15.42736 2.00000
52 -13.92075 2.00000
53 -12.68575 2.00000
54 -12.62850 2.00000
55 -12.62850 2.00000
56 -12.62322 2.00000
57 -12.60305 2.00000
58 -12.34555 2.00000
59 -12.25862 2.00000
60 -12.23330 2.00000
61 -12.23014 2.00000
62 -11.85420 2.00000
63 -11.85420 2.00000
64 -11.64714 2.00000
65 -11.64714 2.00000
66 -11.59723 2.00000
67 -11.54448 2.00000
68 -11.49424 2.00000
69 -11.45180 2.00000
70 -11.17383 2.00000
71 -10.71770 2.00000
72 -10.54024 2.00000
73 -10.54024 2.00000
74 -10.05650 2.00000
75 -9.98872 2.00000
76 -9.74764 2.00000
77 -9.74764 2.00000
78 -9.72811 2.00000
79 -9.61541 2.00000
80 -9.61541 2.00000
81 -9.56325 2.00000
82 -9.47099 2.00000
83 -9.40723 2.00000
84 -9.27486 2.00000
85 -9.27486 2.00000
86 -9.21248 2.00000
87 -9.01531 2.00000
88 -8.96961 2.00000
89 -8.96961 2.00000
90 -8.93963 2.00000
91 -8.87006 2.00000
92 -8.83501 2.00000
93 -8.83501 2.00000
94 -8.78002 2.00000
95 -8.78002 2.00000
96 -8.71882 2.00000
97 -8.35694 2.00000
98 -8.35694 2.00000
99 -8.14983 2.00000
100 -8.14526 2.00000
101 -7.97085 2.00000
102 -7.90008 2.00000
103 -7.90008 2.00000
104 -7.65710 2.00000
105 -7.63203 2.00000
106 -7.38339 2.00000
107 -7.33235 2.00000
108 -7.33235 2.00000
109 -7.03633 2.00000
110 -6.83100 2.00000
111 -6.79120 2.00000
112 -6.70566 2.00000
113 -6.70566 2.00000
114 -6.66922 2.00000
115 -6.59981 2.00000
116 -6.55398 2.00000
117 -6.44520 1.99999
118 -6.44520 1.99999
119 -6.36954 1.99998
120 -6.36954 1.99998
121 -6.26090 1.99993
122 -6.07874 1.99957
123 -6.00560 1.99910
124 -5.95002 1.99843
125 -5.80232 1.99313
126 -5.76855 1.99038
127 -5.76855 1.99038
128 -5.71420 1.98350
129 -5.70232 1.98143
130 -5.63785 1.96492
131 -5.56432 1.92818
132 -5.56432 1.92818
133 -5.23663 1.00669
134 -5.22160 0.93162
135 -5.21908 0.91911
136 -5.20725 0.86070
137 -5.20725 0.86070
138 -5.20184 0.83429
139 -5.09620 0.39851
140 -5.00790 0.18661
141 -5.00790 0.18661
142 -4.87226 0.05165
143 -4.65683 0.00613
144 -4.35913 0.00031
145 -3.93568 0.00000
146 -3.93568 0.00000
147 -3.88073 0.00000
148 -3.82449 0.00000
149 -2.68577 0.00000
150 -2.68577 0.00000
151 -2.38664 0.00000
152 -2.38664 0.00000
153 -1.79078 0.00000
154 -1.67722 0.00000
155 -1.66342 0.00000
156 0.15403 0.00000
157 0.15403 0.00000
158 0.77901 0.00000
159 0.86361 0.00000
160 1.72743 0.00000
161 1.72743 0.00000
162 1.91979 0.00000
163 2.04273 0.00000
164 2.07468 0.00000
165 2.08416 0.00000
166 2.81501 0.00000
167 2.85100 0.00000
Fermi level: -5.23529
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