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PwCalculation: allow regex patterns in detect_important_message (#…
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…771)

The parsing of the stdout of `PwCalculation`s went through the function
`detect_important_message` which compared the output to a list of known
error and warning messages. Here we extend this functionality to also
allow regex patterns.

The direct reason is that for QE v6.8 the error message format in the
case of certain pools not having any k-points changed and was no longer
caught by the fixed pattern. This is now fixed by using a regex pattern
instead.
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@unkcpz
unkcpz authored Mar 1, 2022
1 parent 179d3c7 commit 96356d3
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20 changes: 15 additions & 5 deletions aiida_quantumespresso/parsers/parse_raw/pw.py
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Original file line number Diff line number Diff line change
Expand Up @@ -234,6 +234,9 @@ def get_symmetry_mapping():
return rotations


REG_ERROR_NPOOLS_TOO_HIGH = re.compile(r'\s+some nodes have no k-points.*')


def detect_important_message(logs, line):

message_map = {
Expand All @@ -246,8 +249,8 @@ def detect_important_message(logs, line):
'not orthogonal operation': 'ERROR_SYMMETRY_NON_ORTHOGONAL_OPERATION',
'problems computing cholesky': 'ERROR_COMPUTING_CHOLESKY',
'dexx is negative': 'ERROR_DEXX_IS_NEGATIVE',
'some nodes have no k-points': 'ERROR_NPOOLS_TOO_HIGH',
'too many bands are not converged': 'ERROR_DIAGONALIZATION_TOO_MANY_BANDS_NOT_CONVERGED',
REG_ERROR_NPOOLS_TOO_HIGH: 'ERROR_NPOOLS_TOO_HIGH',
},
'warning': {
'Warning:': None,
Expand All @@ -257,10 +260,17 @@ def detect_important_message(logs, line):

# Match any known error and warning messages
for marker, message in message_map['error'].items():
if marker in line:
if message is None:
message = line
logs.error.append(message)
# Replace with isinstance(marker, re.Pattern) once Python 3.6 is dropped
if hasattr(marker, 'search'):
if marker.match(line):
if message is None:
message = line
logs.error.append(message)
else:
if marker in line:
if message is None:
message = line
logs.error.append(message)

for marker, message in message_map['warning'].items():
if marker in line:
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189 changes: 189 additions & 0 deletions tests/parsers/fixtures/pw/finished_npools_too_high/aiida.out
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Original file line number Diff line number Diff line change
@@ -0,0 +1,189 @@

Program PWSCF v.6.8 starts on 18Jan2022 at 18: 9:56

This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
"P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
"P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote

Parallel version (MPI & OpenMP), running on 16 processor cores
Number of MPI processes: 16
Threads/MPI process: 1

MPI processes distributed on 1 nodes
K-points division: npool = 4
R & G space division: proc/nbgrp/npool/nimage = 4
482439 MiB available memory on the printing compute node when the environment starts

Reading input from aiida.in

Current dimensions of program PWSCF are:
Max number of different atomic species (ntypx) = 10
Max number of k-points (npk) = 40000
Max angular momentum in pseudopotentials (lmaxx) = 4
file Fe.pbe-spn-kjpaw_psl.0.2.1.UPF: wavefunction(s) 3D renormalized
Message from routine setup:
using ibrav=0 with symmetry is DISCOURAGED, use correct ibrav instead
Message from routine divide_et_impera:
suboptimal parallelization: some nodes have no k-points

Subspace diagonalization in iterative solution of the eigenvalue problem:
one sub-group per band group will be used
scalapack distributed-memory algorithm (size of sub-group: 2* 2 procs)


Parallelization info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Min 7364 3686 948 951074 336348 43920
Max 7365 3687 949 951075 336349 43923
Sum 29457 14745 3793 3804297 1345393 175685

Using Slab Decomposition



bravais-lattice index = 0
lattice parameter (alat) = 22.6767 a.u.
unit-cell volume = 11661.1220 (a.u.)^3
number of atoms/cell = 1
number of atomic types = 1
number of electrons = 16.00
number of Kohn-Sham states= 12
kinetic-energy cutoff = 90.0000 Ry
charge density cutoff = 720.0000 Ry
scf convergence threshold = 1.0E-08
mixing beta = 0.7000
number of iterations used = 8 plain mixing
Exchange-correlation= SLA PW PBX PBC
( 1 4 3 4 0 0 0)

celldm(1)= 22.676713 celldm(2)= 0.000000 celldm(3)= 0.000000
celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000

crystal axes: (cart. coord. in units of alat)
a(1) = ( 1.000000 0.000000 0.000000 )
a(2) = ( 0.000000 1.000000 0.000000 )
a(3) = ( 0.000000 0.000000 1.000000 )

reciprocal axes: (cart. coord. in units 2 pi/alat)
b(1) = ( 1.000000 0.000000 0.000000 )
b(2) = ( 0.000000 1.000000 0.000000 )
b(3) = ( 0.000000 0.000000 1.000000 )


PseudoPot. # 1 for Fe read from file:
./pseudo/Fe.pbe-spn-kjpaw_psl.0.2.1.UPF
MD5 check sum: e86618425769142926afa95317d90200
Pseudo is Projector augmented-wave + core cor, Zval = 16.0
Generated using "atomic" code by A. Dal Corso v.5.0.99 svn rev. 10869
Shape of augmentation charge: PSQ
Using radial grid of 1191 points, 6 beta functions with:
l(1) = 0
l(2) = 0
l(3) = 1
l(4) = 1
l(5) = 2
l(6) = 2
Q(r) pseudized with 0 coefficients


atomic species valence mass pseudopotential
Fe 16.00 55.84500 Fe( 1.00)

...... SYMMETRIES REMOVED

Cartesian axes

site n. atom positions (alat units)
1 Fe tau( 1) = ( 0.5000000 0.5000000 0.5000000 )

Crystallographic axes

site n. atom positions (cryst. coord.)
1 Fe tau( 1) = ( 0.5000000 0.5000000 0.5000000 )


...... K-POINTS REMOVED

...... MEMORY INFO REMOVED

...... SCF REMOVED

iteration # 57 ecut= 90.00 Ry beta= 0.70
Davidson diagonalization with overlap

---- Real-time Memory Report at c_bands before calling an iterative solver
1653664 MiB given to the printing process from OS
7 MiB allocation reported by mallinfo(arena+hblkhd)
470965 MiB available memory on the node where the printing process lives
------------------
ethr = 7.38E-10, avg # of iterations = 1.0

negative rho (up, down): 1.661E-03 0.000E+00

total cpu time spent up to now is 729.0 secs

total energy = -328.68767430 Ry
estimated scf accuracy < 0.00000033 Ry

iteration # 58 ecut= 90.00 Ry beta= 0.70
Davidson diagonalization with overlap

---- Real-time Memory Report at c_bands before calling an iterative solver
1653664 MiB given to the printing process from OS
7 MiB allocation reported by mallinfo(arena+hblkhd)
480267 MiB available memory on the node where the printing process lives
------------------
ethr = 7.38E-10, avg # of iterations = 1.0

negative rho (up, down): 1.661E-03 0.000E+00

total cpu time spent up to now is 741.0 secs

End of self-consistent calculation

k = 0.0000 0.0000 0.0000 (168285 PWs) bands (ev):

-90.1257 -56.2677 -56.2677 -56.2677 -4.3037 -4.3037 -4.3037 -4.3037
-4.3037 -4.2897 -0.7954 -0.7954

occupation numbers
1.0000 1.0000 1.0000 1.0000 0.6790 0.6790 0.6790 0.6789
0.6789 0.6052 0.0000 0.0000

the Fermi energy is -4.2709 ev

! total energy = -328.68767430 Ry

total all-electron energy = -2544.984210 Ry
estimated scf accuracy < 2.6E-09 Ry
smearing contrib. (-TS) = -0.02261285 Ry
internal energy E=F+TS = -328.66506144 Ry

The total energy is F=E-TS. E is the sum of the following terms:
one-electron contribution = -367.98720683 Ry
hartree contribution = 181.91266004 Ry
xc contribution = -34.43153795 Ry
ewald contribution = -32.03057422 Ry
one-center paw contrib. = -76.12840247 Ry
-> PAW hartree energy AE = 204.54908170 Ry
-> PAW hartree energy PS = -203.69852858 Ry
-> PAW xc energy AE = -111.08683553 Ry
-> PAW xc energy PS = 34.10787993 Ry
-> total E_H with PAW = 182.76321316 Ry
-> total E_XC with PAW = -111.41049355 Ry

convergence has been achieved in 58 iterations

Writing output data file ./out/aiida.save/

...... TIMING REMOVED

=------------------------------------------------------------------------------=
JOB DONE.
=------------------------------------------------------------------------------=
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