[gpaw-users] python2.7 gpaw-1.4.0 test Errors/results
Alva Dillon
devondillon333 at gmail.com
Wed Jan 16 16:00:56 CET 2019
Hello,
I still had to remove
in libxc.c in c/xc/ line xc_mgga_x_tb09_set_params(self->functional[0], c);
so i expect there to be some problems with the mgga modules, but there is
an issue with other modules and a fatal error in a parallel test.
On Mon, Jan 14, 2019 at 6:45 AM Jens Jørgen Mortensen <jjmo at dtu.dk> wrote:
>
> On 1/14/19 12:11 PM, Alva Dillon wrote:
>
> I got a lot of test errors. Although the build was successful without any
> errors.
>
> (py36) [alvadillon at compute-1-21 gpaw-1.5.0]$ gpaw test -j 4
>
> python-3.6.8
> /home/alvadillon/builds/miniconda2/envs/py36/bin/python
>
> gpaw-1.5.0 /home/alvadillon/builds/gpaw-1.5.0/gpaw/
>
> ase-3.17.0
> /home/alvadillon/.local/lib/python3.6/site-packages/ase-3.17.0-py3.6.egg/ase/
>
> numpy-1.14.3
> /home/gieseking-lab/intel/intelpython3/lib/python3.6/site-packages/numpy/
>
> scipy-1.1.0
> /home/gieseking-lab/intel/intelpython3/lib/python3.6/site-packages/scipy/
>
> _gpaw
> /home/alvadillon/.local/lib/python3.6/site-packages/_
> gpaw.cpython-36m-x86_64-linux-gnu.so
>
> parallel
> /home/alvadillon/builds/miniconda2/envs/py36/bin/gpaw-python
>
> MPI enabled no
>
> scalapack no (MPI unavailable)
>
> Elpa no (MPI unavailable)
>
> FFTW yes
>
> libvdwxc no
>
> PAW-datasets 1: /home/alvadillon/builds/gpaw-setups-0.9.20000
>
> 2: /usr/local/share/gpaw-setups
>
> 3: /usr/share/gpaw-setups
>
> Running tests in /tmp/gpaw-test-hsb1io7n
>
> Jobs: 4, Cores: 1, debug-mode: False
>
>
> =============================================================================
>
> linalg/gemm_complex.py 0.026 OK
>
> ...
>
>
> pw/reallfc.py 0.100 FAILED!
>
>
> #############################################################################
>
> Traceback (most recent call last):
>
> File "/home/alvadillon/builds/gpaw-1.5.0/gpaw/test/__init__.py", line
> 664, in run_one
>
> exec(compile(fd.read(), filename, 'exec'), loc)
>
> File "/home/alvadillon/builds/gpaw-1.5.0/gpaw/test/pw/reallfc.py", line
> 42, in <module>
>
> lfc.add(b, c_axi)
>
> File "/home/alvadillon/builds/gpaw-1.5.0/gpaw/wavefunctions/pw.py", line
> 1567, in add
>
> f_GI = self.expand(q, G1, G2, cc=False)
>
> File "/home/alvadillon/builds/gpaw-1.5.0/gpaw/wavefunctions/pw.py", line
> 1509, in expand
>
> cc, f_GI)
>
> TypeError: function takes exactly 9 arguments (8 given)
>
>
> It looks like your new version 1.5 Python code is picking up the old
> C-code extension module (_gpaw.so). You are getting it from:
>
>
> /home/alvadillon/.local/lib/python3.6/site-packages/_
> gpaw.cpython-36m-x86_64-linux-gnu.so
>
>
> But it must be some left-over from an earlier build of GPAW.
>
>
> Jens Jørgen
>
>
>
--
Thank you,
Alva Dillon
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python-3.6.8 /home/alvadillon/builds/miniconda2/envs/py36/bin/gpaw-python
gpaw-1.5.0 /home/alvadillon/.local/lib/python3.6/site-packages/gpaw/
ase-3.17.0 /home/alvadillon/.local/lib/python3.6/site-packages/ase-3.17.0-py3.6.egg/ase/
numpy-1.14.3 /home/gieseking-lab/intel/intelpython3/lib/python3.6/site-packages/numpy/
scipy-1.1.0 /home/gieseking-lab/intel/intelpython3/lib/python3.6/site-packages/scipy/
_gpaw built-in
parallel /home/alvadillon/.local/bin/gpaw-python
MPI enabled yes
scalapack yes
Elpa no
FFTW yes
libvdwxc no
PAW-datasets 1: /home/alvadillon/builds/gpaw-setups-0.9.20000
2: /usr/local/share/gpaw-setups
3: /usr/share/gpaw-setups
Running tests in /tmp/gpaw-test-02621hwb
Jobs: 1, Cores: 4, debug-mode: False
=============================================================================
linalg/gemm_complex.py 0.321 OK
ase_features/ase3k_version.py 0.057 OK
kpt.py 4.489 OK
mpicomm.py 0.491 OK
pathological/numpy_core_multiarray_dot.py 0.605 OK
eigen/cg2.py 1.350 OK
fd_ops/laplace.py 0.000 SKIPPED
linalg/lapack.py 0.601 OK
linalg/eigh.py 0.169 OK
parallel/submatrix_redist.py 0.311 OK
lfc/second_derivative.py 0.704 OK
parallel/parallel_eigh.py 0.521 OK
lfc/gp2.py 0.765 OK
linalg/blas.py 0.866 OK
Gauss.py 0.380 OK
symmetry/check.py 4.837 OK
fd_ops/nabla.py 0.596 OK
linalg/dot.py 1.029 OK
linalg/mmm.py 0.791 OK
xc/pbe_pw91.py 1.326 OK
fd_ops/gradient.py 1.720 OK
maths/erf.py 0.223 OK
lfc/lf.py 0.284 OK
maths/fsbt.py 9.795 OK
parallel/compare.py 0.537 OK
vdw/libvdwxc_functionals.py 0.000 SKIPPED
radial/integral4.py 6.175 OK
linalg/zher.py 0.166 OK
fd_ops/gd.py 0.425 OK
pw/interpol.py 0.646 OK
poisson/screened_poisson.py 2.247 OK
electronphonon.py 0.000 SKIPPED
xc/xc.py 1.120 FAILED! (rank 0,1,2,3)
#############################################################################
RANK 0,1,2,3:
Traceback (most recent call last):
File "/home/alvadillon/.local/lib/python3.6/site-packages/gpaw/test/__init__.py", line 664, in run_one
exec(compile(fd.read(), filename, 'exec'), loc)
File "/home/alvadillon/.local/lib/python3.6/site-packages/gpaw/test/xc/xc.py", line 83, in <module>
equal(error, 0, 6e-9)
File "/home/alvadillon/.local/lib/python3.6/site-packages/gpaw/test/__init__.py", line 30, in equal
raise AssertionError(msg)
AssertionError: inf != 0 (error: |inf| > 6e-09)
#############################################################################
xc/XC2.py 0.328 OK
radial/yukawa_radial.py 0.123 OK
vdw/potential.py 0.052 OK
radial/lebedev.py 0.098 OK
occupations.py 0.405 OK
lfc/derivatives.py 0.346 OK
pw/reallfc.py 1.659 OK
parallel/pblas.py 0.266 OK
fd_ops/non_periodic.py 0.304 OK
spectrum.py 1.005 OK
pw/lfc.py 0.921 OK
gauss_func.py 2.275 OK
multipoletest.py 0.457 OK
cluster.py 6.096 OK
poisson/poisson.py 0.407 OK
poisson/fastpoisson.py 14.930 FAILED! (rank 0,1,2,3)
#############################################################################
RANK 0:
Traceback (most recent call last):
File "/home/alvadillon/.local/lib/python3.6/site-packages/gpaw/test/__init__.py", line 664, in run_one
exec(compile(fd.read(), filename, 'exec'), loc)
File "/home/alvadillon/.local/lib/python3.6/site-packages/gpaw/test/poisson/fastpoisson.py", line 141, in <module>
assert err < tolerance, err
AssertionError: 2.2252328102973644
#############################################################################
RANK 1:
Traceback (most recent call last):
File "/home/alvadillon/.local/lib/python3.6/site-packages/gpaw/test/__init__.py", line 664, in run_one
exec(compile(fd.read(), filename, 'exec'), loc)
File "/home/alvadillon/.local/lib/python3.6/site-packages/gpaw/test/poisson/fastpoisson.py", line 141, in <module>
assert err < tolerance, err
AssertionError: 2.056641668808078
#############################################################################
RANK 2:
Traceback (most recent call last):
File "/home/alvadillon/.local/lib/python3.6/site-packages/gpaw/test/__init__.py", line 664, in run_one
exec(compile(fd.read(), filename, 'exec'), loc)
File "/home/alvadillon/.local/lib/python3.6/site-packages/gpaw/test/poisson/fastpoisson.py", line 141, in <module>
assert err < tolerance, err
AssertionError: 2.5651275789112353
#############################################################################
RANK 3:
Traceback (most recent call last):
File "/home/alvadillon/.local/lib/python3.6/site-packages/gpaw/test/__init__.py", line 664, in run_one
exec(compile(fd.read(), filename, 'exec'), loc)
File "/home/alvadillon/.local/lib/python3.6/site-packages/gpaw/test/poisson/fastpoisson.py", line 141, in <module>
assert err < tolerance, err
AssertionError: 1.9962495377369367
#############################################################################
poisson/poisson_asym.py 0.767 OK
parallel/arraydict_redist.py 0.318 OK
parallel/scalapack.py 0.204 OK
gauss_wave.py 1.749 OK
fd_ops/transformations.py 0.208 OK
parallel/blacsdist.py 0.240 OK
pbc.py 61.758 OK
atoms_too_close.py 0.214 OK
ext_potential/harmonic.py 2.998 OK
atoms_mismatch.py 0.261 OK
setup_basis_spec.py 0.363 OK
pw/direct.py 0.448 OK
libelpa.py 0.000 SKIPPED
vdw/libvdwxc_spin.py 0.000 SKIPPED
timing.py 0.666 OK
parallel/ut_parallel.py 1.322 OK
lcao/density.py 4.011 OK
pw/stresstest.py 2.031 OK
pw/fftmixer.py 8.081 OK
lcao/fftmixer.py 5.146 OK
symmetry/usesymm.py 4.414 OK
coulomb.py 0.803 OK
xc/xcatom.py 3.021 OK
force_as_stop.py 2.445 OK
vdwradii.py 7.526 OK
ase_features/ase3k.py 7.665 OK
pathological/numpy_zdotc_graphite.py 2.787 OK
utilities/eed.py 16.530 OK
lcao/dos.py 9.506 OK
solvation/nan_radius.py 8.845 OK
solvation/pbc_pos_repeat.py 1.514 OK
lcao/generate_ngto.py 0.000 SKIPPED
reuse_wfs_celldisp.py 16.216 OK
linalg/gemv.py 5.199 OK
fileio/idiotproof_setup.py 6.307 OK
radial/ylexpand.py 8.654 OK
eigen/keep_htpsit.py 5.755 OK
xc/gga_atom.py 4.716 OK
generic/hydrogen.py 10.073 OK
aeatom.py 12.294 OK
ase_features/plt.py 5.302 OK
ds_beta.py 9.650 OK
multipoleH2O.py 6.589 OK
spinorbit_Kr.py 0.000 SKIPPED
stdout.py 3.510 OK
lcao/largecellforce.py 11.886 OK
parallel/scalapack_diag_simple.py 0.583 OK
fixdensity.py 12.048 OK
pseudopotential/ah.py 8.659 OK
lcao/gllb_si.py 6.758 OK
fileio/wfs_io.py 5.195 OK
lrtddft/2.py 6.702 OK
gllbghost.py 6.943 OK
fileio/file_reference.py 5.855 OK
fileio/restart.py 16.142 OK
broydenmixer.py 8.857 OK
pw/fulldiagk.py 13.643 OK
ext_potential/external.py 5.797 OK
ext_potential/external_pw.py 32.814 OK
lcao/atomic_corrections.py 8.754 OK
vdw/libvdwxc_h2.py 0.000 SKIPPED
generic/mixer.py 9.111 OK
parallel/lcao_projections.py 23.978 OK
lcao/h2o.py 7.822 OK
corehole/h2o.py 14.487 OK
fileio/wfs_auto.py 7.447 OK
pw/fulldiag.py 13.317 OK
symmetry/symmetry_ft.py 4.350 OK
response/aluminum_EELS_RPA.py 10.789 OK
poisson/poisson_extended.py 6.726 OK
solvation/vacuum.py 25.739 OK
vdw/libvdwxc_mbeef.py 0.000 SKIPPED
response/graphene_refined_response.py 820.012 OK
pw/par_strategies.py 180.098 OK
pseudopotential/sg15_hydrogen.py 22.273 OK
generic/move_across_cell.py 53.710 OK
parallel/augment_grid.py 49.902 OK
pw/augment_grids.py 57.218 OK
utilities/ewald.py 4.188 OK
symmetry/symmetry.py 4.737 OK
xc/revPBE.py 5.635 OK
xc/nonselfconsistentLDA.py 10.842 OK
response/aluminum_EELS_ALDA.py 7.810 OK
spin/spin_contamination.py 8.649 OK
inducedfield_lrtddft.py 10.866 OK
generic/H_force.py 10.967 OK
symmetry/usesymm2.py 11.864 OK
mgga/mgga_restart.py 7.333 OK
fixocc.py 7.606 OK
spin/spinFe3plus.py 8.547 OK
fermisplit.py 13.106 OK
generic/Cl_minus.py 6.083 OK
lrtddft/pes.py 4.790 OK
generic/proton.py 9.879 OK
parallel/lcao_elpa_kpts.py 0.000 SKIPPED
parallel/lcao_elpa.py 0.000 SKIPPED
corehole/h2o_recursion.py 14.718 OK
xc/nonselfconsistent.py 12.823 OK
spin/spinpol.py 23.828 OK
eigen/cg.py 15.569 OK
parallel/kptpar.py 13.859 OK
utilities/elf.py 7.956 OK
eigen/blocked_rmm_diis.py 17.829 OK
pw/slab.py 144.570 OK
generic/si.py 21.213 OK
lcao/bsse.py 28.077 OK
parallel/lcao_hamiltonian.py 12.109 OK
xc/degeneracy.py 8.227 OK
fileio/refine.py 5.843 OK
solvation/pbc.py 19.800 OK
generic/asym_box.py 16.394 OK
overlap.py 19.831 OK
linalg/gemm.py 14.560 OK
generic/al_chain.py 16.363 OK
fileio/parallel.py 8.397 OK
fixmom.py 13.444 OK
exx/unocc.py 12.909 OK
eigen/davidson.py 27.814 OK
vdw/H_Hirshfeld.py 7.760 OK
parallel/redistribute_grid.py 3.780 OK
aedensity.py 19.043 OK
pw/h.py 17.821 OK
lrtddft/apmb.py 9.593 OK
pseudopotential/hgh_h2o.py 30.016 OK
poisson/poisson_restart.py 0.000 SKIPPED
poisson/poisson_extravacuum.py 23.595 OK
fdtd/ed_wrapper.py 22.919 OK
fdtd/ed_shapes.py 12.424 OK
fdtd/ed.py 22.439 OK
fdtd/ed_inducedfield.py 29.762 OK
inducedfield_td.py 8.454 OK
pw/bulk.py 25.391 OK
gllb/ne.py 22.502 OK
lcao/force.py 19.686 OK
xc/pplda.py 12.332 OK
response/test_unit_sphere_area.py 43.831 OK
rsf_yukawa/lrtddft_short.py 7.343 OK
fileio/restart_density.py 6.481 OK
rpa/rpa_energy_Ni.py 21.638 OK
tddft/be_nltd_ip.py 15.345 OK
ibzqpt.py 21.802 OK
noncollinear/o2.py 0.030 SKIPPED
generic/si_primitive.py 10.629 OK
tddft/ehrenfest_nacl.py 16.715 OK
lcao/fd2lcao_restart.py 23.014 OK
ext_potential/constant_e_field.py 3.199 OK
complex.py 15.057 OK
vdw/quick.py 9.552 OK
pathological/lcao_spos_derivative.py 21.448 OK
lrtddft2/H2O-lcao.py 8.515 OK
lrtddft2/Al2.py 32.991 OK
lcaotddft/simple.py 6.264 OK
lcaotddft/restart.py 32.645 OK
lcaotddft/fxc_is_xc.py 8.414 OK
lcaotddft/fxc_rpa.py 4.698 OK
lcaotddft/fxc_vs_linearize.py 24.450 OK
lcaotddft/replay.py 11.142 OK
lcaotddft/ksdecomp.py 14.770 OK
tddft/fxc_linearize.py 26.252 OK
timelimit.py 15.884 OK
ralda/ralda_energy_N2.py 209.292 OK
parallel/lcao_complicated.py 32.425 OK
generic/bulk.py 30.565 OK
sic/scfsic_h2.py 30.330 OK
kpt_refine.py 293.593 OK
lcao/bulk.py 22.496 OK
reuse_wfs.py 54.946 OK
generic/2Al.py 37.393 OK
lrtddft/kssingles_Be.py 29.876 OK
generic/relax.py 15.494 OK
solvation/adm12.py 41.728 OK
rsf_yukawa/rsf_ivo_sing_mg.py 16.113 OK
solvation/lrtddft.py 9.420 OK
dscf/dscf_lcao.py 32.306 OK
generic/8Si.py 60.876 OK
utilities/partitioning.py 32.744 OK
xc/lxc_xcatom.py 51.887 OK
solvation/sfgcm06.py 12.972 OK
solvation/sss09.py 12.390 OK
tddft/restart.py 37.844 OK
gllb/atomic.py 6.948 OK
generic/guc_force.py 17.930 OK
ralda/ralda_energy_Ni.py 27.763 OK
utilities/simple_stm.py 31.471 OK
ofdft/ofdft_pbc.py 19.189 OK
gllb/restart_band_structure.py 51.219 OK
exx/exx.py 53.436 OK
response/iron_sf_ALDA_gridrep.py 47.199 OK
response/iron_sf_gssALDA_gridrep.py 51.675 OK
Hubbard_U.py 150.431 OK
rpa/rpa_energy_Si.py 54.777 OK
dipole.py 25.573 OK
generic/IP_oxygen.py 33.449 OK
rpa/rpa_energy_Na.py 57.102 OK
parallel/fd_parallel.py 38.632 OK
solvation/poisson.py 21.642 OK
solvation/water_water.py 13.837 OK
xc/pygga.py 31.505 OK
pseudopotential/atompaw.py 49.882 OK
parallel/lcao_parallel.py 28.805 OK
xc/atomize.py 13.749 OK
lrtddft/excited_state.py 59.426 OK
gllb/ne_disc.py 88.660 OK
ofdft/ofdft.py 26.966 OK
response/bse_silicon.py 40.599 OK
tpss.py 9.374 OK
tddft/td_na2.py 100.455 OK
exx/coarse.py 40.304 OK
corehole/si.py 19.287 OK
mgga/mgga_sc.py 365.389 FAILED! (rank 0,1,2,3)
#############################################################################
RANK 0,1,2,3:
Traceback (most recent call last):
File "/home/alvadillon/.local/lib/python3.6/site-packages/gpaw/test/__init__.py", line 664, in run_one
exec(compile(fd.read(), filename, 'exec'), loc)
File "/home/alvadillon/.local/lib/python3.6/site-packages/gpaw/test/mgga/mgga_sc.py", line 11, in <module>
e1 = n.get_potential_energy()
File "/home/alvadillon/.local/lib/python3.6/site-packages/ase-3.17.0-py3.6.egg/ase/atoms.py", line 664, in get_potential_energy
energy = self._calc.get_potential_energy(self)
File "/home/alvadillon/.local/lib/python3.6/site-packages/ase-3.17.0-py3.6.egg/ase/calculators/calculator.py", line 505, in get_potential_energy
energy = self.get_property('energy', atoms)
File "/home/alvadillon/.local/lib/python3.6/site-packages/ase-3.17.0-py3.6.egg/ase/calculators/calculator.py", line 552, in get_property
self.calculate(atoms, [name], system_changes)
File "/home/alvadillon/.local/lib/python3.6/site-packages/gpaw/calculator.py", line 300, in calculate
self.log, self.call_observers)
File "/home/alvadillon/.local/lib/python3.6/site-packages/gpaw/scf.py", line 96, in run
'Did not converge! See text output for help.')
gpaw.KohnShamConvergenceError: Did not converge! See text output for help.
#############################################################################
Hubbard_U_Zn.py 11.933 OK
lrtddft/1.py 51.861 OK
gllb/spin.py 53.822 OK
parallel/fd_parallel_kpt.py Fatal error in PMPI_Comm_create: Other MPI error, error stack:
PMPI_Comm_create(564)...............: MPI_Comm_create(comm=0xc4003072, group=0xc8001315, new_comm=0x7ffc89ee08d8) failed
PMPI_Comm_create(541)...............:
MPIR_Comm_create_intra(215).........:
MPIR_Get_contextid_sparse_group(614): Too many communicators (360/2048 free on this process; ignore_id=0)
Fatal error in PMPI_Comm_create: Other MPI error, error stack:
PMPI_Comm_create(564)...............: MPI_Comm_create(comm=0xc4001118, group=0xc80011aa, new_comm=0x7ffdecdaad68) failed
PMPI_Comm_create(541)...............:
MPIR_Comm_create_intra(215).........:
MPIR_Get_contextid_sparse_group(614): Too many communicators (1360/2048 free on this process; ignore_id=1)
Fatal error in PMPI_Comm_create: Other MPI error, error stack:
PMPI_Comm_create(564)...............: MPI_Comm_create(comm=0xc40043a4, group=0xc80013d9, new_comm=0x7ffdecdef4c8) failed
PMPI_Comm_create(541)...............:
MPIR_Comm_create_intra(215).........:
MPIR_Get_contextid_sparse_group(614): Too many communicators (0/2048 free on this process; ignore_id=0)
Fatal error in PMPI_Comm_create: Other MPI error, error stack:
PMPI_Comm_create(564)...............: MPI_Comm_create(comm=0xc4001318, group=0xc80011f1, new_comm=0x7ffca8412f88) failed
PMPI_Comm_create(541)...............:
MPIR_Comm_create_intra(215).........:
MPIR_Get_contextid_sparse_group(614): Too many communicators (1148/2048 free on this process; ignore_id=1)
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