[gpaw-users] 7 failed tests

Fri Sep 6 20:15:44 CEST 2013

Hi Marcin,
you identified the problem right away. I had a couple of old LDA setups 
laying around in my personal setups folder. After removing them, all the 
7 tests succeeded!

Thank you,
Rasmus

On 09/06/2013 10:40 AM, Marcin Dulak wrote:
> Hi,
>
> On 09/06/2013 07:14 PM, Rasmus Karlsson wrote:
>> (This is a repost from the gpaw-developers list, since I got no 
>> replies there)
>> Hi!
>> After compiling gpaw 0.9.1.10645 with ase version 3.8.0.3237, numpy 
>> version 1.3.0 and scipy version 0.7.0 I get a number of errors in the 
>> tests. I'm using gpaw-setups v 0.9.9672. The cluster uses nodes with 
>> AMD Opteron 6238 (Interlagos) CPUs. Furthermore, I'm using 
>> gcc-compiled lapack (3.4.0) and openblas (0.1), and gcc-compiled 
>> openmpi v 1.6.4.
>>
>> Specifically, the following tests failed (error messages further down 
>> in the email)
>> fileio/hdf5_noncontiguous.py
>> pw/mgo_hybrids.py
>> lcao_h2o.py
>> lcao_force.py
>> IP_oxygen.py
>> dipole.py
>> bse_MoS2_cut.py
>>
>> I have hdf5 version 1.8.10-patch1, but maybe another version is 
>> needed for the latest gpaw. HDF5 is not so important for what I'm 
>> doing, so that problem might be acceptable. Anyway, are there any 
>> ideas as to why the other 6 tests failed?
>>
>> These are the errors (relevant parts of the output files) I get for 
>> each of the tests:
>>
>> pw/mgo_hybrids.py
>> --------------------
>> Traceback (most recent call last):
>>   File "pw/mgo_hybrids.py", line 30, in <module>
>>     de_skn = vxc(calc, hyb_calc) - vxc(calc, 'LDA')
>>   File 
>> "/home/r/rasmusk/pfs/programs/gpaw-0.9.1.10645/gpaw/xc/tools.py", 
>> line 26, in vxc
>>     paw.get_xc_difference(xc)
>>   File 
>> "/home/r/rasmusk/pfs/programs/gpaw-0.9.1.10645/gpaw/aseinterface.py", 
>> line 423, in get_xc_difference
>>     return self.hamiltonian.get_xc_difference(xc, self.density) * 
>> Hartree
>>   File 
>> "/home/r/rasmusk/pfs/programs/gpaw-0.9.1.10645/gpaw/hamiltonian.py", 
>> line 405, in get_xc_difference
>>     xc.calculate_exx()
>>   File 
>> "/home/r/rasmusk/pfs/programs/gpaw-0.9.1.10645/gpaw/xc/hybridg.py", 
>> line 340, in calculate_exx
>>     self.calculate_exx_paw_correction()
>>   File 
>> "/home/r/rasmusk/pfs/programs/gpaw-0.9.1.10645/gpaw/xc/hybridg.py", 
>> line 613, in calculate_exx_paw_correction
>>     self.evc -= np.dot(D_p, setup.X_p)
>> TypeError: unsupported operand type(s) for *: 'float' and 'NoneType'
>>
>> lcao_h2o.py
>> --------------------
>> Dipole Moment: [  7.27763290e-14   7.44357242e-14 -4.80857449e-01]
>> Energy -10.3905075644
>> Ref -10.266984
>> Err 0.123523564376
>> Traceback (most recent call last):
>>   File "lcao_h2o.py", line 24, in <module>
>>     assert err < 1e-4
>> AssertionError
> i'm getting almost the same Err value when using setups 0.8.
> Are you sure you use 0.9?
> echo $GPAW_SETUP_PATH
>
> Best regards,
>
> Marcin
>>
>> lcao_force.py
>> --------------------
>> Forces in eV/Ang:
>>   0 O     1.50949    1.69245   -6.66452
>>   1 H    -0.91270   -1.53450    3.78840
>>   2 H    -0.58858   -0.11066    2.70873
>> Force
>> [[ 1.50948536  1.69244746 -6.66451859]
>>  [-0.91269716 -1.53449586  3.78839681]
>>  [-0.58857688 -0.11065799  2.70872717]]
>>
>> Reference result
>> [[ 1.05200088  1.64950565 -5.01149812]
>>  [-0.70775684 -0.89551937  3.03218888]
>>  [-0.3330413  -0.70650306  1.77179155]]
>>
>> Error
>> [[ 0.45748448  0.04294181  1.65302047]
>>  [ 0.20494032  0.63897649  0.75620793]
>>  [ 0.25553558  0.59584507  0.93693562]]
>>
>> Max error
>> 1.65302046563
>> Traceback (most recent call last):
>>   File "lcao_force.py", line 54, in <module>
>>     assert err < 3e-3
>> AssertionError
>>
>>
>> IP_oxygen.py
>> --------------------
>> Total Magnetic Moment: 3.000000
>> Spin contamination: 0.000000 electrons
>> Local Magnetic Moments:
>> 0 3.0
>>
>> 13.965354077
>> Traceback (most recent call last):
>>   File "IP_oxygen.py", line 23, in <module>
>>     equal(e0, -1.88477, energy_tolerance)
>>   File 
>> "/home/r/rasmusk/pfs/programs/gpaw-0.9.1.10645/gpaw/test/__init__.py", line 
>> 25, in equal
>>     raise AssertionError(msg)
>> AssertionError: -1.69872400425 != -1.88477 (error: |0.186045995755| > 
>> 4e-05)
>>
>> dipole.py
>> --------------------
>> Dipole Moment: [ -5.90227807e+00   1.28376553e+00 -1.18314288e-08]
>> 2.07504659748 2.07692326303
>> Ref value of previous calculation 2.07342988218
>> Value in this calculation 2.07504659748
>> Error 0.00187666554622 0.00161671530144
>> Traceback (most recent call last):
>>   File "dipole.py", line 120, in <module>
>>     assert err2 < 2e-4
>> AssertionError
>>
>> bse_MoS2_cut.py
>> --------------------
>> Calculating phi_qaGp
>>   Finished iq 0 in 0:00:00, estimated 0:00:37 left.
>>   Finished iq 16 in 0:00:08, estimated 0:00:29 left.
>>   Finished iq 32 in 0:00:15, estimated 0:00:22 left.
>>   Finished iq 48 in 0:00:22, estimated 0:00:15 left.
>>   Finished iq 64 in 0:00:29, estimated 0:00:08 left.
>>   Finished iq 80 in 0:00:36, estimated 0:00:01 left.
>> Memory used 248.773438 M
>>
>> Calculating screening interaction kernel.
>>     RPA macroscopic dielectric constant is: 1.008
>>   Finished iq 0 in 0:00:14, estimated 0:02:45 left.
>>   Finished iq 2 in 0:00:23, estimated 0:02:22 left.
>>   Finished iq 4 in 0:00:33, estimated 0:02:13 left.
>>   Finished iq 6 in 0:00:42, estimated 0:02:03 left.
>>   Finished iq 8 in 0:00:51, estimated 0:01:54 left.
>>   Finished iq 10 in 0:01:01, estimated 0:01:44 left.
>>
>> Calculating BSE matrix elements
>>   Finished pair orbital 0 in 0:00:02, estimated 0:02:11 left.
>>   Finished pair orbital 16 in 0:00:27, estimated 0:01:44 left.
>>   Finished pair orbital 32 in 0:00:53, estimated 0:01:19 left.
>>   Finished pair orbital 48 in 0:01:18, estimated 0:00:53 left.
>>   Finished pair orbital 64 in 0:01:44, estimated 0:00:27 left.
>>   Finished pair orbital 80 in 0:02:08, estimated 0:00:03 left.
>> Diagonalizing BSE matrix.
>> Use lapack.
>> Calculating dielectric function.
>>
>> Sum rule:
>> N1 = 0.736282, -95.909544  % error
>> Memory usage: 248.77 MB
>>
>> ============================================================
>> Timing:                               incl.     excl.
>> ...
>>
>> Any suggestions are appreciated.
>>
>> Rasmus
>>
>
>

-- 
Rasmus Karlsson, PhD student
Applied Electrochemistry
School of Chemical Science and Engineering
KTH Royal Institute of Technology
SE-100 44 Stockholm
Sweden