Yambo Community Forum

Dear Developers,

I found the ERROR message during the calculation of dielectric matrix (X):

[ERROR] STOP signal received while in :[05] Dynamic Dielectric Matrix (PPA)
[ERROR][NetCDF] NetCDF: One or more variable sizes violate format constraints

It seems certain size is too big for the program but I don't know why and how to avoid it.

The input is as follows:

# Version 3.2.5 Revision 1034
# http://www.yambo-code.org
#
gw0 # [R GW] GoWo Quasiparticle energy levels
ppa # [R Xp] Plasmon Pole Approximation
HF_and_locXC # [R XX] Hartree-Fock Self-energy and Vxc
em1d # [R Xd] Dynamical Inverse Dielectric Matrix
EXXRLvcs= 9000 RL # [XX] Exchange RL components
% QpntsRXp
1 | 126 | # [Xp] Transferred momenta
%
% BndsRnXp
1 | 200 | # [Xp] Polarization function bands
%
NGsBlkXp= 2000 RL # [Xp] Response block size
% LongDrXp
1.000000 | 0.000000 | 0.000000 | # [Xp] [cc] Electric Field
%
PPAPntXp= 27.21138 eV # [Xp] PPA imaginary energy
% GbndRnge
1 | 200 | # [GW] G[W] bands range
%
GDamping= 0.10000 eV # [GW] G[W] damping
dScStep= 0.10000 eV # [GW] Energy step to evalute Z factors
DysSolver= "n" # [GW] Dyson Equation solver (`n`,`s`,`g`)
%QPkrange # [GW] QP generalized Kpoint/Band indices
1| 29| 10| 25|
%
--------------------------------------------------------------------------------------------------
Part of the output is as follows:

[RD./SAVE//ns.db1]------------------------------------------
Bands : 200
K-points : 126
G-vectors [RL space]: 42095
Components [wavefunctions]: 5298
Symmetries [spatial]: 8
Spinor components : 1
Spin polarizations : 1
Temperature [ev]: 0.0045
Electrons : 42.00000
WF G-vectors : 6579
Max atoms/species : 4
No. of atom species : 2
Magnetic symmetries : no
- S/N 002605 --------------------------- v.03.03.00 r.1887 -

[05] Dynamic Dielectric Matrix (PPA)
====================================

[RESTARTer] Section(s) completed for ./SAVE//ndb.pp :34

[RD./SAVE//ndb.pp]------------------------------------------
Brillouin Zone Q/K grids (IBZ/BZ): 126 640 126 640
RL vectors (WF): 6579
Coulomb cutoff potential :none
Electronic Temperature [K]: 52.62912
Bosonic Temperature [K]: 52.62912
PPA diel. fun. energies :Slater exchange(X)+Perdew & Zunger(C)
wavefunctions :Slater exchange(X)+Perdew & Zunger(C)
Global Gauge :length
X matrix size : 2005
X band range : 1 200
X e/h energy range [ev]:-1.000000 -1.000000
X Time ordering :c
X xc-Kernel :none
X Drude frequency : 0.00 0.00
X poles [o/o]: 100.0000
Rl vectors in the sum : 6579
[r,Vnl] included :no
Field direction :0.1000E-4 0.000 0.000
BZ energy Random IM :no
BZ energy RIM points :0
PPA Im energy [ev]: 27.21138
- S/N 002605 --------------------------- v.03.03.00 r.1887 -
[X-CG] R(p) Tot o/o(of R) : 831398 2416792 100
[FFT-X] Mesh size: 27 27 20

[WF loader] Normalization (few states) min/max :0.524E-10 1.00

----------------------------------------------------------------------------------

Let me know if any suggestions or more information needed.

Thanks!

Yuan Ping
Materials Postdoc Fellow
Joint Center for Artificial Photosynthesis (JCAP)
Lawrence Berkeley National Laboratory &
California Institute of Technology

Dear Yuan,
as you argued, this kind of error is usually due to big size files, which are not supported by standard netcdf.
Possible solution are:
1) Compile the code enabling Large File Support, it should be --enable-netcdf-LFS option. I'm not sure, but in order to enable that it is needed the hdf5 support (type ./configure -h for instructions.
2) Easier solution, if you not have already tried, run yambo using (> yambo -S). With this (-S) option yambo will fragment the databases in pieces, so producing many files of reasonable size, so avoiding to handle a single huge database file.

Just a remark, for the input you posted it looks you are using a very ancient version of yambo, since then several bugs have been solved and various features have been added to the code.

Best,
Daniele