Yambo Community Forum

Dear all,

After a initialization, I performed a runlevel of "yambo -c -g -n -p p":
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rim_cut # [R RIM CUT] Coulomb interaction
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
RandQpts=1000000 # [RIM] Number of random q-points in the BZ
RandGvec=1 RL # [RIM] Coulomb interaction RS components
CUTGeo= "box z" # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere
% CUTBox
0.000 | 0.000 | 25.056 | # [CUT] [au] Box sides
%
CUTRadius= 0.000000 # [CUT] [au] Sphere/Cylinder radius
CUTCylLen= 0.000000 # [CUT] [au] Cylinder length
EXXRLvcs= 13787 RL # [XX] Exchange RL components
% QpntsRXp
1 | 91 | # [Xp] Transferred momenta
%
% BndsRnXp
1 | 300 | # [Xp] Polarization function bands
%
NGsBlkXp= 400 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 | 300 | # [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| 91| 12|22|
%
%QPerange # [GW] QP generalized Kpoint/Energy indices
1| 91| 0.0|-1.0|
%
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In the log file "l_HF_and_locXC_em1d_ppa_gw0_rim_cut", it printed:

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<---> [01] Files & I/O Directories
<---> [02] CORE Variables Setup
<---> [02.01] Unit cells
<---> [02.02] Symmetries
<---> [02.03] RL shells
<---> [02.04] K-grid lattice
<---> [02.05] Energies [ev] & Occupations
<---> [03] Transferred momenta grid
<---> [04] Coloumb potential Random Integration (RIM)
<---> [04.01] RIM initialization
<---> Random points | | [000%] --(E) --(X)
<03s> Random points |####################| [100%] 03s(E) 03s(X)
<03s> [04.02] RIM integrals
<03s> Momenta loop | | [000%] --(E) --(X)
<04s> P01: Momenta loop |####################| [100%] --(E) --(X)
<04s> [05] Coloumb potential CutOff :box
<04s> Box | | [000%] --(E) --(X)
<09s> P01: Box |############## | [073%] 05s(E) 06s(X)
<11s> P01: Box |####################| [100%] 06s(E) 06s(X)
<12s> [06] Bare local and non-local Exchange-Correlation
<13s> [M 1.638 Gb] Alloc WF (1.611)
<16s> [FFT-HF/Rho] Mesh size: 27 27 69
<16s> [WF-HF/Rho loader] Wfs (re)loading | | [000%] --(E) --(X)
<22s> [WF-HF/Rho loader] Wfs (re)loading |# | [009%] 05s(E) 54s(X)
<27s> [WF-HF/Rho loader] Wfs (re)loading |### | [019%] 10s(E) 52s(X)
<32s> [WF-HF/Rho loader] Wfs (re)loading |##### | [029%] 15s(E) 52s(X)

<37s> [WF-HF/Rho loader] Wfs (re)loading |####### | [039%] 20s(E) 52s(X)
[ERROR] STOP signal received while in :[06] Bare local and non-local Exchange-Correlation
[ERROR][NetCDF] NetCDF: Variable not found
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So, could you please tell me what happened to my calculation?

Thank you very much!

Dear Wei

from the info you gave I cannot understand what is the problem with your calculation.

I ran a job similar to yours without any problem.

Please try to give us all the info and inputs needed to eventually reproduce your problem also including the revision you are using, compiler, machine etc.

Before that please check for all the obvious things (e.g. if you change the value of some variables, check they are compatible with the original DFT calculation etc.
Also try to change the parameters to make e.g. your job smaller to see if the problem persist.

Best,
m

Dear Myrta,

Thank you for your reply!
I have found that if I use p2y -S -N to generate databse file SAVE the error will not appear, but p2y -N it appears.

Nice that you found a solution and it is working.

myrta gruning wrote:I have found that if I use p2y -S -N to generate databse file SAVE the error will not appear, but p2y -N it appears.

That means that you were working with quite large databases with too many variables for netcdf to handle them. -S is fragmenting the databases and avoiding the problem.

Best,
m

Dear Myrta,
Thank you very much!

Dear All,

[ERROR] STOP signal received while in :[06] Bare local and non-local Exchange-Correlation
[ERROR]Allocation of WF%c failed

I have encountered the same problem. But I think p2y -S -N variables are no longer supported by YAMBO (v4.5.2) at least by p2y -H.
So, how to solve this problem? Is p2y -U will help? Input file attached (sorry for the very long input file, yambo part is from step-10). Error occurs after step-13

with many thanks and best regards
Soumyadeep

Dear Soumyadeep,
at first sight it seems a memory issue.

You are actually calculating a very large number of QP corrections (more than a thousand!).
First, are you really interested in calculating corrections for deep states? (bands starting from 1). Usually one is interested in GW bands correction across the gap. Next you can try to split your calculations in different step, i.e. many runs containing fewer corrections in %QPkrange

At the end you can merge the results using ypp. In order to do that you have to pay attention to not overwrite the ndb.QP databases, so you need to
put in different directories or rename them.

I do not know how many CPU you are using, anyway defining a parallel strategy in input parallelising over bands (b) in SE_CPU helps in distributing memory e.g.
Best,
Daniele