[QE-users] DFT+U+V neighbour allocation extremely slow and not parallelized

[julien_barbaud at sjtu.edu.cn]

Dear QE users,

 

I am currently trying to run calculations on a 324-atom crystal system using
DFT+U+V (I'm running a recompiled version of QE 7.2 with an increased natx
parameter). More specifically, I am trying to use only the V parameter on
the combination of two specific atomic orbitals which are supposed to form a
polaronic dimer (the Hubbard potential is helping to localize the polaronic
charge on the dimer after tuning). This worked well on smaller systems.

The issue that I'm facing with the large system is that the calculation is
taking very long to initiate (~20 000 seconds), while the iterations
themselves are relatively fast (~3000 seconds).This seems strange that the
preliminary calculations take so much longer than the actual iterations. On
smaller systems (96 atoms), I was not observing that trend, the bottleneck
was the iterations as expected and there was barely any initialization time.

The most concerning aspect is that this bottleneck does not seem to be
effectively distributed in parallel, because no matter how many nodes I use,
the pre-iteration calculations always seem to take about 20 000 seconds
(meanwhile, the iteration time does decrease when using more nodes)

The routine taking up all that time is the Hubbard routine "alloc_neigh". I
thought it might have been due to some memory issues, but looking at the
memory usage of the nodes during the job, it seems to have only used about
30% of memory according to slurm "seff" utility. I have also experimented
with different IO settings to try to reduce memory usage without success.

 

Is there a way to speed up that part of the calculation, or at least to
distribute it over several nodes? Am I doing something wrong in my input? 

Additionally, it seems that the program is calculating Hubbard projectors
for every single atom of the species, even though I am only applying a V
parameter on two hand-picked atoms, which seems very wasteful indeed. Is
there a way to force the program to drop the Hubbard calculations on the
atoms of the same species which do not receive a V value?

 

I have attached the input and output file of an example job (charge has been
set to 0 in that particular one, but same problem happens when adding the
polaronic charge)

 

Thanks in advance!

Julien

 

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20250505/91615f19/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: large_q0.in
Type: application/octet-stream
Size: 24482 bytes
Desc: not available
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20250505/91615f19/attachment.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: large_q0.44033235.out
Type: application/octet-stream
Size: 424197 bytes
Desc: not available
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20250505/91615f19/attachment-0001.obj>