GW and BSE calculations with larger k-point mesh

Concerns issues with computing quasiparticle corrections to the DFT eigenvalues - i.e., the self-energy within the GW approximation (-g n), or considering the Hartree-Fock exchange only (-x)

Moderators: Davide Sangalli, andrea.ferretti, myrta gruning, andrea marini, Daniele Varsano

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nileshkumar
Posts: 3
Joined: Thu May 12, 2022 2:32 pm

GW and BSE calculations with larger k-point mesh

Post by nileshkumar » Thu May 04, 2023 3:29 pm

Hello YAMBO developers and users
I am trying to calculate GW quasiparticle energies and BSE spectra for a 2D material. I have the unit cell structure of 7 atoms. I am trying this calculation with a 24*24*1 k-points grid. When I run it with 8 CPUs on 1 node then it is working but I faced a time issue for the calculation. But when I increased the number of CPUs with higher nodes, then the calculation stopped (maybe memory issues). Please help me with how I can make a suitable parallelization of CPUs for this specific calculation.
Thank you
Nilesh Kumar
Ph.D. Scholar
University of Ostrava
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Daniele Varsano
Posts: 3975
Joined: Tue Mar 17, 2009 2:23 pm
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Re: GW and BSE calculations with larger k-point mesh

Post by Daniele Varsano » Sat May 06, 2023 9:29 am

Dear Nilesh,
If it is a memory issue, you can set a suitable parallelization strategy in the input file to distribute memory.
Can you post the input file together with submission script and error message of the problematic case?

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
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nileshkumar
Posts: 3
Joined: Thu May 12, 2022 2:32 pm

Re: GW and BSE calculations with larger k-point mesh

Post by nileshkumar » Sat May 06, 2023 11:30 am

Hello Mr. Daniele
I was trying to attach the file as attachments but it is not supporting. So I mentioned all the necessary details here,
1. Input file for GW calculation-

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#  __      __   ______   __       __  _______    ______               
# |  \    /  \ /      \ |  \     /  \|       \  /      \              
#  \$$\  /  $$|  $$$$$$\| $$\   /  $$| $$$$$$$\|  $$$$$$\             
#   \$$\/  $$ | $$__| $$| $$$\ /  $$$| $$__/ $$| $$  | $$             
#    \$$  $$  | $$    $$| $$$$\  $$$$| $$    $$| $$  | $$             
#     \$$$$   | $$$$$$$$| $$\$$ $$ $$| $$$$$$$\| $$  | $$             
#     | $$    | $$  | $$| $$ \$$$| $$| $$__/ $$| $$__/ $$             
#     | $$    | $$  | $$| $$  \$ | $$| $$    $$ \$$    $$             
#      \$$     \$$   \$$ \$$      \$$ \$$$$$$$   \$$$$$$              
#                                                                     
# Version 5.1.0 Revision 21422 Hash (prev commit) fde6e2a07           
#                        Branch is                                    
#               MPI+SLEPC+HDF5_MPI_IO Build                           
#                http://www.yambo-code.org                            
#
rim_cut                          # [R] Coulomb potential
HF_and_locXC                     # [R] Hartree-Fock
gw0                              # [R] GW approximation
ppa                              # [R][Xp] Plasmon Pole Approximation for the Screened Interaction
dyson                            # [R] Dyson Equation solver
em1d                             # [R][X] Dynamically Screened Interaction
StdoHash=  40                    # [IO] Live-timing Hashes
Nelectro= 56.00000               # Electrons number
ElecTemp= 0.000000         eV    # Electronic Temperature
BoseTemp=-1.000000         eV    # Bosonic Temperature
OccTresh= 0.100000E-4            # Occupation treshold (metallic bands)
NLogCPUs=0                       # [PARALLEL] Live-timing CPU`s (0 for all)
DBsIOoff= "none"                 # [IO] Space-separated list of DB with NO I/O. DB=(DIP,X,HF,COLLs,J,GF,CARRIERs,OBS,W,SC,BS,ALL)
DBsFRAGpm= "none"                # [IO] Space-separated list of +DB to FRAG and -DB to NOT FRAG. DB=(DIP,X,W,HF,COLLS,K,BS,QINDX,RT,ELP
FFTGvecs= 70            Ry    # [FFT] Plane-waves
#WFbuffIO                      # [IO] Wave-functions buffered I/O
PAR_def_mode= "balanced"         # [PARALLEL] Default distribution mode ("balanced"/"memory"/"workload")
X_and_IO_CPU= "1 1 16 4 4"                 # [PARALLEL] CPUs for each role
X_and_IO_ROLEs= "q g k c v"               # [PARALLEL] CPUs roles (q,g,k,c,v)
X_and_IO_nCPU_LinAlg_INV=-1      # [PARALLEL] CPUs for Linear Algebra (if -1 it is automatically set)
DIP_CPU= "16 4 4"                      # [PARALLEL] CPUs for each role
DIP_ROLEs= "k c v"                    # [PARALLEL] CPUs roles (k,c,v)
SE_CPU= "16 4 4"                       # [PARALLEL] CPUs for each role
SE_ROLEs= "q qp b"                     # [PARALLEL] CPUs roles (q,qp,b)
RandQpts=1000000                       # [RIM] Number of random q-points in the BZ
RandGvec= 100                RL    # [RIM] Coulomb interaction RS components
#QpgFull                       # [F RIM] Coulomb interaction: Full matrix
% Em1Anys
 0.000000 | 0.000000 | 0.000000 |        # [RIM] X Y Z Static Inverse dielectric matrix Anysotropy
%
IDEm1Ref=0                       # [RIM] Dielectric matrix reference component 1(x)/2(y)/3(z)
CUTGeo= "box z"                   # [CUT] Coulomb Cutoff geometry: box/cylinder/sphere/ws/slab X/Y/Z/XY..
% CUTBox
 0.000000 | 0.000000 | 41.53774 |        # [CUT] [au] Box sides
%
CUTRadius= 0.000000              # [CUT] [au] Sphere/Cylinder radius
CUTCylLen= 0.000000              # [CUT] [au] Cylinder length
CUTwsGvec= 0.700000              # [CUT] WS cutoff: number of G to be modified
#CUTCol_test                   # [CUT] Perform a cutoff test in R-space
EXXRLvcs= 70           Ry    # [XX] Exchange    RL components
VXCRLvcs= 70           Ry    # [XC] XCpotential RL components
#UseNLCC                       # [XC] If present, add NLCC contributions to the charge density
Chimod= "HARTREE"                # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
ChiLinAlgMod= "LIN_SYS"          # [X] inversion/lin_sys,cpu/gpu
XfnQPdb= "none"                  # [EXTQP Xd] Database action
XfnQP_INTERP_NN= 1               # [EXTQP Xd] Interpolation neighbours (NN mode)
XfnQP_INTERP_shells= 20.00000    # [EXTQP Xd] Interpolation shells (BOLTZ mode)
XfnQP_DbGd_INTERP_mode= "NN"     # [EXTQP Xd] Interpolation DbGd mode
% XfnQP_E
 0.000000 | 1.000000 | 1.000000 |        # [EXTQP Xd] E parameters  (c/v) eV|adim|adim
%
XfnQP_Z= ( 1.000000 , 0.000000 )         # [EXTQP Xd] Z factor  (c/v)
XfnQP_Wv_E= 0.000000       eV    # [EXTQP Xd] W Energy reference  (valence)
% XfnQP_Wv
 0.000000 | 0.000000 | 0.000000 |        # [EXTQP Xd] W parameters  (valence) eV| 1|eV^-1
%
XfnQP_Wv_dos= 0.000000     eV    # [EXTQP Xd] W dos pre-factor  (valence)
XfnQP_Wc_E= 0.000000       eV    # [EXTQP Xd] W Energy reference  (conduction)
% XfnQP_Wc
 0.000000 | 0.000000 | 0.000000 |        # [EXTQP Xd] W parameters  (conduction) eV| 1 |eV^-1
%
XfnQP_Wc_dos= 0.000000     eV    # [EXTQP Xd] W dos pre-factor  (conduction)
ShiftedPaths= ""                 # [DIP] Shifted grids paths (separated by a space)
% QpntsRXp
  1 | 61 |                           # [Xp] Transferred momenta
%
% BndsRnXp
    1 |  300 |                       # [Xp] Polarization function bands
%
NGsBlkXp= 14                Ry    # [Xp] Response block size
CGrdSpXp= 100.0000               # [Xp] [o/o] Coarse grid controller
% EhEngyXp
-1.000000 |-1.000000 |         eV    # [Xp] Electron-hole energy range
%
% LongDrXp
 1.000000 | 1.000000 | 0.000000 |        # [Xp] [cc] Electric Field
%
PPAPntXp= 27.21138         eV    # [Xp] PPA imaginary energy
XTermKind= "BG"                # [X] X terminator ("none","BG" Bruneval-Gonze)
XTermEn= 40.00000          eV    # [X] X terminator energy (only for kind="BG")
#OptDipAverage                 # [Xd] Average Xd along the non-zero Electric Field directions
#QPsymmtrz                     # [GW] Force symmetrization of states with the same energy
GfnQPdb= "none"                  # [EXTQP G] Database action
GfnQP_INTERP_NN= 1               # [EXTQP G] Interpolation neighbours (NN mode)
GfnQP_INTERP_shells= 20.00000    # [EXTQP G] Interpolation shells (BOLTZ mode)
GfnQP_DbGd_INTERP_mode= "NN"     # [EXTQP G] Interpolation DbGd mode
% GfnQP_E
 0.000000 | 1.000000 | 1.000000 |        # [EXTQP G] E parameters  (c/v) eV|adim|adim
%
GfnQP_Z= ( 1.000000 , 0.000000 )         # [EXTQP G] Z factor  (c/v)
GfnQP_Wv_E= 0.000000       eV    # [EXTQP G] W Energy reference  (valence)
% GfnQP_Wv
 0.000000 | 0.000000 | 0.000000 |        # [EXTQP G] W parameters  (valence) eV| 1|eV^-1
%
GfnQP_Wv_dos= 0.000000     eV    # [EXTQP G] W dos pre-factor  (valence)
GfnQP_Wc_E= 0.000000       eV    # [EXTQP G] W Energy reference  (conduction)
% GfnQP_Wc
 0.000000 | 0.000000 | 0.000000 |        # [EXTQP G] W parameters  (conduction) eV| 1 |eV^-1
%
GfnQP_Wc_dos= 0.000000     eV    # [EXTQP G] W dos pre-factor  (conduction)
BoseCut= 0.100000                # [BOSE] Finite T Bose function cutoff
% GbndRnge
    1 | 300 |                       # [GW] G[W] bands range
%
GDamping= 0.200000         eV    # [GW] G[W] damping
dScStep= 0.100000          eV    # [GW] Energy step to evaluate Z factors
GTermKind= "none"                # [GW] GW terminator ("none","BG" Bruneval-Gonze,"BRS" Berger-Reining-Sottile)
GTermEn= 40.81708          eV    # [GW] GW terminator energy (only for kind="BG")
DysSolver= "n"                   # [GW] Dyson Equation solver ("n","s","g")
GWoIter=0                        # [GW] GWo self-consistent (evGWo) iterations on eigenvalues
GWIter=0                         # [GW] GW  self-consistent (evGW)  iterations on eigenvalues
SCEtresh= 0.010000         eV    # [SC] Energy convergence threshold for SC-GW
#NewtDchk                      # [GW] Test dSc/dw convergence
ExtendOut                     # [GW] Print all variables in the output file
#OnMassShell                   # [F GW] On mass shell approximation
#QPExpand                      # [F GW] The QP corrections are expanded all over the BZ
%QPkrange                        # [GW] QP generalized Kpoint/Band indices
1|61|45|61|
%
%QPerange                        # [GW] QP generalized Kpoint/Energy indices
1|61| 0.000000|-1.000000|
%
2. the submit script is here-

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#!/bin/bash
#PBS -A OPEN-24-46
#PBS -N yambo
#PBS -q qlong
#PBS -l select=8:mpiprocs=36
#PBS -l walltime=144:00:00
#PBS -j oe

hostname
date

module load OpenMPI/4.0.3-GCC-9.3.0
cd $PBS_O_WORKDIR

#p2y
#yambo
#yambo -r -fatlog -x -p p -g n -V all -F gw.in
mpirun -np 256 yambo -F gw.in -J gw.out -C report
3. the output error file is here,

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cn48.barbora.it4i.cz
Sat May  6 12:10:16 CEST 2023
--------------------------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 215 with PID 1446841 on node cn98 exited on signal 9 (Killed).
--------------------------------------------------------------------------
6 total processes killed (some possibly by mpirun during cleanup)
cn99.barbora.it4i.cz: # PBS Epilogue Report
cn99.barbora.it4i.cz: # Issues found in kernel log
cn99.barbora.it4i.cz: [161946.381129] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn99.barbora.it4i.cz: [161947.798359] Out of memory: Killed process 801261 (yambo) total-vm:6301728kB, anon-rss:5435732kB, file-rss:0kB, shmem-rss:3896kB, UID:7916 pgtables:10856kB oom_score_adj:0
cn99.barbora.it4i.cz: [161948.536194] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn99.barbora.it4i.cz: [161949.944615] Out of memory: Killed process 801254 (yambo) total-vm:7314192kB, anon-rss:5641280kB, file-rss:0kB, shmem-rss:3988kB, UID:7916 pgtables:11268kB oom_score_adj:0
cn99.barbora.it4i.cz: [161950.551119] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn99.barbora.it4i.cz: [161951.968622] Out of memory: Killed process 801225 (yambo) total-vm:7314712kB, anon-rss:5808548kB, file-rss:0kB, shmem-rss:3472kB, UID:7916 pgtables:11588kB oom_score_adj:0
cn99.barbora.it4i.cz: [161952.621832] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn99.barbora.it4i.cz: [161954.044314] Out of memory: Killed process 801281 (yambo) total-vm:7312608kB, anon-rss:5957592kB, file-rss:0kB, shmem-rss:3460kB, UID:7916 pgtables:11876kB oom_score_adj:0
cn99.barbora.it4i.cz: [161954.740102] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn99.barbora.it4i.cz: [161956.127949] Out of memory: Killed process 801222 (yambo) total-vm:7314704kB, anon-rss:6140932kB, file-rss:0kB, shmem-rss:3628kB, UID:7916 pgtables:12248kB oom_score_adj:0
cn99.barbora.it4i.cz: [161959.373742] kthreadd invoked oom-killer: gfp_mask=0x6082c2(GFP_KERNEL|__GFP_HIGHMEM|__GFP_NOWARN|__GFP_ZERO), order=0, oom_score_adj=0
cn99.barbora.it4i.cz: [161960.706503] Out of memory: Killed process 801280 (yambo) total-vm:7313648kB, anon-rss:6381496kB, file-rss:0kB, shmem-rss:3444kB, UID:7916 pgtables:12704kB oom_score_adj:0
cn99.barbora.it4i.cz: [161961.504801] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn99.barbora.it4i.cz: [161962.901959] Out of memory: Killed process 801252 (yambo) total-vm:7313396kB, anon-rss:6653896kB, file-rss:0kB, shmem-rss:3880kB, UID:7916 pgtables:13240kB oom_score_adj:0
cn90.barbora.it4i.cz: # PBS Epilogue Report
cn90.barbora.it4i.cz: # Issues found in kernel log
cn90.barbora.it4i.cz: [1881636.919998] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn90.barbora.it4i.cz: [1881638.366127] Out of memory: Killed process 273064 (yambo) total-vm:7313124kB, anon-rss:5390044kB, file-rss:0kB, shmem-rss:3360kB, UID:7916 pgtables:10768kB oom_score_adj:0
cn90.barbora.it4i.cz: [1881639.722032] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn90.barbora.it4i.cz: [1881641.128085] Out of memory: Killed process 273054 (yambo) total-vm:7312340kB, anon-rss:5543400kB, file-rss:0kB, shmem-rss:3356kB, UID:7916 pgtables:11072kB oom_score_adj:0
cn90.barbora.it4i.cz: [1881641.969390] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn90.barbora.it4i.cz: [1881643.364261] Out of memory: Killed process 272990 (yambo) total-vm:6301988kB, anon-rss:5877584kB, file-rss:0kB, shmem-rss:3436kB, UID:7916 pgtables:11720kB oom_score_adj:0
cn90.barbora.it4i.cz: [1881644.732927] ibms_mad_agent invoked oom-killer: gfp_mask=0x6200ca(GFP_HIGHUSER_MOVABLE), order=0, oom_score_adj=0
cn90.barbora.it4i.cz: [1881646.141366] Out of memory: Killed process 273066 (yambo) total-vm:7312604kB, anon-rss:6022940kB, file-rss:0kB, shmem-rss:3368kB, UID:7916 pgtables:12008kB oom_score_adj:0
cn90.barbora.it4i.cz: [1881646.824997] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn90.barbora.it4i.cz: [1881648.228590] Out of memory: Killed process 272986 (yambo) total-vm:7316304kB, anon-rss:6060552kB, file-rss:0kB, shmem-rss:3660kB, UID:7916 pgtables:12080kB oom_score_adj:0
cn90.barbora.it4i.cz: [1881650.481638] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn90.barbora.it4i.cz: [1881651.855823] Out of memory: Killed process 272998 (yambo) total-vm:7314456kB, anon-rss:6269372kB, file-rss:0kB, shmem-rss:3528kB, UID:7916 pgtables:12492kB oom_score_adj:0
cn91.barbora.it4i.cz: # PBS Epilogue Report
cn91.barbora.it4i.cz: # Issues found in kernel log
cn91.barbora.it4i.cz: [697703.060750] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn91.barbora.it4i.cz: [697704.468088] Out of memory: Killed process 1800738 (yambo) total-vm:6299084kB, anon-rss:5339656kB, file-rss:0kB, shmem-rss:3212kB, UID:7916 pgtables:10660kB oom_score_adj:0
cn91.barbora.it4i.cz: [697706.057215] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn91.barbora.it4i.cz: [697707.458098] Out of memory: Killed process 1800727 (yambo) total-vm:7312364kB, anon-rss:5585304kB, file-rss:0kB, shmem-rss:3284kB, UID:7916 pgtables:11148kB oom_score_adj:0
cn91.barbora.it4i.cz: [697707.976593] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn91.barbora.it4i.cz: [697709.391896] Out of memory: Killed process 1800729 (yambo) total-vm:7312340kB, anon-rss:5724940kB, file-rss:0kB, shmem-rss:3264kB, UID:7916 pgtables:11428kB oom_score_adj:0
cn91.barbora.it4i.cz: [697710.103304] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn91.barbora.it4i.cz: [697711.486198] Out of memory: Killed process 1800736 (yambo) total-vm:6299756kB, anon-rss:5847800kB, file-rss:0kB, shmem-rss:3220kB, UID:7916 pgtables:11660kB oom_score_adj:0
cn91.barbora.it4i.cz: [697712.329209] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn91.barbora.it4i.cz: [697713.695857] Out of memory: Killed process 1800716 (yambo) total-vm:7314460kB, anon-rss:6058012kB, file-rss:0kB, shmem-rss:3296kB, UID:7916 pgtables:12084kB oom_score_adj:0
cn91.barbora.it4i.cz: [697714.453906] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn91.barbora.it4i.cz: [697715.810939] Out of memory: Killed process 1800709 (yambo) total-vm:7313124kB, anon-rss:6347164kB, file-rss:0kB, shmem-rss:3264kB, UID:7916 pgtables:12640kB oom_score_adj:0
cn91.barbora.it4i.cz: [697717.964331] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn91.barbora.it4i.cz: [697719.312565] Out of memory: Killed process 1800708 (yambo) total-vm:7314704kB, anon-rss:6691032kB, file-rss:0kB, shmem-rss:3292kB, UID:7916 pgtables:13316kB oom_score_adj:0
cn59.barbora.it4i.cz: # PBS Epilogue Report
cn59.barbora.it4i.cz: # Issues found in kernel log
cn59.barbora.it4i.cz: [1806539.905358] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn59.barbora.it4i.cz: [1806541.326459] Out of memory: Killed process 3941956 (yambo) total-vm:7314172kB, anon-rss:5355484kB, file-rss:0kB, shmem-rss:3312kB, UID:7916 pgtables:10704kB oom_score_adj:0
cn59.barbora.it4i.cz: [1806542.575819] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn59.barbora.it4i.cz: [1806543.995877] Out of memory: Killed process 3941991 (yambo) total-vm:6365076kB, anon-rss:5801600kB, file-rss:0kB, shmem-rss:2980kB, UID:7916 pgtables:11572kB oom_score_adj:0
cn59.barbora.it4i.cz: [1806549.355318] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn59.barbora.it4i.cz: [1806550.774951] Out of memory: Killed process 3941988 (yambo) total-vm:6300812kB, anon-rss:5690684kB, file-rss:0kB, shmem-rss:3476kB, UID:7916 pgtables:11352kB oom_score_adj:0
cn59.barbora.it4i.cz: [1806551.421019] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn59.barbora.it4i.cz: [1806552.840724] Out of memory: Killed process 3941970 (yambo) total-vm:7315496kB, anon-rss:5900704kB, file-rss:0kB, shmem-rss:3672kB, UID:7916 pgtables:11776kB oom_score_adj:0
cn59.barbora.it4i.cz: [1806556.461055] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn59.barbora.it4i.cz: [1806557.871159] Out of memory: Killed process 3942012 (yambo) total-vm:7310516kB, anon-rss:6088080kB, file-rss:0kB, shmem-rss:2988kB, UID:7916 pgtables:12132kB oom_score_adj:0
cn59.barbora.it4i.cz: [1806559.194579] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn59.barbora.it4i.cz: [1806560.593263] Out of memory: Killed process 3941978 (yambo) total-vm:7315244kB, anon-rss:6369896kB, file-rss:0kB, shmem-rss:3604kB, UID:7916 pgtables:12688kB oom_score_adj:0
cn59.barbora.it4i.cz: System error
cn98.barbora.it4i.cz: # PBS Epilogue Report
cn98.barbora.it4i.cz: # Issues found in kernel log
cn98.barbora.it4i.cz: [351522.539098] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn98.barbora.it4i.cz: [351523.947279] Out of memory: Killed process 1446841 (yambo) total-vm:7311020kB, anon-rss:5431760kB, file-rss:0kB, shmem-rss:2856kB, UID:7916 pgtables:10840kB oom_score_adj:0
cn98.barbora.it4i.cz: [351524.530026] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn98.barbora.it4i.cz: [351525.938131] Out of memory: Killed process 1446761 (yambo) total-vm:7313908kB, anon-rss:5584324kB, file-rss:0kB, shmem-rss:3500kB, UID:7916 pgtables:11144kB oom_score_adj:0
cn98.barbora.it4i.cz: [351526.898038] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn98.barbora.it4i.cz: [351528.298460] Out of memory: Killed process 1446771 (yambo) total-vm:7314448kB, anon-rss:5750620kB, file-rss:0kB, shmem-rss:3500kB, UID:7916 pgtables:11480kB oom_score_adj:0
cn98.barbora.it4i.cz: [351529.953387] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn98.barbora.it4i.cz: [351531.358892] Out of memory: Killed process 1446764 (yambo) total-vm:7314712kB, anon-rss:5910536kB, file-rss:0kB, shmem-rss:3516kB, UID:7916 pgtables:11788kB oom_score_adj:0
cn98.barbora.it4i.cz: [351532.819466] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn98.barbora.it4i.cz: [351534.215452] Out of memory: Killed process 1446772 (yambo) total-vm:7316024kB, anon-rss:6125908kB, file-rss:0kB, shmem-rss:3548kB, UID:7916 pgtables:12216kB oom_score_adj:0
cn98.barbora.it4i.cz: [351535.490184] mad/handler invoked oom-killer: gfp_mask=0x6200ca(GFP_HIGHUSER_MOVABLE), order=0, oom_score_adj=0
cn98.barbora.it4i.cz: [351536.906057] Out of memory: Killed process 1446803 (yambo) total-vm:7314188kB, anon-rss:6393212kB, file-rss:0kB, shmem-rss:3912kB, UID:7916 pgtables:12736kB oom_score_adj:0
cn98.barbora.it4i.cz: [351541.191143] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn98.barbora.it4i.cz: [351542.553790] Out of memory: Killed process 1446825 (yambo) total-vm:7313400kB, anon-rss:6703660kB, file-rss:0kB, shmem-rss:3452kB, UID:7916 pgtables:13332kB oom_score_adj:0
cn60.barbora.it4i.cz: # PBS Epilogue Report
cn60.barbora.it4i.cz: # Issues found in kernel log
cn60.barbora.it4i.cz: [1755733.475081] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn60.barbora.it4i.cz: [1755734.899513] Out of memory: Killed process 351207 (yambo) total-vm:6302784kB, anon-rss:5329924kB, file-rss:0kB, shmem-rss:3456kB, UID:7916 pgtables:10648kB oom_score_adj:0
cn60.barbora.it4i.cz: [1755735.412500] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn60.barbora.it4i.cz: [1755736.820157] Out of memory: Killed process 351197 (yambo) total-vm:7315760kB, anon-rss:5501428kB, file-rss:0kB, shmem-rss:3956kB, UID:7916 pgtables:10992kB oom_score_adj:0
cn60.barbora.it4i.cz: [1755737.898513] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn60.barbora.it4i.cz: [1755739.329351] Out of memory: Killed process 351235 (yambo) total-vm:7312616kB, anon-rss:5673540kB, file-rss:0kB, shmem-rss:3336kB, UID:7916 pgtables:11316kB oom_score_adj:0
cn60.barbora.it4i.cz: [1755740.376220] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn60.barbora.it4i.cz: [1755741.798103] Out of memory: Killed process 351200 (yambo) total-vm:7314704kB, anon-rss:5808332kB, file-rss:0kB, shmem-rss:3692kB, UID:7916 pgtables:11592kB oom_score_adj:0
cn60.barbora.it4i.cz: [1755742.952718] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn60.barbora.it4i.cz: [1755744.358852] Out of memory: Killed process 351204 (yambo) total-vm:6301728kB, anon-rss:5991416kB, file-rss:0kB, shmem-rss:3472kB, UID:7916 pgtables:11932kB oom_score_adj:0
cn60.barbora.it4i.cz: [1755747.062628] yambo invoked oom-killer: gfp_mask=0x6200ca(GFP_HIGHUSER_MOVABLE), order=0, oom_score_adj=0
cn60.barbora.it4i.cz: [1755748.488439] Out of memory: Killed process 351215 (yambo) total-vm:7315492kB, anon-rss:6207780kB, file-rss:0kB, shmem-rss:3856kB, UID:7916 pgtables:12368kB oom_score_adj:0
cn60.barbora.it4i.cz: [1755749.679994] mad/handler invoked oom-killer: gfp_mask=0x6200ca(GFP_HIGHUSER_MOVABLE), order=0, oom_score_adj=0
cn60.barbora.it4i.cz: [1755751.102421] Out of memory: Killed process 351223 (yambo) total-vm:7312612kB, anon-rss:6494304kB, file-rss:0kB, shmem-rss:3224kB, UID:7916 pgtables:12932kB oom_score_adj:0
cn60.barbora.it4i.cz: [1755752.399894] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn60.barbora.it4i.cz: [1755753.801679] Out of memory: Killed process 351211 (yambo) total-vm:7315504kB, anon-rss:6784816kB, file-rss:0kB, shmem-rss:3532kB, UID:7916 pgtables:13504kB oom_score_adj:0
cn48.barbora.it4i.cz: # PBS Epilogue Report
cn48.barbora.it4i.cz: # Issues found in kernel log
cn48.barbora.it4i.cz: [1900015.497187] yambo invoked oom-killer: gfp_mask=0x7080c0(GFP_KERNEL_ACCOUNT|__GFP_ZERO), order=0, oom_score_adj=0
cn48.barbora.it4i.cz: [1900016.951951] Out of memory: Killed process 601689 (yambo) total-vm:7313936kB, anon-rss:5321700kB, file-rss:0kB, shmem-rss:3688kB, UID:7916 pgtables:10632kB oom_score_adj:0
cn48.barbora.it4i.cz: [1900018.663468] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn48.barbora.it4i.cz: [1900020.100254] Out of memory: Killed process 601707 (yambo) total-vm:7314700kB, anon-rss:5701004kB, file-rss:0kB, shmem-rss:3628kB, UID:7916 pgtables:11384kB oom_score_adj:0
cn48.barbora.it4i.cz: [1900020.883627] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn48.barbora.it4i.cz: [1900022.330629] Out of memory: Killed process 601699 (yambo) total-vm:7314448kB, anon-rss:5840600kB, file-rss:0kB, shmem-rss:3652kB, UID:7916 pgtables:11664kB oom_score_adj:0
cn48.barbora.it4i.cz: [1900022.928544] yambo invoked oom-killer: gfp_mask=0x6280ca(GFP_HIGHUSER_MOVABLE|__GFP_ZERO), order=0, oom_score_adj=0
cn48.barbora.it4i.cz: [1900024.375939] Out of memory: Killed process 601693 (yambo) total-vm:6301876kB, anon-rss:6002104kB, file-rss:0kB, shmem-rss:3804kB, UID:7916 pgtables:11964kB oom_score_adj:0
4. the log file is here-

Code: Select all

_|      _|   _|_|   _|      _|  _|_|_|     _|_|
  _|  _|   _|    _| _|_|  _|_| _|    _| _|    _|
    _|     _|_|_|_| _|  _|  _| _|_|_|   _|    _|
    _|     _|    _| _|      _| _|    _| _|    _|
    _|     _|    _| _|      _| _|_|_|     _|_|

 <---> P1: [01] MPI/OPENMP structure, Files & I/O Directories
 <---> P1-cn48.barbora.it4i.cz: MPI Cores-Threads   : 256(CPU)-1(threads)-1(threads@X)-1(threads@DIP)-1(threads@SE)-1(threads@RT)-1(threads@K)-1(threads@NL)
 <---> P1-cn48.barbora.it4i.cz: MPI Cores-Threads   : DIP(environment)-16 4 4(CPUs)-k c v(ROLEs)
 <---> P1-cn48.barbora.it4i.cz: MPI Cores-Threads   : X_and_IO(environment)-1 1 16 4 4(CPUs)-q g k c v(ROLEs)
 <---> P1-cn48.barbora.it4i.cz: MPI Cores-Threads   : SE(environment)-16 4 4(CPUs)-q qp b(ROLEs)
 <---> P1-cn48.barbora.it4i.cz: [02] CORE Variables Setup
 <---> P1-cn48.barbora.it4i.cz: [02.01] Unit cells
 <---> P1-cn48.barbora.it4i.cz: [02.02] Symmetries
 <---> P1-cn48.barbora.it4i.cz: [02.03] Reciprocal space
 <---> P1-cn48.barbora.it4i.cz: [02.04] K-grid lattice
 <---> P1-cn48.barbora.it4i.cz: Grid dimensions      :  24  24
 <---> P1-cn48.barbora.it4i.cz: [02.05] Energies & Occupations
 <---> P1-cn48.barbora.it4i.cz: [03] Transferred momenta grid and indexing
 <---> P1-cn48.barbora.it4i.cz: [04] Coloumb potential Random Integration (RIM)
 <---> P1-cn48.barbora.it4i.cz: [04.01] RIM initialization
 <---> P1-cn48.barbora.it4i.cz: Random points |                                        | [000%] --(E) --(X)
 <---> P1-cn48.barbora.it4i.cz: Random points |########################################| [100%] --(E) --(X)
 <02s> P1-cn48.barbora.it4i.cz: [04.02] RIM integrals
 <02s> P1-cn48.barbora.it4i.cz: Momenta loop |                                        | [000%] --(E) --(X)
 <04s> P1-cn48.barbora.it4i.cz: Momenta loop |########################################| [100%] 02s(E) 02s(X)
 <04s> P1-cn48.barbora.it4i.cz: [05] Coloumb potential CutOffbox
 <04s> P1-cn48.barbora.it4i.cz: Box |                                        | [000%] --(E) --(X)
 <06s> P1-cn48.barbora.it4i.cz: Box |########################################| [100%] --(E) --(X)
 <06s> P1-cn48.barbora.it4i.cz: [06] Dipoles
 <06s> P1-cn48.barbora.it4i.cz: [PARALLEL DIPOLES for K(ibz) on 16 CPU] Loaded/Total (Percentual):4/61(7%)
 <06s> P1-cn48.barbora.it4i.cz: [PARALLEL DIPOLES for CON bands on 4 CPU] Loaded/Total (Percentual):75/300(25%)
 <06s> P1-cn48.barbora.it4i.cz: [PARALLEL DIPOLES for VAL bands on 4 CPU] Loaded/Total (Percentual):14/56(25%)
 <06s> P1-cn48.barbora.it4i.cz: [DIP] Checking dipoles header
 <06s> P1-cn48.barbora.it4i.cz: [DIP] Database not correct or missing. To be computed
 <06s> P1-cn48.barbora.it4i.cz: [x,Vnl] computed using 262 projectors
 <06s> P1-cn48.barbora.it4i.cz: [WARNING] [x,Vnl] slows the Dipoles computation. To neglect it rename the ns.kb_pp file
 <07s> P1-cn48.barbora.it4i.cz: Dipoles: P, V and iR (T) |                                        | [000%] --(E) --(X)
 <07s> P1-cn48.barbora.it4i.cz: [PARALLEL distribution for Wave-Function states] Loaded/Total(Percentual):75/300(25%)
 <18s> P1-cn48.barbora.it4i.cz: Dipoles: P, V and iR (T) |#                                       | [002%] 11s(E) 07m-47s(X)
 <32s> P1-cn48.barbora.it4i.cz: Dipoles: P, V and iR (T) |##########                              | [025%] 25s(E) 01m-39s(X)
 <45s> P1-cn48.barbora.it4i.cz: Dipoles: P, V and iR (T) |####################                    | [050%] 38s(E) 01m-17s(X)
 <58s> P1-cn48.barbora.it4i.cz: Dipoles: P, V and iR (T) |##############################          | [075%] 51s(E) 01m-09s(X)
 <01m-00s> P1-cn48.barbora.it4i.cz: Dipoles: P, V and iR (T) |########################################| [100%] 53s(E) 53s(X)
 <01m-08s> P1-cn48.barbora.it4i.cz: [DIP] Writing dipoles header
 <01m-09s> P1-cn48.barbora.it4i.cz: [07] Dynamic Dielectric Matrix (PPA)
 <01m-16s> P1-cn48.barbora.it4i.cz: [WARNING] Response block size reduced to 1299    RL (7124    mHa)
 <01m-16s> P1-cn48.barbora.it4i.cz: [PARALLEL Response_G_space_and_IO for K(bz) on 16 CPU] Loaded/Total (Percentual):36/576(6%)
 <01m-16s> P1-cn48.barbora.it4i.cz: [PARALLEL Response_G_space_and_IO for Q(ibz) on 1 CPU] Loaded/Total (Percentual):61/61(100%)
 <01m-16s> P1-cn48.barbora.it4i.cz: [PARALLEL Response_G_space_and_IO for K-q(ibz) on 1 CPU] Loaded/Total (Percentual):61/61(100%)
 <01m-16s> P1-cn48.barbora.it4i.cz: [LA] SERIAL linear algebra
 <01m-16s> P1-cn48.barbora.it4i.cz: [PARALLEL Response_G_space_and_IO for K(ibz) on 1 CPU] Loaded/Total (Percentual):61/61(100%)
 <01m-16s> P1-cn48.barbora.it4i.cz: [PARALLEL Response_G_space_and_IO for CON bands on 4 CPU] Loaded/Total (Percentual):75/300(25%)
 <01m-16s> P1-cn48.barbora.it4i.cz: [PARALLEL Response_G_space_and_IO for VAL bands on 4 CPU] Loaded/Total (Percentual):14/56(25%)
 <01m-16s> P1-cn48.barbora.it4i.cz: [PARALLEL distribution for RL vectors(X) on 1 CPU] Loaded/Total (Percentual):1687401/1687401(100%)
 <01m-17s> P1-cn48.barbora.it4i.cz: [DIP] Checking dipoles header
The calculation stopped at this line " [DIP] Checking dipoles header".
Please let me know what can I do solve this issue?
Nilesh Kumar
Ph.D. Scholar
University of Ostrava
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User avatar
Daniele Varsano
Posts: 3975
Joined: Tue Mar 17, 2009 2:23 pm
Contact:
Contact Daniele Varsano

Re: GW and BSE calculations with larger k-point mesh

Post by Daniele Varsano » Mon May 08, 2023 8:37 am

Dear Nilesh,

this is not really comfortable to read, you can share files renaming them with a supported suffix as e.g. file.txt
Anyway, a good parallelization strategy to share memory among cpu, considering you are using 288 CPUs:

Code: Select all

X_and_IO_CPU= "1 1 1 36 8" # [PARALLEL] CPUs for each role
X_and_IO_ROLEs= "q g k c v" 

SE_CPU= "1 8 36" # [PARALLEL] CPUs for each role
SE_ROLEs= "q qp b" # [PARALLEL] CPUs roles (q,qp,b)
Furthermore, I strongly advise you to set:

Code: Select all

XTermKind= "none" # [X] X terminator ("none","BG" Bruneval-Gonze)

as this is very memory intensive and not particularly efficient.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
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Harshita
Posts: 11
Joined: Thu May 25, 2023 12:02 pm

Re: GW and BSE calculations with larger k-point mesh

Post by Harshita » Sun Apr 28, 2024 2:53 pm

Dear Team,

I am also facing similar problem while interpolating band structures, which is supposedly arising from virtual memory issue. I tried using more nodes and less cores, so as to use higher memory, but all in vain.

The calculation was stopping every time at
<14s> P1: [05.01] G0W0 on the real axis
<14s> P1: Self_Energy parallel ENVIRONMENT is incomplete. Switching to defaults
<14s> P1: [PARALLEL Self_Energy for QPs on 3 CPU] Loaded/Total (Percentual):10260/30780(33%)
<14s> P1: [PARALLEL Self_Energy for Q(ibz) on 1 CPU] Loaded/Total (Percentual):81/81(100%)
<14s> P1: [PARALLEL Self_Energy for G bands on 2 CPU] Loaded/Total (Percentual):190/380(50%)
<15s> P1: [PARALLEL distribution for Wave-Function states] Loaded/Total(Percentual):20520/30780(67%)

It was creating the error file "yambo.80s-56187,node9.btr" which shows:

yambo:55185 terminated with signal 11 at PC=4af805 SP=7ffd064bf6c0. Backtrace: /apps/scratch/compile/yambo-5.1/yambo-5.1.1/bin/yambo[0x4af805] /apps/scratch/compile/yambo-5.1/yambo-5.1.1/bin/yambo[0x497eeb] /apps/scratch/compile/yambo-5.1/yambo-5.1.1/bin/yambo[0x493469] /apps/scratch/compile/yambo-5.1/yambo-5.1.1/bin/yambo[0x40bc25] /apps/scratch/compile/yambo-5.1/yambo-5.1.1/bin/yambo[0x73f525] /apps/scratch/compile/yambo-5.1/yambo-5.1.1/bin/yambo[0x406875] /usr/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b59338823d5] /apps/scratch/compile/yambo-5.1/yambo-5.1.1/bin/yambo[0x4066a9]

After seeing this forum, I tried using:

X_and_IO_CPU= "1 1 1 48 4"
X_and_IO_ROLEs= "q g k c v"

SE_CPU= "1 4 48" # [PARALLEL] CPUs for each role
SE_ROLEs= "q qp b" # [PARALLEL] CPUs roles (q,qp,b)

Now, the "yambo.80s-56187,node9.btr" files are not created, still the calculation is stopping at the same place.

Any help would be highly appreciated.

Thanks and regards,
Harshita
Harshita, Research Scholar, INST
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Daniele Varsano
Posts: 3975
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Re: GW and BSE calculations with larger k-point mesh

Post by Daniele Varsano » Fri May 03, 2024 8:50 am

Dear Harshita,

to distribute memory the best parallelization strategy is to assign all the tasks in the b channel:

Code: Select all

SE_CPU= "1 1 ncpu" # [PARALLEL] CPUs for each role
SE_ROLEs= "q qp b" # [PARALLEL] CPUs roles (q,qp,b)
Please note that from the log you posted it seems you are using 6 mpi task, instead in the input file you are assigning 192 tasks.
The input variable should be consistent with the used resource otherwise Yambo switch to its default distribution, and it can be not the most efficient in terms of memory distribution.

BTW, how many QP particle are you calculating (%QPkrange) ?

If the problem persists, you can try to recompile Yambo using the flag --enable-memory-profile:
./configure --enable-memory-profile --other options

in this way, you can track the memory and see how much resource you would need.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
Top
Harshita
Posts: 11
Joined: Thu May 25, 2023 12:02 pm

Re: GW and BSE calculations with larger k-point mesh

Post by Harshita » Fri May 03, 2024 3:13 pm

Dear Daniele,

Thanks for your response. I have corrected the mpi tasks in accordance to the input file, still the error persists.

Below is my input file:


HF_and_locXC # [R] Hartree-Fock
gw0 # [R] GW approximation
dyson # [R] Dyson Equation solver
EXXRLvcs= 165 RL # [XX] Exchange RL components
VXCRLvcs= 165 RL # [XC] XCpotential RL components
% GbndRnge
0 | 380 | # [GW] G[W] bands range
%
% BndsRnXd
0 | 380 | # [Xd] Polarization function bands
%
NGsBlkXd= 4 Ry # [Xd] Response block size
% DmRngeXd
0.050000 | 0.050000 | eV # [Xd] Damping range
%
ETStpsXd= 800 # [Xd] Total Energy steps
EMStpsXd= 100.0000 # [Xd] [o/o] Memory Energy steps
DrudeWXd= ( 0.000000 , 0.000000 ) eV # [Xd] Drude plasmon
% LongDrXd
1.000000 | 0.000000 | 0.000000 | # [Xd] [cc] Electric Field
%
GTermKind= "none" # [GW] GW terminator ("none","BG" Bruneval-Gonze,"BRS" Berger-Reining-Sottile)
DysSolver= "n" # [GW] Dyson Equation solver ("n","s","g")
%QPkrange # [GW] QP generalized Kpoint/Band indices
1|1|175|200|
%

X_and_IO_CPU= "1 1 1 16 1"
X_and_IO_ROLEs= "q g k c v"

SE_CPU= "1 1 16" # [PARALLEL] CPUs for each role
SE_ROLEs= "q qp b" # [PARALLEL] CPUs roles (q,qp,b)


And the script:

mpirun -ppn 4 -hostfile $PBS_NODEFILE -np 16 /apps/scratch/compile/yambo-5.1/yambo-5.1.1/bin/yambo -F gw_ppa_all_Bz.in -J all_Bz



Just to mention, the system is metallic and I haven't added the Drude term, I hope that isn't causing the calculation to run.

Thanks and regards,
Harshita
Harshita, Research Scholar, INST
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Daniele Varsano
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Re: GW and BSE calculations with larger k-point mesh

Post by Daniele Varsano » Mon May 06, 2024 9:04 am

Dear Harhista,

the Drude term is harmless, and it is not the source of the problem.
Some comments on your input file:
1) It seems that you are doing a full-frequency calculation (real axis), this is computationally very intensive, are you sure that you cannot opt for the plasmon-pole approximation that it is somehow the standard for a gw calculation? This input file is generated using yambo -gw0 p
2) Bands range: the number of bands should start from 1 and not from zero.
3) You can attach in the forum (by rename it with e.g. *.txt) the report and log file, this can help to spot the problem.
4) In order to spot if it is a memory problem, you can lower the QPkrange calculating, for instance just for a couple of bands. Note that it is possible to split the calculation in many runs with different number of bands and then merge the calculated databases.
5) Not related with your problem, EXXRLvcs and VXCRLvcs have a very low value and are most probably not at convergence.
6) You can update the code to the latest version and eventually to compile it with the --enable-memory-profile option.

Best,
Daniele
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
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