Running optical spectrum on parallel
Posted: Wed Mar 30, 2022 3:29 am
Hi all,
I am following the steps in this tutorial http://www.yambo-code.org/wiki/index.ph ... parameters for the optical absorption.
I'm using 8 cpus but based on r_screen_dipoles_em1s file it say 1 for cores, threads, nodes, ... etc so why it does not show that I'm running it on 8 cpus?
Also how to check the progress of my job, I see nothing in the log, err, out files I included in the submit_job.
thank you in advance!
I am following the steps in this tutorial http://www.yambo-code.org/wiki/index.ph ... parameters for the optical absorption.
I'm using 8 cpus but based on r_screen_dipoles_em1s file it say 1 for cores, threads, nodes, ... etc so why it does not show that I'm running it on 8 cpus?
Also how to check the progress of my job, I see nothing in the log, err, out files I included in the submit_job.
thank you in advance!
Code: Select all
ooooo oooo .. ooo ooo ooooooooo. .oooo.
`88. .8" .88. `88. .88 `88" `Y8b dP" `Yb
`88. .8" .8"88. 888b d"88 88 888 88 88
`88.8" .8" `88. 8 Y88. .P 88 88oooo888" 88 88
`88" .88ooo888. 8 `888" 88 88 `88b 88 88
88 .8" `88. 8 Y 88 88 .88P `8b d8"
o88o88o 888o8 88 o88bood8P" `Ybod8P"
Version 5.0.4 Revision 19595 Hash 896bffc02
Branch is
MPI+HDF5_IO Build
http://www.yambo-code.org
03/29/2022 at 13:04 yambo @ submit-1.chtc.wisc.edu
==================================================
Cores : 1
Threads per core : 1
Threads total : 1
Nodes Computing : 1
Nodes IO : 1
Fragmented WFs : yes
CORE databases : .
Additional I/O : .
Communications : .
Input file : 02_screening.in
Report file : ./r_screen_dipoles_em1s
Verbose log/report : no
Precision : SINGLE
[RD./SAVE//ns.db1]--------------------------------------------------------------
Bands : 40
K-points : 286
G-vectors : 21559 [RL space]
Components : 2730 [wavefunctions]
Symmetries : 48 [spatial]
Spinor components : 1
Spin polarizations : 1
Temperature : 0.000000 [eV]
Electrons : 44.00000
WF G-vectors : 3431
Max atoms/species : 3
No. of atom species : 3
Exact exchange fraction in XC : 0.000000
Exact exchange screening in XC : 0.000000
Magnetic symmetries : no
- S/N 009369 ---------------------------------------------- v.05.00.04 r.19595 -
[02] CORE Variables Setup
=========================
[02.04] K-grid lattice
======================
Compatible Grid is : 3D
Base K vectors : K_min[ 1 ] K_min[ 2 ] K_min[ 3 ]
K_min[ 1 ] : 0.000000 0.050000 0.000000 [rlu]
K_min[ 2 ] : 0.050000 0.000000 0.000000 [rlu]
K_min[ 3 ] : 0.000000 0.000000 -0.050000 [rlu]
Grid dimensions : 20 20 20
K lattice UC volume : 0.689179E-4 [a.u.]
[02.05] Energies & Occupations
==============================
[X] === General ===
[X] Electronic Temperature : 0.000000 0.000000 [eV K]
[X] Bosonic Temperature : 0.000000 0.000000 [eV K]
[X] Finite Temperature mode : no
[X] El. density : 0.65998E+24 [cm-3]
[X] Fermi Level : 4.528345 [eV]
[X] === Gaps and Widths ===
[X] Conduction Band Min : 1.534023 [eV]
[X] Valence Band Max : 0.000000 [eV]
[X] Filled Bands : 22
[X] Empty Bands : 23 40
[X] Direct Gap : 2.253872 [eV]
[X] Direct Gap localized at k-point : 1
[X] Indirect Gap : 1.534023 [eV]
[X] Indirect Gap between k-points : 286 1
[X] Last valence band width : 0.719849 [eV]
[X] 1st conduction band width : 3.714666 [eV]Code: Select all
## Submit file options for running your program
executable =run_script
log = 02_screening.log
output = 02_screening.out
error = 02_screening.err
# arguments = (if you want to pass any to the shell script)
should_transfer_files = YES
when_to_transfer_output = ON_EXIT
transfer_input_files =pwscf.save/
requirements = (HasChtcSoftware == true)
request_cpus = 8
request_memory =32GB
request_disk = 32GB
queue 1Code: Select all
#!/bin/bash
. /etc/profile.d/modules.sh
module load OpenMPI/3.1.4-GCC-8.3.0
mpirun -np 8 ./yambo -F <02_screening.inCode: Select all
#
# __ __ ________ ___ __ __ _______ ______
# /_/\/_/\ /_______/\ /__//_//_/\ /_______/\ /_____/\
# \ \ \ \ \\::: _ \ \\::\| \| \ \\::: _ \ \\:::_ \ \
# \:\_\ \ \\::(_) \ \\:. \ \\::(_) \/_\:\ \ \ \
# \::::_\/ \:: __ \ \\:.\-/\ \ \\:: _ \ \\:\ \ \ \
# \::\ \ \:.\ \ \ \\. \ \ \ \\::(_) \ \\:\_\ \ \
# \__\/ \__\/\__\/ \__\/ \__\/ \_______\/ \_____\/
#
#
# Version 5.0.4 Revision 19595 Hash 896bffc02
# Branch is
# MPI+HDF5_IO Build
# http://www.yambo-code.org
#
screen # [R] Inverse Dielectric Matrix
em1s # [R][Xs] Statically Screened Interaction
dipoles # [R] Oscillator strenghts (or dipoles)
Chimod= "HARTREE" # [X] IP/Hartree/ALDA/LRC/PF/BSfxc
% BndsRnXs
1 | 40 | # [Xs] Polarization function bands
%
NGsBlkXs= 4 RL # [Xs] Response block size
% LongDrXs
1.000000 | 1.000000 | 1.000000 | # [Xs] [cc] Electric Field
%
XTermKind= "none" # [X] X terminator ("none","BG" Bruneval-Gonze)