[QE-users] [SUSPECT ATTACHMENT REMOVED] Error in routine divide_et_impera (1):
Abdulla Bin Afif
abdulla.binafif at ntnu.no
Tue May 5 09:42:31 CEST 2020
Hi Michal and QE friends,
Thanks for the helpful suggestions , the advice worked.
When the nk (last second line) was changed from 4 to 1 in the submit script, the SCF calculations were executed. I guess this was the way to change the npool.
/////////////////////////////////////////////////////////
#!/bin/bash
#SBATCH --partition=CPUQ
#SBATCH --account=iv-mtp
#SBATCH --time=99:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --mem=48000
#SBATCH --job-name="hello_test"
#SBATCH --output=job_%j.out
#SBATCH --error=job_%j.err
#SBATCH --mail-user=abdulla.binafif at ntnu.no
#SBATCH --mail-type=NONE
echo "The working directory is $SLURM_SUBMIT_DIR"
echo "Running QE with: $cmd on $SLURM_JOB_NODELIST in directory "`pwd`
pwscf=/share/apps/software/QuantumESPRESSO/6.4.1-intel-2019a/bin/pw.x
input=TMA.pw.in
cd $SLURM_SUBMIT_DIR
echo "Job started at "`date`
mpiexec -np 24 $pwscf -nk 1 < $input > $SLURM_SUBMIT_DIR/TMA.pw.out
echo "Job finished at "`date`
////////////////////////////////////////////////////////////////////////////////////////////////////
Thanks and Regards,
Abdulla
>-----Original Message-----
>From: Michal Krompiec <michal.krompiec at gmail.com>
>Sent: Monday, May 4, 2020 1:05 PM
>To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>;
>Abdulla Bin Afif <abdulla.binafif at ntnu.no>
>Subject: Re: [QE-users] [SUSPECT ATTACHMENT REMOVED] Error in routine
>divide_et_impera (1):
>
>Dear Abdulla,
>No need to run on 1 processor. The error is caused by the fact that the
>number of k-points (1) is not divisible by the number of MPI pools
>(4 in your case). Run with -npool 1 instead of -npool 4.
>Best,
>Michal Krompiec
>Merck KGaA
>
>On Mon, 4 May 2020 at 11:59, Offermans Willem <willem.offermans at vito.be>
>wrote:
>>
>> Dear Abdulla and Quantum Espresso friend,
>>
>> From the error message you showed I got the impression that there is
>> something wrong in the way you run mpi. If you run parallel along kpoints
>(111), then some nodes will be workless.
>>
>> Run on 1 processor (not parallel) and the error message might disappear.
>>
>> If I recall correctly, you can also run in parallel along the bands. That might
>be an alternative, if you insist on running in parallel.
>>
>>
>>
>> > On 3 May 2020, at 23:21, Abdulla Bin Afif <abdulla.binafif at ntnu.no>
>wrote:
>> >
>> > Hi QE community members,
>> >
>> >
>> > When I conduct scf calculation on an organometallic TMA
>(trimethylaluminium), it shows an error.
>> >
>> > For molecules we consider Kpoints 11100, with this its gives the below
>error and when the Kpoints are changed to 33300 there is no error, I am not
>sure why it’s not working with 111000.
>> >
>> > I have a considered TMA compound inside a unit cell of 15A.
>> >
>> >
>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> > Error in routine divide_et_impera (1):
>> > some nodes have no k-points
>> >
>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>%%%%%%%%%%%%%%%%%%%%%%
>> > %%%%%%%%%%
>> > &CONTROL
>> > calculation = 'scf',
>> > outdir = '.',
>> > prefix = 'calc',
>> > pseudo_dir = '.',
>> > tprnfor = .true.,
>> > tstress = .true.,
>> > /
>> > &SYSTEM
>> > degauss = 0.00734986475817d0,
>> > ecutrho = 367.493237909d0,
>> > ecutwfc = 36.7493237909d0,
>> > ibrav=1,
>> > celldm(1)=28.3459,
>> > nat = 13,
>> > ntyp = 3,
>> > occupations = 'smearing',
>> > smearing = 'cold',
>> > input_dft='PBE',
>> > /
>> > &ELECTRONS
>> > diagonalization='david',
>> > conv_thr=7.34986475817e-07,
>> > mixing_mode='plain',
>> > electron_maxstep=100,
>> > mixing_beta=0.7d0,
>> > /
>> > ATOMIC_SPECIES
>> > Al 26.98154 Al.UPF,
>> > C 12.011 C.UPF,
>> > H 1.00794 H.UPF,
>> > ATOMIC_POSITIONS {crystal}
>> > Al 0.5344800000 0.5466800000 0.5342700000
>> > C 0.4242100000 0.6103500000 0.5344500000
>> > C 0.6447600000 0.6103500000 0.5344500000
>> > C 0.5344800000 0.4193500000 0.5344500000
>> > H 0.4032300000 0.6226500000 0.4659700000
>> > H 0.3735600000 0.5709800000 0.5685900000
>> > H 0.4329000000 0.6737500000 0.5688800000
>> > H 0.6657400000 0.6222700000 0.6029900000
>> > H 0.6954000000 0.5711800000 0.5000900000
>> > H 0.6360700000 0.6739400000 0.5003700000
>> > H 0.5343200000 0.3950300000 0.4659700000
>> > H 0.5939000000 0.3951800000 0.5685900000
>> > H 0.4752400000 0.3951800000 0.5688800000
>> > K_POINTS (automatic)
>> > 1 1 1 0 0 0
>> >
>> >
>> > Output
>> >
>> > This program is part of the open-source Quantum ESPRESSO suite
>> > for quantum simulation of materials; please cite
>> > "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
>> > "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
>> > URL http://www.quantum-espresso.org",
>> > in publications or presentations arising from this work. More details at
>> > http://www.quantum-espresso.org/quote
>> >
>> > Parallel version (MPI & OpenMP), running on 24 processor cores
>> > Number of MPI processes: 24
>> > Threads/MPI process: 1
>> >
>> > MPI processes distributed on 1 nodes
>> > K-points division: npool = 4
>> > R & G space division: proc/nbgrp/npool/nimage = 6
>> > Waiting for input...
>> > Reading input from standard input
>> >
>> > Current dimensions of program PWSCF are:
>> > Max number of different atomic species (ntypx) = 10
>> > Max number of k-points (npk) = 40000
>> > Max angular momentum in pseudopotentials (lmaxx) = 3
>> >
>> > IMPORTANT: XC functional enforced from input :
>> > Exchange-correlation = PBE ( 1 4 3 4 0 0)
>> > Using LIBXC version = 4 3 4
>> > Any further DFT definition will be discarded
>> > Please, verify this is what you really want
>> >
>> >
>> > Subspace diagonalization in iterative solution of the eigenvalue
>problem:
>> > a serial algorithm will be used
>> >
>> >
>> >
>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> > Error in routine divide_et_impera (1):
>> > some nodes have no k-points
>> >
>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>%%%%%%%%%%%%%%%%%%%%%%
>> > %%%%%%%%%%
>> >
>> > stopping ...
>> >
>> >
>> > Thanks and Regards,
>> >
>> > Abdulla Bin Afif
>> > Ph.D. Candidate
>> > Norwegian University of Science and Technology (NTNU) MTP -
>> > Department of Mechanical and Industrial Engineering Richard
>> > Birkelandsvei 2b
>> > NO-7491 Trondheim. Norway
>> >
>> > Email: abdulla.binafif at ntnu.no
>> > Mobil: +47 41348358
>> >
>> > _______________________________________________
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