[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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