[QE-users] Error when computing the band structure
Paolo Giannozzi
p.giannozzi at gmail.com
Thu Jun 4 12:06:27 CEST 2020
I mean that the problem _might_ come from the setting of your cluster. In
recent versions of the code, all files are read by just one processors, but
in your version there might be still a few files (the xml data file is one
of those) that are read by alI processors.
Paolo
On Thu, Jun 4, 2020 at 11:48 AM Kenan Song <kenan.song at kaust.edu.sa> wrote:
> Dear Paolo,
>
> Do you mean that this problem comes from the settings of the cluster
> system, which restricts some CPUs from entering the .save folder? Thank you.
>
> Kind regards,
>
> Kenan Song
>
> On Thu, Jun 4, 2020 at 12:18 PM Paolo Giannozzi <p.giannozzi at gmail.com>
> wrote:
>
>> The number of processors does not affect the reading of data files,
>> unless there are processors cannot access the disk where data files are
>> stored.
>>
>> Paolo
>>
>>
>> On Thu, Jun 4, 2020 at 4:07 AM Mostafa Marzouk <
>> mostafamarzokphysics at gmail.com> wrote:
>>
>>> Dear Mr. Song,
>>> I think this problem is related to the number of tasks and nodes,
>>> *You can try to reduce the number of nodes from 8 to become 4 nodes*,
>>> and then let me know if the problem has been solved or not.
>>> Regards,
>>> Mostaf Marzouk
>>>
>>>
>>> On Thu, Jun 4, 2020 at 3:26 AM Kenan Song <kenan.song at kaust.edu.sa>
>>> wrote:
>>>
>>>> Dear All,
>>>>
>>>> I tried to compute the band structure but received error information.
>>>>
>>>> Here is my input file.
>>>>
>>>> &bands
>>>> prefix='Bulk_Co3Sn2S2',
>>>> outdir='./',
>>>> filband='band.dat'
>>>> no_overlap=.true.
>>>> /
>>>>
>>>> Here is the error file.
>>>>
>>>>
>>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>> songk0a at cdl4:/project/k1364/Col/Co3Sn2S2> squeue -u songk0a
>>>> JOBID USER ACCOUNT NAME ST REASON
>>>> START_TIME TIME TIME_LEFT NODES
>>>> songk0a at cdl4:/project/k1364/Col/Co3Sn2S2> cat CRASH
>>>>
>>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>> songk0a at cdl4:/project/k1364/Col/Co3Sn2S2> cat nscf_band.out
>>>> Program BANDS v.6.5 starts on 4Jun2020 at 4:22:14
>>>> 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), running on 256 processors
>>>> MPI processes distributed on 8 nodes
>>>> R & G space division: proc/nbgrp/npool/nimage = 256
>>>> Reading xml data from directory:
>>>> ./Bulk_Co3Sn2S2.save/
>>>>
>>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>> Error in routine read_xml_file (1):
>>>> fatal error reading xml file
>>>>
>>>> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>>>> stopping ...
>>>>
>>>> Here is script that I use for the job submission.
>>>>
>>>> #!/bin/bash
>>>> #SBATCH --partition=workq
>>>> #SBATCH --job-name="espresso"
>>>> #SBATCH --nodes=8
>>>> #SBATCH --time=24:00:00
>>>> #SBATCH --exclusive
>>>> #SBATCH --err=std.err
>>>> #SBATCH --output=std.out
>>>> #----------------------------------------------------------#
>>>> #export ESPRESSO_USE="" # This is the default
>>>> #export ESPRESSO_USE=_scalapack # This is the scalapack version
>>>> module load espresso/6.5
>>>> export OMP_NUM_THREADS=1
>>>> #----------------------------------------------------------#
>>>> echo "The job "${SLURM_JOB_ID}" is running on "${SLURM_JOB_NODELIST}
>>>> #----------------------------------------------------------#
>>>> srun --ntasks=256 --hint=nomultithread --ntasks-per-node=32
>>>> --ntasks-per-socket=16 --ntasks-per-core=1 --mem-bind=v,local
>>>> /sw/xc40cle7/espresso/6.5/cle7_intel19.0.1/qe-6.5/bin/bands.x <
>>>> nscf_band.in > nscf_band.out
>>>> rm -r pr.*
>>>>
>>>> I have my data-file-schema.xml file in .save folder so I do not know
>>>> why the code could not find this file.
>>>>
>>>> Would anyone please provide some solutions? Thank you very much.
>>>>
>>>> Kind regards,
>>>>
>>>> Kieran
>>>>
>>>> ------------------------------
>>>> This message and its contents, including attachments are intended
>>>> solely for the original recipient. If you are not the intended recipient or
>>>> have received this message in error, please notify me immediately and
>>>> delete this message from your computer system. Any unauthorized use or
>>>> distribution is prohibited. Please consider the environment before printing
>>>> this email._______________________________________________
>>>> Quantum ESPRESSO is supported by MaX (
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>>>> users mailing list users at lists.quantum-espresso.org
>>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>
>>>
>>>
>>> --
>>> *Kind Regards;Sincerely;Mostafa *
>>> _______________________________________________
>>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso
>>> )
>>> users mailing list users at lists.quantum-espresso.org
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>
>>
>>
>> --
>> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>> _______________________________________________
>> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
>> users mailing list users at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
> ------------------------------
> This message and its contents, including attachments are intended solely
> for the original recipient. If you are not the intended recipient or have
> received this message in error, please notify me immediately and delete
> this message from your computer system. Any unauthorized use or
> distribution is prohibited. Please consider the environment before printing
> this email._______________________________________________
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu/quantum-espresso)
> users mailing list users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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