[QE-users] Error in routine davcio (10)?
Vasilios Passias
billy.passias at gmail.com
Tue Sep 8 01:55:22 CEST 2020
Thanks Paolo, I thought I solved this problem: previously I had a number
of "nested" directories for each surface I wanted to relax, i.e Surface3
was inside Surface 2, which was inside Surface 1, and Surface 1 was inside
the master directory. For each directory, I ran relaxation calculations
using the restart setting, but all of the directories had the same prefix
for the .wfc files.
So then I moved each of these surfaces to separate directories inside the
master directory, and for each surface I assigned a unique prefix for the
.wfc files.
"Apparently the *.wfc files produced by the code when stopping cleanly for
time limit are not there."
When I tried restarting the relaxation calculations for one surface I got
the same error, *error in routine davcio (10)*. The output file said *error
while reading from* *file* for the following files:
./SurfaceO6.wfc2, ./SurfaceO6.wfc3 , ./SurfaceO6.wfc4 ,
./SurfaceO6.wfc5 , ./SurfaceO6.wfc6 , ./SurfaceO6.wfc7 ,
./SurfaceO6.wfc8, ./SurfaceO6.wfc9, ./SurfaceO6.wfc11 ,
./SurfaceO6.wfc13, ./SurfaceO6.wfc15 , ./SurfaceO6.wfc17
But in the screenshot of this folder *all of these files are there.*
Note that saving files may take some time: if you are using a batch system,
the time limit of the batch queue must be larger than the time limit
specified in "max_seconds"
In the output file I did found:
* Message from routine readpp:*
* file ./SurfaceO6.save/Bi.rel-pbe-dn-kjpaw_psl.1.0.0.UPF not found
Message from routine readpp: file
./SurfaceO6.save/Na.rel-pbe-spn-kjpaw_psl.0.2.UPF not found*
This is accurate; I could not find these files. So I think this is related
to an issue with saving the files. My max_seconds is 61 hours, but the
walltime is 72 hours. Is the batch queue the walltime? What is a batch
system?
Thank you for your time and input.
On Sun, Aug 30, 2020 at 1:00 PM Paolo Giannozzi <p.giannozzi at gmail.com>
wrote:
> I am quite sure that restart under normally encountered conditions works,
> although I cannot rule out that it may fail in some particular cases.
> Apparently the *.wfc files produced by the code when stopping cleanly for
> time limit are not there. You should have a look at the output of the
> previous run, check where the code stopped, look for any suspicious or
> missing message. Note that saving files may take some time: if you are
> using a batch system, the time limit of the batch queue must be larger than
> the time limit specified in "max_seconds"
>
> Paolo
>
> On Fri, Aug 28, 2020 at 11:22 PM Vasilios Passias <billy.passias at gmail.com>
> wrote:
>
>> There was a problem with the files I attached in my previous email, so I
>> will input them in here:
>>
>> My input file:
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>> *&CONTROL calculation = 'relax', restart_mode = 'restart', pseudo_dir =
>> '/home/passias2/qe-6.3/pseudo/' etot_conv_thr = 1.0d-4, forc_conv_thr =
>> 1.0d-3, max_seconds = 2.196d+5/&SYSTEM ibrav = 0, nat = 56, ntyp =
>> 2, occupations = 'smearing', smearing = 'marzari-vanderbilt', degauss =
>> 1.0d-3, ecutwfc = 25.0, ecutrho = 100.0, noncolin = .true. lspinorb =
>> .true./&ELECTRONS conv_thr = 1.0d-8, mixing_beta = 0.1/&IONSion_dynamics =
>> 'bfgs'/ATOMIC_SPECIES Bi 208.980 Bi.rel-pbe-dn-kjpaw_psl.1.0.0.UPF Na
>> 22.989 Na.rel-pbe-spn-kjpaw_psl.0.2.UPFK_POINTS automatic8 8 1 0 0
>> 0CELL_PARAMETERS angstrom5.44800000000000 0.00000000000000
>> 0.000000000000000.00000000000000 9.65500000000000
>> 0.000000000000000.00000000000000 0.00000000000000
>> 51.45404266545082ATOMIC_POSITIONS angstromNa 0.0000000000 2.4137500000
>> 10.0000000000 Na 0.0000000000 7.2412500000 10.0000000000 Na 2.7240000000
>> 5.6288650000 11.5727021333 Na 0.0000000000 0.8013650000 13.1454042665 Na
>> 0.0000000000 4.0261350000 13.1454042665 Na 2.7240000000 8.8536350000
>> 11.5727021333 Bi 2.7240000000 2.4137500000 11.5727021333 Bi 0.0000000000
>> 7.2412500000 13.1454042665 Na 2.7240000000 2.4137500000 14.7181063998 Na
>> 2.7240000000 7.2412500000 14.7181063998 Na 0.0000000000 5.6288650000
>> 16.2908085331 Na 2.7240000000 0.8013650000 17.8635106664 Na 2.7240000000
>> 4.0261350000 17.8635106664 Na 0.0000000000 8.8536350000 16.2908085331 Bi
>> 0.0000000000 2.4137500000 16.2908085331 Bi 2.7240000000 7.2412500000
>> 17.8635106664 Na 0.0000000000 2.4137500000 19.4362127996 Na 0.0000000000
>> 7.2412500000 19.4362127996 Na 2.7240000000 5.6288650000 21.0089149329 Na
>> 0.0000000000 0.8013650000 22.5816170662 Na 0.0000000000 4.0261350000
>> 22.5816170662 Na 2.7240000000 8.8536350000 21.0089149329 Bi 2.7240000000
>> 2.4137500000 21.0089149329 Bi 0.0000000000 7.2412500000 22.5816170662 Na
>> 2.7240000000 2.4137500000 24.1543191995 Na 2.7240000000 7.2412500000
>> 24.1543191995 Na 0.0000000000 5.6288650000 25.7270213327 Na 2.7240000000
>> 0.8013650000 27.2997234660 Na 2.7240000000 4.0261350000 27.2997234660 Na
>> 0.0000000000 8.8536350000 25.7270213327 Bi 0.0000000000 2.4137500000
>> 25.7270213327 Bi 2.7240000000 7.2412500000 27.2997234660 Na 0.0000000000
>> 2.4137500000 28.8724255993 Na 0.0000000000 7.2412500000 28.8724255993 Na
>> 2.7240000000 5.6288650000 30.4451277325 Na 0.0000000000 0.8013650000
>> 32.0178298658 Na 0.0000000000 4.0261350000 32.0178298658 Na 2.7240000000
>> 8.8536350000 30.4451277325 Bi 2.7240000000 2.4137500000 30.4451277325 Bi
>> 0.0000000000 7.2412500000 32.0178298658 Na 2.7240000000 2.4137500000
>> 33.5905319991 Na 2.7240000000 7.2412500000 33.5905319991 Na 0.0000000000
>> 5.6288650000 35.1632341324 Na 2.7240000000 0.8013650000 36.7359362656 Na
>> 2.7240000000 4.0261350000 36.7359362656 Na 0.0000000000 8.8536350000
>> 35.1632341324 Bi 0.0000000000 2.4137500000 35.1632341324 Bi 2.7240000000
>> 7.2412500000 36.7359362656 Na 2.7240000000 2.4137500000 5.2818936002 Na
>> 2.7240000000 7.2412500000 5.2818936001Na 0.0000000000 5.6288650000
>> 6.8545957335 Na 2.7240000000 0.8013650000 8.4272978666 Na 2.7240000000
>> 4.0261350000 8.4272978666Na 0.0000000000 8.8536350000 6.8545957335 Bi
>> 0.0000000000 2.4137500000 6.8545957335 Bi 2.7240000000 7.2412500000
>> 8.4272978667 *
>>
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>> My output file:
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>> * The initial density is read from file :
>> ./pwscf.save/charge-density negative rho (up, down): 3.771E-01
>> 0.000E+00 Starting wfcs from file Checking if some PAW data can be
>> deallocated... total cpu time spent up to now is 15.7 secs
>> Self-consistent Calculation iteration # 1 ecut= 25.00 Ry
>> beta= 0.10 Calculation restarted from kpoint # 20 Davidson
>> diagonalization with
>> overlap %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> Error in routine davcio (10): error while reading from file
>> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc11" %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> stopping
>> ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> Error in routine davcio (10): error while reading from file
>> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc3" %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> stopping
>> ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> Error in routine davcio (10): error while reading from file
>> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc13" %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> stopping
>> ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> Error in routine davcio (10): error while reading from file
>> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc14" %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> stopping
>> ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> Error in routine davcio (10): error while reading from file
>> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc10" %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> stopping
>> ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> Error in routine davcio (10): error while reading from file
>> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc5" %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> stopping
>> ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> Error in routine davcio (10): error while reading from file
>> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc2" %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> stopping
>> ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> Error in routine davcio (10): error while reading from file
>> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc17" %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> stopping
>> ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> Error in routine davcio (10): error while reading from file
>> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc16" %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> stopping
>> ... %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> Error in routine davcio (10): error while reading from file
>> "/projects/wagner/vpassias2/Investigation_1/Na3Bi_100/Na3Bi_100_nlayer7_vac20A_2D_band_plot/Original_Structure/SurfaceO8_move_down_37Na/./pwscf.wfc20" %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>> stopping ...*
>>
>>
>> Other relevant information:
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>> *Warning: Process to core binding is enabled and OMP_NUM_THREADS is set
>> to non-zero (1) valueIf your program has OpenMP sections, this can cause
>> over-subscription of cores and consequently poor performanceTo avoid this,
>> please re-run your application after setting MV2_ENABLE_AFFINITY=0Use
>> MV2_USE_THREAD_WARNING=0 to suppress this message[cli_12]: aborting
>> job:application called MPI_Abort(MPI_COMM_WORLD, 1) - process
>> 12[mpiexec at golub220] HYDT_bscd_pbs_wait_for_completion
>> (tools/bootstrap/external/pbs_wait.c:67): tm_poll(obit_event) failed with
>> TM error 17002[mpiexec at golub220] HYDT_bsci_wait_for_completion
>> (tools/bootstrap/src/bsci_wait.c:23): launcher returned error waiting for
>> completion[proxy:0:0 at golub220] HYD_pmcd_pmip_control_cmd_cb
>> (pm/pmiserv/pmip_cb.c:911): assert (!closed) failed[proxy:0:0 at golub220]
>> HYDT_dmxu_poll_wait_for_event (tools/demux/demux_poll.c:76): callback
>> returned error status[proxy:0:0 at golub220] main (pm/pmiserv/pmip.c:202):
>> demux engine error waiting for event*
>>
>>
>>
>> On Fri, Aug 28, 2020 at 2:40 PM Vasilios Passias <billy.passias at gmail.com>
>> wrote:
>>
>>> Hello fellow quantum espresso users.
>>>
>>> Recently, I tried running a relaxation calculation. The convergence
>>> thresholds on the total energy and total force are such that I need to run
>>> this relaxation calculation multiple times. The first relaxation run, with
>>> restart_mode = 'from_scratch' , ran fine for the max_time I had set.
>>>
>>> Then I set restart_mode = 'restart' and I ran this relaxation
>>> calculation again, expecting it to continue where it left off.
>>>
>>> Instead I got the following error: error in routine davcio (10):
>>> error while reading from file.
>>>
>>> All of the files associated with this error are in the same folder as my
>>> input and output files. Why is this happening? Should I just re-run this
>>> calculation?
>>>
>>> I have my input, output, job submission, and crash files attached in
>>> this email.
>>>
>>>
>>> Thank you for your time and input.
>>>
>> _______________________________________________
>> 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
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