[QE-users] Error in routine davcio (10)?

Sun Aug 30 19:59:21 CEST 2020

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:
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> 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 ...*
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> 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.
>>
> _______________________________________________
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-- 
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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