<div dir="ltr"><div>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.</div><div><br></div><div>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. </div><div><br></div><div><font color="#741b47">"Apparently the *.wfc files produced by the code when stopping cleanly for time limit are not there."</font> <br></div><div><br></div><div>When I tried restarting the relaxation calculations for one surface I got the same error, <i>error in routine davcio (10)</i>. The output file said <i>error while reading from</i> <i>file</i> for the following files: </div><div><br></div><div>./SurfaceO6.wfc2,
./SurfaceO6.wfc3 ,
./SurfaceO6.wfc4 ,
./SurfaceO6.wfc5 ,
./SurfaceO6.wfc6 ,
./SurfaceO6.wfc7 , <br></div><div>./SurfaceO6.wfc8, ./SurfaceO6.wfc9,
./SurfaceO6.wfc11 ,
./SurfaceO6.wfc13,
./SurfaceO6.wfc15 ,
./SurfaceO6.wfc17
<br></div><div><br></div><div>But in the screenshot of this folder <u>all of these files are there.</u></div><div><div><br></div></div><div><br></div><div><font color="#741b47">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"</font><font color="#4c1130"> </font> <br></div><div><br></div><div>In the output file I did found: </div><div><br></div><div><i> Message from routine readpp:</i></div><i> file ./SurfaceO6.save/Bi.rel-pbe-dn-kjpaw_psl.1.0.0.UPF not found<br> Message from routine readpp:<br> file ./SurfaceO6.save/Na.rel-pbe-spn-kjpaw_psl.0.2.UPF not found</i><div><br></div><div>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?</div><div><br></div><div>Thank you for your time and input. </div><div><div><br></div><div><br></div><div> </div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Sun, Aug 30, 2020 at 1:00 PM Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com">p.giannozzi@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div>I am quite sure that restart under normally encountered conditions works, although I cannot rule out that it may fail in some particular cases. <br></div><div>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"<br></div><div><br></div><div>Paolo<br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Aug 28, 2020 at 11:22 PM Vasilios Passias <<a href="mailto:billy.passias@gmail.com" target="_blank">billy.passias@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">There was a problem with the files I attached in my previous email, so I will input them in here:<div><br></div><div>My input file:</div><div><i><br></i></div><div><i>&CONTROL<br> calculation = 'relax',<br> restart_mode = 'restart',<br> pseudo_dir = '/home/passias2/qe-6.3/pseudo/'<br> etot_conv_thr = 1.0d-4,<br> forc_conv_thr = 1.0d-3,<br> max_seconds = 2.196d+5<br>/<br>&SYSTEM<br> ibrav = 0,<br> nat = 56,<br> ntyp = 2,<br> occupations = 'smearing',<br> smearing = 'marzari-vanderbilt',<br> degauss = 1.0d-3,<br> ecutwfc = 25.0,<br> ecutrho = 100.0,<br> noncolin = .true.<br> lspinorb = .true.<br>/<br>&ELECTRONS<br> conv_thr = 1.0d-8,<br> mixing_beta = 0.1<br>/<br>&IONS<br>ion_dynamics = 'bfgs'<br>/<br><br>ATOMIC_SPECIES<br> Bi 208.980 Bi.rel-pbe-dn-kjpaw_psl.1.0.0.UPF<br> Na 22.989 Na.rel-pbe-spn-kjpaw_psl.0.2.UPF<br><br>K_POINTS automatic<br>8 8 1 0 0 0<br><br>CELL_PARAMETERS angstrom<br>5.44800000000000 0.00000000000000 0.00000000000000<br>0.00000000000000 9.65500000000000 0.00000000000000<br>0.00000000000000 0.00000000000000 51.45404266545082<br><br>ATOMIC_POSITIONS angstrom<br>Na 0.0000000000 2.4137500000 10.0000000000 <br>Na 0.0000000000 7.2412500000 10.0000000000 <br>Na 2.7240000000 5.6288650000 11.5727021333 <br>Na 0.0000000000 0.8013650000 13.1454042665 <br>Na 0.0000000000 4.0261350000 13.1454042665 <br>Na 2.7240000000 8.8536350000 11.5727021333 <br>Bi 2.7240000000 2.4137500000 11.5727021333 <br>Bi 0.0000000000 7.2412500000 13.1454042665 <br>Na 2.7240000000 2.4137500000 14.7181063998 <br>Na 2.7240000000 7.2412500000 14.7181063998 <br>Na 0.0000000000 5.6288650000 16.2908085331 <br>Na 2.7240000000 0.8013650000 17.8635106664 <br>Na 2.7240000000 4.0261350000 17.8635106664 <br>Na 0.0000000000 8.8536350000 16.2908085331 <br>Bi 0.0000000000 2.4137500000 16.2908085331 <br>Bi 2.7240000000 7.2412500000 17.8635106664 <br>Na 0.0000000000 2.4137500000 19.4362127996 <br>Na 0.0000000000 7.2412500000 19.4362127996 <br>Na 2.7240000000 5.6288650000 21.0089149329 <br>Na 0.0000000000 0.8013650000 22.5816170662 <br>Na 0.0000000000 4.0261350000 22.5816170662 <br>Na 2.7240000000 8.8536350000 21.0089149329 <br>Bi 2.7240000000 2.4137500000 21.0089149329 <br>Bi 0.0000000000 7.2412500000 22.5816170662 <br>Na 2.7240000000 2.4137500000 24.1543191995 <br>Na 2.7240000000 7.2412500000 24.1543191995 <br>Na 0.0000000000 5.6288650000 25.7270213327 <br>Na 2.7240000000 0.8013650000 27.2997234660 <br>Na 2.7240000000 4.0261350000 27.2997234660 <br>Na 0.0000000000 8.8536350000 25.7270213327 <br>Bi 0.0000000000 2.4137500000 25.7270213327 <br>Bi 2.7240000000 7.2412500000 27.2997234660 <br>Na 0.0000000000 2.4137500000 28.8724255993 <br>Na 0.0000000000 7.2412500000 28.8724255993 <br>Na 2.7240000000 5.6288650000 30.4451277325 <br>Na 0.0000000000 0.8013650000 32.0178298658 <br>Na 0.0000000000 4.0261350000 32.0178298658 <br>Na 2.7240000000 8.8536350000 30.4451277325 <br>Bi 2.7240000000 2.4137500000 30.4451277325 <br>Bi 0.0000000000 7.2412500000 32.0178298658 <br>Na 2.7240000000 2.4137500000 33.5905319991 <br>Na 2.7240000000 7.2412500000 33.5905319991 <br>Na 0.0000000000 5.6288650000 35.1632341324 <br>Na 2.7240000000 0.8013650000 36.7359362656 <br>Na 2.7240000000 4.0261350000 36.7359362656 <br>Na 0.0000000000 8.8536350000 35.1632341324 <br>Bi 0.0000000000 2.4137500000 35.1632341324 <br>Bi 2.7240000000 7.2412500000 36.7359362656 <br>Na 2.7240000000 2.4137500000 5.2818936002 <br>Na 2.7240000000 7.2412500000 5.2818936001<br>Na 0.0000000000 5.6288650000 6.8545957335 <br>Na 2.7240000000 0.8013650000 8.4272978666 <br>Na 2.7240000000 4.0261350000 8.4272978666<br>Na 0.0000000000 8.8536350000 6.8545957335 <br>Bi 0.0000000000 2.4137500000 6.8545957335 <br>Bi 2.7240000000 7.2412500000 8.4272978667 </i><br></div><div><br></div><div><br></div><div>My output file:</div><div><br></div><div><i> The initial density is read from file :<br> ./pwscf.save/charge-density<br><br><br> negative rho (up, down): 3.771E-01 0.000E+00<br> Starting wfcs from file<br> Checking if some PAW data can be deallocated... <br><br> total cpu time spent up to now is 15.7 secs<br><br> Self-consistent Calculation<br><br> iteration # 1 ecut= 25.00 Ry beta= 0.10<br> Calculation restarted from kpoint # 20<br> Davidson diagonalization with overlap<br><br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br> Error in routine davcio (10):<br> 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"<br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br><br> stopping ...<br><br><br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br> Error in routine davcio (10):<br> 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"<br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br><br> stopping ...<br><br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br> Error in routine davcio (10):<br> 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"<br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br><br> stopping ...<br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br> Error in routine davcio (10):<br> 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"<br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br><br> stopping ...<br><br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br> Error in routine davcio (10):<br> 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"<br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br><br> stopping ...<br><br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br> Error in routine davcio (10):<br> 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"<br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br><br> stopping ...<br><br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br> Error in routine davcio (10):<br> 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"<br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br><br> stopping ...<br><br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br> Error in routine davcio (10):<br> 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"<br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br><br> stopping ...<br><br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br> Error in routine davcio (10):<br> 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"<br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br><br> stopping ...<br><br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br> Error in routine davcio (10):<br> 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"<br> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br><br> stopping ...<br></i></div><div><br></div><div><br></div><div>Other relevant information:</div><div><br></div><div><i>Warning: Process to core binding is enabled and OMP_NUM_THREADS is set to non-zero (1) value<br>If your program has OpenMP sections, this can cause over-subscription of cores and consequently poor performance<br>To avoid this, please re-run your application after setting MV2_ENABLE_AFFINITY=0<br>Use MV2_USE_THREAD_WARNING=0 to suppress this message<br>[cli_12]: aborting job:<br>application called MPI_Abort(MPI_COMM_WORLD, 1) - process 12<br>[mpiexec@golub220] HYDT_bscd_pbs_wait_for_completion (tools/bootstrap/external/pbs_wait.c:67): tm_poll(obit_event) failed with TM error 17002<br>[mpiexec@golub220] HYDT_bsci_wait_for_completion (tools/bootstrap/src/bsci_wait.c:23): launcher returned error waiting for completion<br>[proxy:0:0@golub220] HYD_pmcd_pmip_control_cmd_cb (pm/pmiserv/pmip_cb.c:911): assert (!closed) failed<br>[proxy:0:0@golub220] HYDT_dmxu_poll_wait_for_event (tools/demux/demux_poll.c:76): callback returned error status<br>[proxy:0:0@golub220] main (pm/pmiserv/pmip.c:202): demux engine error waiting for event</i><br></div><div><br></div><div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Aug 28, 2020 at 2:40 PM Vasilios Passias <<a href="mailto:billy.passias@gmail.com" target="_blank">billy.passias@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hello fellow quantum espresso users. <div><br></div><div>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.</div><div><br></div><div>Then I set restart_mode = 'restart' and I ran this relaxation calculation again, expecting it to continue where it left off. </div><div><br></div><div>Instead I got the following error: error in routine davcio (10): error while reading from file.</div><div><br></div><div>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?</div><div><br></div><div>I have my input, output, job submission, and crash files attached in this email. <br></div><div><br></div><div><br></div><div>Thank you for your time and input.</div></div>
</blockquote></div>
_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote></div><br clear="all"><br>-- <br><div dir="ltr"><div dir="ltr"><div><div dir="ltr"><div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>Phone +39-0432-558216, fax +39-0432-558222<br><br></div></div></div></div></div>
_______________________________________________<br>
Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
users mailing list <a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a><br>
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