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</o:shapelayout></xml><![endif]--></head><body bgcolor=white lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Well actually, this remark may be much closer to solve my problem than you might think !<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I tried to run the simulation again on the cluster without the assume_isolated=’2D’ flag, and the parallelization was efficient this time. It seemed to scale well with growing number of procs. So thank you very much for this suggestion.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>However, this raised other questions that I was not able to find an answer to:<o:p></o:p></span></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l1 level1 lfo2'><![if !supportLists]><span style='font-size:11.0pt;font-family:Symbol;color:#1F497D'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Where does the information about the need to center the system come from? I could not find track of it in the INPUT_PW documentation. I only quickly glanced over the paper mentioned as reference in the ‘2D’ flag, but I don’t suppose that such technical details would be explained there ( as I imagine that it is more relevant to the particular coding implementation in quantum espresso than the general method described in the article)<o:p></o:p></span></p><p class=MsoListParagraph style='text-indent:-18.0pt;mso-list:l1 level1 lfo2'><![if !supportLists]><span style='font-size:11.0pt;font-family:Symbol;color:#1F497D'><span style='mso-list:Ignore'>·<span style='font:7.0pt "Times New Roman"'> </span></span></span><![endif]><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I tried to correct the assume_isolated, but I might have misunderstood how to center the system. I just took the atom with “highest z” zh and the one with “lowest z” zl, and made sure to shift the whole so that the average (zh+zl)/2=0. This did not work. However, this particular example being made of a slab and a 2d layer over it, this means, among others, that the slab itself is not centered, and I am unsure whether this is the correct way to do it<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Best,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Julien<o:p></o:p></span></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:windowtext'>From:</span></b><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:windowtext'> Thomas Brumme [mailto:thomas.brumme@uni-leipzig.de] <br><b>Sent:</b> mercredi 10 avril 2019 18:19<br><b>To:</b> Quantum Espresso users Forum; Julien Barbaud<br><b>Subject:</b> Re: [QE-users] unefficient parallelization of scf calculation<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal style='margin-bottom:12.0pt'>Dear Julien,<br><br>I can't give any valuable input for your question regarding the parallelization, but I think your<br>input is wrong. Using assume_isolated needs the system to be centered around z=0.<br><br>Regards<br><br>Thomas<o:p></o:p></p><div><p class=MsoNormal>On 4/10/19 11:36 AM, Julien Barbaud wrote:<o:p></o:p></p></div><blockquote style='margin-top:5.0pt;margin-bottom:5.0pt'><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I am starting to use a hpc cluster of my university, but I am very green on parallel computation.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I have made a first test (test #1) on a very small-scale simulation (relaxation of a GO sheet with 19 atoms, with respect to the gamma point). The calculation took 3m20s to run on 1 proc on my personal computer. On the cluster with 4 proc and default parallel options, it took 1m5s, and on 8 proc it took 44s. This seems like a reasonable behavior, and at least shows that raising the number of procs does reduce computation time in this case (with obvious limitations if too many procs for the job).<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>However I tried with another test, a bit bigger (test #2). This example is a scf calculation with 120 atoms (still with respect to the gamma point). In this case, the parallelization brings absolutely no improvement. In fact, although the <i>outfile</i> confirms that the code is running on N procs, it has similar performances as if it was running on 1 proc (sometimes even worse actually, but probably not in a significant manner, as the times are fluctuating a bit from 1 run to another)<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I tried to run this same input file on my personal computer both on 1 and 2 cores. Turns out that it takes 10376s to run 10 iterations on 1 core, while it takes 6777s on two cores, so it seems that the parallelization is doing ok on my computer.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I have tried to run with different number of cores on the hpc, and different parallelization options (like for instance –nb 4), but nothing seems to improve the time<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Basically, I am stuck with those 2 seemingly conflicting facts:<o:p></o:p></p><ul type=disc><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1'>Parallelization seems to have no particular problem on the hpc cluster because test #1 gives good results<o:p></o:p></li><li class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0 level1 lfo1'>Parallelization seems to have no particular problem with the particular input file #2 because it seems to scale reasonably with proc number on my individual computer<o:p></o:p></li></ul><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>However, combining both and running this file in parallel on the hpc cluster ends up not working correctly…<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I included below the input file and output file of test #2. I also included as well as the slurm script that I use to submit the calculation to the job manager, in case it helps (test2.scf.slurm.txt)<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Any suggestion on what is going wrong would be very welcome.<o:p></o:p></p><p>Julien<o:p></o:p></p><p><o:p> </o:p></p><p><b><span style='font-size:18.0pt'>----------------------------------test2.in---------------------------------------</span></b><o:p></o:p></p><p><o:p> </o:p></p><p style='margin-bottom:12.0pt'>&CONTROL<br> title = '# Quantum Espresso PWSCF output snapshot # 0'<br> pseudo_dir = '/lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/' ,<br> prefix='bonding_scf'<br> calculation = 'scf'<br> outdir='./outslurm'<br>/<br> <br>&SYSTEM<br> nat= 120<br> ntyp= 7<br> ibrav= 0<br> ecutwfc= 50, ecutrho=400,<br> occupations='smearing', smearing='mv', degauss=1.0d-3<br> assume_isolated='2D'<br>/<br> <br>&ELECTRONS<br> mixing_beta = 0.5<br> conv_thr = 1.0d-7<br> electron_maxstep=1<br>/<br> <br>&IONS<br>/<br> <br>&CELL<br>/<br> <br>ATOMIC_SPECIES<br>C 12.011 C.pbesol-n-kjpaw_psl.1.0.0.UPF<br>N 14.007 N.pbesol-n-kjpaw_psl.0.1.UPF<br>H 1.008 H.pbesol-kjpaw_psl.0.1.UPF<br>Pb 207.2 Pb.pbesol-dn-kjpaw_psl.1.0.0.UPF<br>I 126.9 I.pbesol-n-kjpaw_psl.1.0.0.UPF<br>O 15.999 O.pbesol-n-kjpaw_psl.1.0.0.UPF<br>Cl 35.450 Cl.pbesol-n-kjpaw_psl.1.0.0.UPF<br> <br> <br>CELL_PARAMETERS angstrom<br> 6.40743642 0.00000000 0.00000000<br> 0.00000000 12.53119000 0.00000000<br> 0.00000000 0.00000000 39.01263233<br> <br> <br>ATOMIC_POSITIONS angstrom<br>C 3.20373698 3.26295456 22.67510117<br>N 4.36830205 2.66824164 22.67510117<br>N 2.03914607 2.66824164 22.67510117<br>H 3.20373076 4.35970913 22.67510117<br>H 5.20200492 3.26227865 22.67510117<br>H 4.49794030 1.65118734 22.67510117<br>H 1.90952027 1.65118734 22.67510117<br>H 1.20545622 3.26227865 22.67510117<br>Pb 6.40746106 6.04808537 19.50631617<br>I 3.20373108 6.16571088 19.50631617<br>I 6.40746051 2.89948619 19.50631617<br>I 0.00000101 5.76270558 22.67510117<br>C 3.20373698 9.52854956 22.67510117<br>N 4.36830205 8.93383664 22.67510117<br>N 2.03914607 8.93383664 22.67510117<br>H 3.20373076 10.62530413 22.67510117<br>H 5.20200492 9.52787365 22.67510117<br>H 4.49794030 7.91678234 22.67510117<br>H 1.90952027 7.91678234 22.67510117<br>H 1.20545622 9.52787365 22.67510117<br>Pb 6.40746106 12.31368037 19.50631617<br>I 3.20373108 12.43130588 19.50631617<br>I 6.40746051 9.16508119 19.50631617<br>I 0.00000101 12.02830057 22.67510117<br>C 3.20373698 3.26295456 29.01264528<br>N 4.36830205 2.66824164 29.01264528<br>N 2.03914607 2.66824164 29.01264528<br>H 3.20373076 4.35970913 29.01264528<br>H 5.20200492 3.26227865 29.01264528<br>H 4.49794030 1.65118734 29.01264528<br>H 1.90952027 1.65118734 29.01264528<br>H 1.20545622 3.26227865 29.01264528<br>Pb 6.40746106 6.04808537 25.84386028<br>I 3.20373108 6.16571088 25.84386028<br>I 6.40746051 2.89948619 25.84386028<br>I 0.00000101 5.76270558 29.01264528<br>C 3.20373698 9.52854956 29.01264528<br>N 4.36830205 8.93383664 29.01264528<br>N 2.03914607 8.93383664 29.01264528<br>H 3.20373076 10.62530413 29.01264528<br>H 5.20200492 9.52787365 29.01264528<br>H 4.49794030 7.91678234 29.01264528<br>H 1.90952027 7.91678234 29.01264528<br>H 1.20545622 9.52787365 29.01264528<br>Pb 6.40746106 12.31368037 25.84386028<br>I 3.20373108 12.43130588 25.84386028<br>I 6.40746051 9.16508119 25.84386028<br>I 0.00000101 12.02830057 29.01264528<br>C 3.20373698 3.26295456 35.35018939<br>N 4.36830205 2.66824164 35.35018939<br>N 2.03914607 2.66824164 35.35018939<br>H 3.20373076 4.35970913 35.35018939<br>H 5.20200492 3.26227865 35.35018939<br>H 4.49794030 1.65118734 35.35018939<br>H 1.90952027 1.65118734 35.35018939<br>H 1.20545622 3.26227865 35.35018939<br>Pb 6.40746106 6.04808537 32.18140439<br>I 3.20373108 6.16571088 32.18140439<br>I 6.40746051 2.89948619 32.18140439<br>I 0.00000101 5.76270558 35.35018939<br>C 3.20373698 9.52854956 35.35018939<br>N 4.36830205 8.93383664 35.35018939<br>N 2.03914607 8.93383664 35.35018939<br>H 3.20373076 10.62530413 35.35018939<br>H 5.20200492 9.52787365 35.35018939<br>H 4.49794030 7.91678234 35.35018939<br>H 1.90952027 7.91678234 35.35018939<br>H 1.20545622 9.52787365 35.35018939<br>Pb 6.40746106 12.31368037 32.18140439<br>I 3.20373108 12.43130588 32.18140439<br>I 6.40746051 9.16508119 32.18140439<br>I 0.00000101 12.02830057 35.35018939<br>C -2.65922562 1.02746622 13.15267801<br>C -1.57082020 2.76789659 14.15213700<br>C -1.55249267 1.43382279 13.92545145<br>C -2.76678501 3.43396657 13.80880118<br>C -0.51572401 0.59007742 14.27042957<br>C 0.45127539 2.57771266 15.36479250<br>C 0.54032636 1.13871696 14.89500427<br>C -0.61858466 3.46111062 14.87552012<br>C 1.75850840 0.45260751 14.42517077<br>C 2.51877126 2.72823145 14.25997933<br>C 2.54527275 1.46853929 13.80948684<br>C 1.69149484 3.42061251 15.24764489<br>C -2.84434923 4.73311498 13.75015587<br>C -1.79251576 6.80155604 13.82062727<br>C -1.71556103 5.46156288 14.02089871<br>C -2.79591766 7.89012407 13.91075998<br>C -0.67171524 4.85078215 14.72657807<br>C 0.42299842 7.09269756 14.52980725<br>C 0.31418038 5.75006370 15.32008815<br>C -0.54822530 7.37927093 13.62065670<br>C 1.58501883 4.93901110 15.15192558<br>C 1.95672818 6.38683569 12.97082740<br>C 2.39800998 5.48893963 14.08928384<br>C 2.19010582 7.82391704 13.36789777<br>C -2.58931431 9.73216977 11.12323260<br>C -1.53736385 11.49261513 12.63531287<br>C -1.43991415 10.25590370 11.85590265<br>C -2.46212319 12.58463568 12.27360914<br>C -0.60003148 9.34961386 12.41523759<br>C 0.61521796 10.90977347 13.68739727<br>C 0.56702168 9.72454135 13.05961564<br>C -0.57311928 11.74387481 13.77090253<br>C 1.73778864 8.96596466 12.44952664<br>C 2.44039831 11.26999757 12.43362532<br>C 2.66220529 10.00525725 12.01318349<br>C 1.83430055 11.66382030 13.76046404<br>Cl -0.00001799 6.04797424 17.07363791<br>Cl 1.25165378 8.40223027 10.76754187<br>O -1.79125675 11.13196776 14.04477237<br>O 2.87346590 12.19705486 11.50562577<br>O 2.66595523 5.77705032 15.51329335<br>O 1.68196546 5.86106544 11.91469705<br>O 2.44111071 11.89613785 15.06748010<br>O 3.89019144 8.86144083 14.58391140<br>O -2.48663871 8.96018517 10.18744705<br>O -0.74483722 7.99628057 12.39035840<br>O 1.51084248 7.88917390 14.66305294<br>O 1.28942315 2.85893197 16.48674549<br> <br><br>K_POINTS gamma<o:p></o:p></p><p><o:p> </o:p></p><p><o:p> </o:p></p><p><b><span style='font-size:18.0pt'>-----------------------------------------------------test2.out--------------------------------------------</span></b><o:p></o:p></p><p><o:p> </o:p></p><p><br> Program PWSCF v.6.3 starts on 10Apr2019 at 15:35:34 <br><br> This program is part of the open-source Quantum ESPRESSO suite<br> for quantum simulation of materials; please cite<br> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);<br> "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);<br> URL <a href="http://www.quantum-espresso.org">http://www.quantum-espresso.org</a>", <br> in publications or presentations arising from this work. More details at<br> <a href="http://www.quantum-espresso.org/quote">http://www.quantum-espresso.org/quote</a><br><br> Parallel version (MPI), running on 8 processors<br><br> MPI processes distributed on 1 nodes<br> R & G space division: proc/nbgrp/npool/nimage = 8<br> Reading input from /lustre/home/acct-mseyxd/mseyxd/QE/GO-Cl/FAPBI3_bonding/scf/1x2x3_matching/bonding.scf.in<br>Warning: card &IONS ignored<br>Warning: card / ignored<br>Warning: card &CELL ignored<br>Warning: card / ignored<br><br> Current dimensions of program PWSCF are:<br> Max number of different atomic species (ntypx) = 10<br> Max number of k-points (npk) = 40000<br> Max angular momentum in pseudopotentials (lmaxx) = 3<br> file C.pbesol-n-kjpaw_psl.1.0.0.UPF: wavefunction(s) 2S 2P renormalized<br> file N.pbesol-n-kjpaw_psl.0.1.UPF: wavefunction(s) 2P renormalized<br> file H.pbesol-kjpaw_psl.0.1.UPF: wavefunction(s) 1S renormalized<br> file Pb.pbesol-dn-kjpaw_psl.1.0.0.UPF: wavefunction(s) 6S 6P 5D renormalized<br> file I.pbesol-n-kjpaw_psl.1.0.0.UPF: wavefunction(s) 5S renormalized<br> file O.pbesol-n-kjpaw_psl.1.0.0.UPF: wavefunction(s) 2S 2P renormalized<br> file Cl.pbesol-n-kjpaw_psl.1.0.0.UPF: wavefunction(s) 3S 3P renormalized<br><br> gamma-point specific algorithms are used<br><br> Subspace diagonalization in iterative solution of the eigenvalue problem:<br> a serial algorithm will be used<br><br><br> Parallelization info<br> --------------------<br> sticks: dense smooth PW G-vecs: dense smooth PW<br> Min 1140 570 141 356988 126222 15758<br> Max 1142 572 142 357012 126236 15798<br> Sum 9123 4565 1135 2856023 1009807 126259<br><br><br> Title: <br> # Quantum Espresso PWSCF output snapshot # 0 <br><br><br> bravais-lattice index = 0<br> lattice parameter (alat) = 12.1083 a.u.<br> unit-cell volume = 21138.7101 (a.u.)^3<br> number of atoms/cell = 120<br> number of atomic types = 7<br> number of electrons = 542.00<br> number of Kohn-Sham states= 325<br> kinetic-energy cutoff = 50.0000 Ry<br> charge density cutoff = 400.0000 Ry<br> convergence threshold = 1.0E-07<br> mixing beta = 0.5000<br> number of iterations used = 8 plain mixing<br> Exchange-correlation = SLA PW PSX PSC ( 1 4 10 8 0 0)<br><br> celldm(1)= 12.108300 celldm(2)= 0.000000 celldm(3)= 0.000000<br> celldm(4)= 0.000000 celldm(5)= 0.000000 celldm(6)= 0.000000<br><br> crystal axes: (cart. coord. in units of alat)<br> a(1) = ( 1.000000 0.000000 0.000000 ) <br> a(2) = ( 0.000000 1.955726 0.000000 ) <br> a(3) = ( 0.000000 0.000000 6.088649 ) <br><br> reciprocal axes: (cart. coord. in units 2 pi/alat)<br> b(1) = ( 1.000000 0.000000 0.000000 ) <br> b(2) = ( 0.000000 0.511319 0.000000 ) <br> b(3) = ( 0.000000 0.000000 0.164240 ) <br><br><br> PseudoPot. # 1 for C read from file:<br> /lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/C.pbesol-n-kjpaw_psl.1.0.0.UPF<br> MD5 check sum: f9b2fe17d1f478429498b05d17159f9e<br> Pseudo is Projector augmented-wave + core cor, Zval = 4.0<br> Generated using "atomic" code by A. Dal Corso v.6.3<br> Shape of augmentation charge: PSQ<br> Using radial grid of 1073 points, 4 beta functions with: <br> l(1) = 0<br> l(2) = 0<br> l(3) = 1<br> l(4) = 1<br> Q(r) pseudized with 0 coefficients <br><br><br> PseudoPot. # 2 for N read from file:<br> /lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/N.pbesol-n-kjpaw_psl.0.1.UPF<br> MD5 check sum: 15bd223d5d75e9eda893d0f4e6bdad1b<br> Pseudo is Projector augmented-wave + core cor, Zval = 5.0<br> Generated using "atomic" code by A. Dal Corso v.6.3<br> Shape of augmentation charge: PSQ<br> Using radial grid of 1085 points, 4 beta functions with: <br> l(1) = 0<br> l(2) = 0<br> l(3) = 1<br> l(4) = 1<br> Q(r) pseudized with 0 coefficients <br><br><br> PseudoPot. # 3 for H read from file:<br> /lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/H.pbesol-kjpaw_psl.0.1.UPF<br> MD5 check sum: 27a6b98f1514c59d399e798f1258b8b7<br> Pseudo is Projector augmented-wave, Zval = 1.0<br> Generated using "atomic" code by A. Dal Corso v.5.0.2 svn rev. 9415<br> Shape of augmentation charge: PSQ<br> Using radial grid of 929 points, 2 beta functions with: <br> l(1) = 0<br> l(2) = 0<br> Q(r) pseudized with 0 coefficients <br><br><br> PseudoPot. # 4 for Pb read from file:<br> /lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/Pb.pbesol-dn-kjpaw_psl.1.0.0.UPF<br> MD5 check sum: 56da3be0db09ba43f309b470f7bff7d1<br> Pseudo is Projector augmented-wave + core cor, Zval = 14.0<br> Generated using "atomic" code by A. Dal Corso v.6.3<br> Shape of augmentation charge: PSQ<br> Using radial grid of 1281 points, 6 beta functions with: <br> l(1) = 0<br> l(2) = 0<br> l(3) = 1<br> l(4) = 1<br> l(5) = 2<br> l(6) = 2<br> Q(r) pseudized with 0 coefficients <br><br><br> PseudoPot. # 5 for I read from file:<br> /lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/I.pbesol-n-kjpaw_psl.1.0.0.UPF<br> MD5 check sum: 6038403ff9b03366b27f71806436e734<br> Pseudo is Projector augmented-wave + core cor, Zval = 7.0<br> Generated using "atomic" code by A. Dal Corso v.6.3<br> Shape of augmentation charge: PSQ<br> Using radial grid of 1247 points, 6 beta functions with: <br> l(1) = 0<br> l(2) = 0<br> l(3) = 1<br> l(4) = 1<br> l(5) = 2<br> l(6) = 2<br> Q(r) pseudized with 0 coefficients <br><br><br> PseudoPot. # 6 for O read from file:<br> /lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/O.pbesol-n-kjpaw_psl.1.0.0.UPF<br> MD5 check sum: cb766521a97cf798d01896eaf7ac9a0a<br> Pseudo is Projector augmented-wave + core cor, Zval = 6.0<br> Generated using "atomic" code by A. Dal Corso v.6.3<br> Shape of augmentation charge: PSQ<br> Using radial grid of 1095 points, 4 beta functions with: <br> l(1) = 0<br> l(2) = 0<br> l(3) = 1<br> l(4) = 1<br> Q(r) pseudized with 0 coefficients <br><br><br> PseudoPot. # 7 for Cl read from file:<br> /lustre/home/acct-mseyxd/mseyxd/QE/qe-6.3/pseudo/Cl.pbesol-n-kjpaw_psl.1.0.0.UPF<br> MD5 check sum: 939a64fc035742408689cdf8470f8314<br> Pseudo is Projector augmented-wave + core cor, Zval = 7.0<br> Generated using "atomic" code by A. Dal Corso v.6.3<br> Shape of augmentation charge: PSQ<br> Using radial grid of 1157 points, 6 beta functions with: <br> l(1) = 0<br> l(2) = 0<br> l(3) = 1<br> l(4) = 1<br> l(5) = 2<br> l(6) = 2<br> Q(r) pseudized with 0 coefficients <br><br><br> atomic species valence mass pseudopotential<br> C 4.00 12.01100 C ( 1.00)<br> N 5.00 14.00700 N ( 1.00)<br> H 1.00 1.00800 H ( 1.00)<br> Pb 14.00 207.20000 Pb( 1.00)<br> I 7.00 126.90000 I ( 1.00)<br> O 6.00 15.99900 O ( 1.00)<br> Cl 7.00 35.45000 Cl( 1.00)<br><br> No symmetry found<br><br><br><br> Cartesian axes<br><br> site n. atom positions (alat units)<br> 1 C tau( 1) = ( 0.5000029 0.5092449 3.5388726 )<br> 2 N tau( 2) = ( 0.6817550 0.4164289 3.5388726 )<br> 3 N tau( 3) = ( 0.3182468 0.4164289 3.5388726 )<br> 4 H tau( 4) = ( 0.5000020 0.6804140 3.5388726 )<br> 5 H tau( 5) = ( 0.8118699 0.5091394 3.5388726 )<br> 6 H tau( 6) = ( 0.7019875 0.2576986 3.5388726 )<br> 7 H tau( 7) = ( 0.2980163 0.2576986 3.5388726 )<br> 8 H tau( 8) = ( 0.1881339 0.5091394 3.5388726 )<br> 9 Pb tau( 9) = ( 1.0000038 0.9439166 3.0443246 )<br> 10 I tau( 10) = ( 0.5000020 0.9622742 3.0443246 )<br> 11 I tau( 11) = ( 1.0000038 0.4525189 3.0443246 )<br> 12 I tau( 12) = ( 0.0000002 0.8993777 3.5388726 )<br> 13 C tau( 13) = ( 0.5000029 1.4871079 3.5388726 )<br> 14 N tau( 14) = ( 0.6817550 1.3942919 3.5388726 )<br> 15 N tau( 15) = ( 0.3182468 1.3942919 3.5388726 )<br> 16 H tau( 16) = ( 0.5000020 1.6582770 3.5388726 )<br> 17 H tau( 17) = ( 0.8118699 1.4870024 3.5388726 )<br> 18 H tau( 18) = ( 0.7019875 1.2355616 3.5388726 )<br> 19 H tau( 19) = ( 0.2980163 1.2355616 3.5388726 )<br> 20 H tau( 20) = ( 0.1881339 1.4870024 3.5388726 )<br> 21 Pb tau( 21) = ( 1.0000038 1.9217796 3.0443246 )<br> 22 I tau( 22) = ( 0.5000020 1.9401372 3.0443246 )<br> 23 I tau( 23) = ( 1.0000038 1.4303819 3.0443246 )<br> 24 I tau( 24) = ( 0.0000002 1.8772407 3.5388726 )<br> 25 C tau( 25) = ( 0.5000029 0.5092449 4.5279646 )<br> 26 N tau( 26) = ( 0.6817550 0.4164289 4.5279646 )<br> 27 N tau( 27) = ( 0.3182468 0.4164289 4.5279646 )<br> 28 H tau( 28) = ( 0.5000020 0.6804140 4.5279646 )<br> 29 H tau( 29) = ( 0.8118699 0.5091394 4.5279646 )<br> 30 H tau( 30) = ( 0.7019875 0.2576986 4.5279646 )<br> 31 H tau( 31) = ( 0.2980163 0.2576986 4.5279646 )<br> 32 H tau( 32) = ( 0.1881339 0.5091394 4.5279646 )<br> 33 Pb tau( 33) = ( 1.0000038 0.9439166 4.0334166 )<br> 34 I tau( 34) = ( 0.5000020 0.9622742 4.0334166 )<br> 35 I tau( 35) = ( 1.0000038 0.4525189 4.0334166 )<br> 36 I tau( 36) = ( 0.0000002 0.8993777 4.5279646 )<br> 37 C tau( 37) = ( 0.5000029 1.4871079 4.5279646 )<br> 38 N tau( 38) = ( 0.6817550 1.3942919 4.5279646 )<br> 39 N tau( 39) = ( 0.3182468 1.3942919 4.5279646 )<br> 40 H tau( 40) = ( 0.5000020 1.6582770 4.5279646 )<br> 41 H tau( 41) = ( 0.8118699 1.4870024 4.5279646 )<br> 42 H tau( 42) = ( 0.7019875 1.2355616 4.5279646 )<br> 43 H tau( 43) = ( 0.2980163 1.2355616 4.5279646 )<br> 44 H tau( 44) = ( 0.1881339 1.4870024 4.5279646 )<br> 45 Pb tau( 45) = ( 1.0000038 1.9217796 4.0334166 )<br> 46 I tau( 46) = ( 0.5000020 1.9401372 4.0334166 )<br> 47 I tau( 47) = ( 1.0000038 1.4303819 4.0334166 )<br> 48 I tau( 48) = ( 0.0000002 1.8772407 4.5279646 )<br> 49 C tau( 49) = ( 0.5000029 0.5092449 5.5170566 )<br> 50 N tau( 50) = ( 0.6817550 0.4164289 5.5170566 )<br> 51 N tau( 51) = ( 0.3182468 0.4164289 5.5170566 )<br> 52 H tau( 52) = ( 0.5000020 0.6804140 5.5170566 )<br> 53 H tau( 53) = ( 0.8118699 0.5091394 5.5170566 )<br> 54 H tau( 54) = ( 0.7019875 0.2576986 5.5170566 )<br> 55 H tau( 55) = ( 0.2980163 0.2576986 5.5170566 )<br> 56 H tau( 56) = ( 0.1881339 0.5091394 5.5170566 )<br> 57 Pb tau( 57) = ( 1.0000038 0.9439166 5.0225086 )<br> 58 I tau( 58) = ( 0.5000020 0.9622742 5.0225086 )<br> 59 I tau( 59) = ( 1.0000038 0.4525189 5.0225086 )<br> 60 I tau( 60) = ( 0.0000002 0.8993777 5.5170566 )<br> 61 C tau( 61) = ( 0.5000029 1.4871079 5.5170566 )<br> 62 N tau( 62) = ( 0.6817550 1.3942919 5.5170566 )<br> 63 N tau( 63) = ( 0.3182468 1.3942919 5.5170566 )<br> 64 H tau( 64) = ( 0.5000020 1.6582770 5.5170566 )<br> 65 H tau( 65) = ( 0.8118699 1.4870024 5.5170566 )<br> 66 H tau( 66) = ( 0.7019875 1.2355616 5.5170566 )<br> 67 H tau( 67) = ( 0.2980163 1.2355616 5.5170566 )<br> 68 H tau( 68) = ( 0.1881339 1.4870024 5.5170566 )<br> 69 Pb tau( 69) = ( 1.0000038 1.9217796 5.0225086 )<br> 70 I tau( 70) = ( 0.5000020 1.9401372 5.0225086 )<br> 71 I tau( 71) = ( 1.0000038 1.4303819 5.0225086 )<br> 72 I tau( 72) = ( 0.0000002 1.8772407 5.5170566 )<br> 73 C tau( 73) = ( -0.4150218 0.1603553 2.0527208 )<br> 74 C tau( 74) = ( -0.2451558 0.4319819 2.2087050 )<br> 75 C tau( 75) = ( -0.2422954 0.2237748 2.1733265 )<br> 76 C tau( 76) = ( -0.4318084 0.5359346 2.1551211 )<br> 77 C tau( 77) = ( -0.0804884 0.0920926 2.2271668 )<br> 78 C tau( 78) = ( 0.0704299 0.4023002 2.3979625 )<br> 79 C tau( 79) = ( 0.0843280 0.1777180 2.3246433 )<br> 80 C tau( 80) = ( -0.0965417 0.5401709 2.3216025 )<br> 81 C tau( 81) = ( 0.2744480 0.0706378 2.2513170 )<br> 82 C tau( 82) = ( 0.3931012 0.4257914 2.2255358 )<br> 83 C tau( 83) = ( 0.3972373 0.2291930 2.1552281 )<br> 84 C tau( 84) = ( 0.2639893 0.5338504 2.3796795 )<br> 85 C tau( 85) = ( -0.4439138 0.7386909 2.1459684 )<br> 86 C tau( 86) = ( -0.2797555 1.0615097 2.1569667 )<br> 87 C tau( 87) = ( -0.2677453 0.8523788 2.1882228 )<br> 88 C tau( 88) = ( -0.4363551 1.2314011 2.1710336 )<br> 89 C tau( 89) = ( -0.1048337 0.7570551 2.2983573 )<br> 90 C tau( 90) = ( 0.0660168 1.1069478 2.2676475 )<br> 91 C tau( 91) = ( 0.0490337 0.8974047 2.3909856 )<br> 92 C tau( 92) = ( -0.0855608 1.1516729 2.1257576 )<br> 93 C tau( 93) = ( 0.2473718 0.7708248 2.3647407 )<br> 94 C tau( 94) = ( 0.3053839 0.9967849 2.0243396 )<br> 95 C tau( 95) = ( 0.3742542 0.8566514 2.1988956 )<br> 96 C tau( 96) = ( 0.3418069 1.2210682 2.0863099 )<br> 97 C tau( 97) = ( -0.4041108 1.5188867 1.7359880 )<br> 98 C tau( 98) = ( -0.2399343 1.7936370 1.9719763 )<br> 99 C tau( 99) = ( -0.2247255 1.6006251 1.8503348 )<br> 100 C tau( 100) = ( -0.3842603 1.9640672 1.9155257 )<br> 101 C tau( 101) = ( -0.0936461 1.4591817 1.9376295 )<br> 102 C tau( 102) = ( 0.0960162 1.7026737 2.1361737 )<br> 103 C tau( 103) = ( 0.0884943 1.5176961 2.0381967 )<br> 104 C tau( 104) = ( -0.0894460 1.8328508 2.1492063 )<br> 105 C tau( 105) = ( 0.2712143 1.3993061 1.9429809 )<br> 106 C tau( 106) = ( 0.3808697 1.7588934 1.9404992 )<br> 107 C tau( 107) = ( 0.4154868 1.5615071 1.8748814 )<br> 108 C tau( 108) = ( 0.2862768 1.8203568 2.1475771 )<br> 109 Cl tau( 109) = ( -0.0000028 0.9438992 2.6646597 )<br> 110 Cl tau( 110) = ( 0.1953439 1.3113248 1.6804758 )<br> 111 O tau( 111) = ( -0.2795590 1.7373513 2.1919488 )<br> 112 O tau( 112) = ( 0.4484580 1.9035780 1.7956676 )<br> 113 O tau( 113) = ( 0.4160721 0.9016165 2.4211389 )<br> 114 O tau( 114) = ( 0.2625021 0.9147286 1.8595108 )<br> 115 O tau( 115) = ( 0.3809809 1.8566143 2.3515614 )<br> 116 O tau( 116) = ( 0.6071370 1.3829932 2.2760915 )<br> 117 O tau( 117) = ( -0.3880864 1.3984041 1.5899412 )<br> 118 O tau( 118) = ( -0.1162457 1.2479688 1.9337466 )<br> 119 O tau( 119) = ( 0.2357952 1.2312528 2.2884430 )<br> 120 O tau( 120) = ( 0.2012385 0.4461897 2.5730642 )<br><br> number of k points= 1 Marzari-Vanderbilt smearing, width (Ry)= 0.0010<br> cart. coord. in units 2pi/alat<br> k( 1) = ( 0.0000000 0.0000000 0.0000000), wk = 2.0000000<br><br> Dense grid: 1428012 G-vectors FFT dimensions: ( 80, 160, 480)<br><br> Smooth grid: 504904 G-vectors FFT dimensions: ( 60, 108, 360)<br><br> Estimated max dynamical RAM per process > 965.66 MB<br><br> Estimated total dynamical RAM > 7.54 GB<br> ----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D<br> The code is running with the 2D cutoff<br> Please refer to:<br> Sohier, T., Calandra, M., & Mauri, F. (2017), <br> Density functional perturbation theory for gated two-dimensional heterostructures:<br> Theoretical developments and application to flexural phonons in graphene.<br> Physical Review B, 96(7), 75448. <a href="https://doi.org/10.1103/PhysRevB.96.075448">https://doi.org/10.1103/PhysRevB.96.075448</a><br> ----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D----2D<br><br> Check: negative/imaginary core charge= -0.000002 0.000000<br><br> Initial potential from superposition of free atoms<br> Check: negative starting charge= -0.001132<br><br> starting charge 541.98383, renormalised to 542.00000<br><br> negative rho (up, down): 1.132E-03 0.000E+00<br> Starting wfcs are 420 randomized atomic wfcs<br> Checking if some PAW data can be deallocated... <br><br> total cpu time spent up to now is 125.6 secs<br><br> Self-consistent Calculation<br><br> iteration # 1 ecut= 50.00 Ry beta= 0.50<br> Davidson diagonalization with overlap<br> c_bands: 3 eigenvalues not converged<br> ethr = 1.00E-02, avg # of iterations = 40.0<br><br> negative rho (up, down): 1.031E-05 0.000E+00<br><br> total cpu time spent up to now is 2094.5 secs<br><br> total energy = 82142.85683667 Ry<br> Harris-Foulkes estimate = -53335.51769720 Ry<br> estimated scf accuracy < 111068.31785845 Ry<br><br> End of self-consistent calculation<br><br> convergence NOT achieved after 1 iterations: stopping<br><br> Writing output data file bonding_scf.save/<br><br> init_run : 119.18s CPU 120.33s WALL ( 1 calls)<br> electrons : 1961.71s CPU 1969.12s WALL ( 1 calls)<br><br> Called by init_run:<br> wfcinit : 52.26s CPU 52.44s WALL ( 1 calls)<br> potinit : 19.26s CPU 19.33s WALL ( 1 calls)<br> hinit0 : 36.63s CPU 36.68s WALL ( 1 calls)<br><br> Called by electrons:<br> c_bands : 1919.78s CPU 1923.97s WALL ( 1 calls)<br> sum_band : 28.22s CPU 30.08s WALL ( 1 calls)<br> v_of_rho : 2.26s CPU 2.35s WALL ( 2 calls)<br> newd : 20.58s CPU 22.50s WALL ( 2 calls)<br> PAW_pot : 4.00s CPU 4.00s WALL ( 2 calls)<br> mix_rho : 0.23s CPU 0.24s WALL ( 1 calls)<br><br> Called by c_bands:<br> init_us_2 : 0.22s CPU 0.27s WALL ( 3 calls)<br> regterg : 1919.41s CPU 1923.60s WALL ( 2 calls)<br><br> Called by sum_band:<br> sum_band:bec : 0.00s CPU 0.00s WALL ( 1 calls)<br> addusdens : 16.57s CPU 17.94s WALL ( 1 calls)<br><br> Called by *egterg:<br> h_psi : 680.38s CPU 682.69s WALL ( 43 calls)<br> s_psi : 259.57s CPU 259.75s WALL ( 43 calls)<br> g_psi : 0.93s CPU 0.94s WALL ( 40 calls)<br> rdiaghg : 52.76s CPU 52.86s WALL ( 41 calls)<br><br> Called by h_psi:<br> h_psi:pot : 679.62s CPU 681.90s WALL ( 43 calls)<br> h_psi:calbec : 255.27s CPU 255.54s WALL ( 43 calls)<br> vloc_psi : 164.42s CPU 166.01s WALL ( 43 calls)<br> add_vuspsi : 259.93s CPU 260.35s WALL ( 43 calls)<br><br> General routines<br> calbec : 263.20s CPU 263.88s WALL ( 44 calls)<br> fft : 2.33s CPU 2.43s WALL ( 23 calls)<br> ffts : 0.09s CPU 0.09s WALL ( 3 calls)<br> fftw : 128.50s CPU 130.07s WALL ( 10237 calls)<br> interpolate : 0.25s CPU 0.26s WALL ( 2 calls)<br> davcio : 0.00s CPU 0.10s WALL ( 3 calls)<br><br> Parallel routines<br> fft_scatt_xy : 23.50s CPU 23.55s WALL ( 10263 calls)<br> fft_scatt_yz : 10.98s CPU 12.22s WALL ( 10263 calls)<br><br> PWSCF : 34m45.53s CPU 34m55.12s WALL<br><br><br> This run was terminated on: 16:10:30 10Apr2019 <br><br>=------------------------------------------------------------------------------=<br> JOB DONE.<br>=------------------------------------------------------------------------------=<o:p></o:p></p><p><o:p> </o:p></p><p><o:p> </o:p></p><p><o:p> </o:p></p><p><o:p> </o:p></p><p><o:p> </o:p></p><p><b><span style='font-size:13.5pt'>-----------------------------------------------------SLURM command-------------------------------------</span></b><o:p></o:p></p><p><o:p> </o:p></p><p style='margin-bottom:12.0pt'>#!/bin/bash<br><br>#SBATCH --job-name=QE_GO-Cl_bonding_scf<br>#SBATCH --partition=cpu<br>#SBATCH --mail-type=end<br>#SBATCH <a href="mailto:--mail-user=julien_barbaud@sjtu.edu.cn">--mail-user=julien_barbaud@sjtu.edu.cn</a><br>#SBATCH --output=bonding.scf.slurm.out<br>#SBATCH --error=bonding.scf.slurm.err<br>#SBATCH -p cpu<br>#SBATCH -n 8 <br>#SBATCH --ntasks-per-node=8<br><br>ulimit -l unlimited<br>ulimit -s unlimited<br><br>INPUT=$HOME/QE/GO-Cl/FAPBI3_bonding/scf/1x2x3_matching/bonding.scf.in<br>EXEC=$HOME/QE/qe-6.3/bin/pw.x<br><br>srun --mpi=pmi2 $EXEC -in $INPUT <o:p></o:p></p><p class=MsoNormal><br><br><o:p></o:p></p><pre>_______________________________________________<o:p></o:p></pre><pre>users mailing list<o:p></o:p></pre><pre><a href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><o:p></o:p></pre><pre><a href="https://lists.quantum-espresso.org/mailman/listinfo/users">https://lists.quantum-espresso.org/mailman/listinfo/users</a><o:p></o:p></pre></blockquote><p class=MsoNormal><br><br><o:p></o:p></p><pre>-- <o:p></o:p></pre><pre>Dr. rer. nat. Thomas Brumme<o:p></o:p></pre><pre>Wilhelm-Ostwald-Institute for Physical and Theoretical Chemistry<o:p></o:p></pre><pre>Leipzig University<o:p></o:p></pre><pre>Phillipp-Rosenthal-Strasse 31<o:p></o:p></pre><pre>04103 Leipzig<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>Tel: +49 (0)341 97 36456<o:p></o:p></pre><pre><o:p> </o:p></pre><pre>email: <a href="mailto:thomas.brumme@uni-leipzig.de">thomas.brumme@uni-leipzig.de</a><o:p></o:p></pre></div></body></html>