<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Try to relaunch it on just one processor, usually it is very fast and it does not require parallelization.<div class=""><br class=""></div><div class="">Giovanni</div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 23 Sep 2015, at 00:06, Huang, Xu <<a href="mailto:xu-huang@uiowa.edu" class="">xu-huang@uiowa.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; direction: ltr; font-family: Tahoma; font-size: 10pt;" class="">Dear all,<br class=""><br class="">I'm using QE to plot the layer-averaged potential for hematite (Fe2O3) surface slabs. I did scf (pw.x) first, then got the potential (pp.x), and finally tried to make layer-averaged potential (average.x) along surface normal. The first 2 steps were successful and finished in ~10 minutes. But in the last step, the output file of average.x just stopped at the beginning for several days without any new update like this:<br class="">----------------------<br class=""> Program AVERAGE v.5.1.1 starts on 20Sep2015 at 16:58:27<span class="Apple-converted-space"> </span><br class=""><br class=""> This program is part of the open-source Quantum ESPRESSO suite<br class=""> for quantum simulation of materials; please cite<br class=""> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);<br class=""> URL<span class="Apple-converted-space"> </span><a href="http://www.quantum-espresso.org/" class="">http://www.quantum-espresso.org</a>",<span class="Apple-converted-space"> </span><br class=""> in publications or presentations arising from this work. More details at<br class=""> <span class="Apple-converted-space"> </span><a href="http://www.quantum-espresso.org/quote" class="">http://www.quantum-espresso.org/quote</a><br class=""><br class=""> Parallel version (MPI), running on 16 processors<br class=""> R & G space division: proc/nbgrp/npool/nimage = 16<br class=""> Reading header from file Fe2O3.potential<br class=""><br class=""> Info: using nr1, nr2, nr3 values from input<br class=""><br class=""> Info: using nr1s, nr2s, nr3s values from input<br class="">----------------------<br class=""><br class="">And currently the all the files in the working directory are:<br class=""> 2779 Sep 20 16:48 QEneonscript_pot_avg<br class=""> 2 Sep 20 16:49 results<br class=""> 2150 Sep 20 16:49 Fe2O3.scf.in<br class=""> 19 Sep 20 16:58 temp<br class=""> 127237 Sep 20 16:58 Fe2O3.scf.out<br class=""> 138 Sep 20 16:58 Fe2O3.pp.in<br class=""> 16051771 Sep 20 16:58 Fe2O3.potential<br class=""> 2263 Sep 20 16:58 Fe2O3.pp.out<br class=""> 39 Sep 20 16:58 Fe2O3.avg.in<br class=""> 696 Sep 20 16:59 Fe2O3.avg.out<br class=""><br class="">I'm very confused about it. I don't know if I missed anything in the script for the last step. Here I added the entire run script (QEneonscript_pot_avg) of this calculation with all 3 steps below. Thank you very much for helping me with this!<br class=""><br class="">Regards,<br class="">Xu Huang<br class=""><br class="">Below is the QEneonscript_pot_avg file:<br class="">-----------------------------------------------------------<br class="">#!/bin/bash<br class="">#$ -S /bin/bash<br class="">#$ -N uhv_pot<br class="">#$ -cwd<br class="">#$ -q UI<br class="">#$ -l std_mem<br class="">#$ -pe 16cpn 16<br class=""><br class="">module load espresso/5.1.1<br class="">BIN_DIR=/opt/quantum-espresso/5.1.1/<br class=""><br class="">temp=$PWD/temp<br class="">mkdir -p $temp<br class=""><br class="">results=$PWD/results<br class="">mkdir -p $results<br class=""><br class="">cat > Fe2O3.scf.in <<EOF<br class="">&CONTROL<br class=""> calculation = 'scf',<br class=""> pseudo_dir = '/Users/xhuang3/pwf/',<br class=""> outdir='$temp/',<br class=""> prefix = 'Fe2O3',<br class="">/<br class="">&SYSTEM<br class=""> ibrav = 4,<br class=""> celldm(1) = 9.536271655,<br class=""> celldm(3) = 6.000000000,<br class=""> nat = 30,<br class=""> ntyp = 3,<br class=""> ecutwfc = 35,<br class=""> ecutrho = 280,<br class=""> occupations = 'smearing',<br class=""> smearing = 'mp',<br class=""> degauss = 0.02,<br class=""> nspin = 2,<br class=""> starting_magnetization(1) = 0.5,<br class=""> starting_magnetization(2) = -0.5,<br class="">/<br class="">&ELECTRONS<br class=""> mixing_beta = 0.4,<br class=""> conv_thr = 1.0d-6,<br class="">/<br class="">ATOMIC_SPECIES<br class=""> Fe1 1.0 Fe.pbe-nd-rrkjus.UPF<br class=""> Fe2 1.0 Fe.pbe-nd-rrkjus.UPF<br class=""> O 1.0 O.pbe-rrkjus.UPF<br class="">ATOMIC_POSITIONS {crystal}<br class="">Fe1 0.333333330 0.333333330 0.019799034<br class="">Fe2 0.666666670 0.000000000 0.060629428<br class="">Fe2 0.000000000 0.666666670 0.075292861<br class="">Fe1 0.333333330 0.333333330 0.135189943<br class="">Fe1 0.666666670 0.000000000 0.155817104<br class="">Fe2 0.000000000 0.666666670 0.210485936<br class="">Fe2 0.333333330 0.333333330 0.232350369<br class="">Fe1 0.666666670 0.000000000 0.287045648<br class="">Fe1 0.000000000 0.666666670 0.307656149<br class="">Fe2 0.333333330 0.333333330 0.367558597<br class="">Fe2 0.666666670 0.000000000 0.382170005<br class="">Fe1 0.000000000 0.666666670 0.423088504<br class="">O -0.008926107 -0.020983988 0.031308650<br class="">O 0.321275458 0.675592765 0.031308650<br class="">O 0.687650647 0.345391225 0.031308650<br class="">O -0.021172740 0.313345511 0.106625540<br class="">O 0.667851616 0.687839421 0.106625540<br class="">O 0.353321125 -0.001184934 0.106625540<br class="">O 0.024534827 0.024970890 0.183306362<br class="">O 0.333769369 0.642131830 0.183306362<br class="">O 0.641695804 0.332897279 0.183306362<br class="">O -0.000469120 0.357826954 0.259526509<br class="">O 0.691629403 0.667135802 0.259526509<br class="">O 0.308839717 -0.024962756 0.259526509<br class="">O -0.019998485 0.001310105 0.336192461<br class="">O 0.354641930 0.686665178 0.336192461<br class="">O 0.665356554 0.312024717 0.336192461<br class="">O 0.012004812 0.324454789 0.411508891<br class="">O 0.645783306 0.654661835 0.411508891<br class="">O 0.342211883 0.020883376 0.411508891<br class="">K_POINTS (automatic)<br class=""> 4 4 1 1 1 1<br class="">EOF<br class=""><br class="">mpirun -n 16 $BIN_DIR/pw.x < Fe2O3.scf.in > Fe2O3.scf.out<br class=""><br class="">cat > Fe2O3.pp.in <<EOF<br class="">&inputpp<br class=""> prefix = 'Fe2O3'<br class=""> outdir='$temp/',<br class=""> filplot = 'Fe2O3.potential'<br class=""> plot_num = 1<br class="">/<br class="">EOF<br class=""><br class="">mpirun -n 16 $BIN_DIR/pp.x < Fe2O3.pp.in > Fe2O3.pp.out<br class=""><br class="">### average calculation<br class="">cat > Fe2O3.avg.in <<EOF<br class="">1<br class="">Fe2O3.potential<br class="">1.0d0<br class="">480<br class="">3<br class="">4.000000<br class="">EOF<br class=""><br class="">mpirun -n 16 $BIN_DIR/average.x < Fe2O3.avg.in > Fe2O3.avg.out<br class=""><br class="">mv Fe2O3.* $results/<br class=""><br class=""></div><span style="font-family: Helvetica; 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-- <br class=""><br class="">Giovanni Cantele, PhD<br class="">CNR-SPIN<br class="">c/o Dipartimento di Fisica<br class="">Universita' di Napoli "Federico II"<br class="">Complesso Universitario M. S. Angelo - Ed. 6<br class="">Via Cintia, I-80126, Napoli, Italy<br class="">e-mail: <a href="mailto:giovanni.cantele@spin.cnr.it" class="">giovanni.cantele@spin.cnr.it</a><br class="">Phone: +39 081 676910<br class="">Skype contact: giocan74<br class=""><br class="">ResearcherID: <a href="http://www.researcherid.com/rid/A-1951-2009" class="">http://www.researcherid.com/rid/A-1951-2009</a><br class="">Web page: <a href="http://people.na.infn.it/~cantele" class="">http://people.na.infn.it/~cantele</a><br class="">
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