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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">I changed the ppn down to 1 and restart the last part. It's successful and finished just in a few seconds. Thank you very much!<br>
<br>
Xu Huang<br>
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<div style="direction: ltr;" id="divRpF852036"><font face="Tahoma" size="2" color="#000000"><b>From:</b> pw_forum-bounces@pwscf.org [pw_forum-bounces@pwscf.org] on behalf of Giovanni Cantele [giovanni.cantele@spin.cnr.it]<br>
<b>Sent:</b> Wednesday, September 23, 2015 2:45 AM<br>
<b>To:</b> PWSCF Forum<br>
<b>Subject:</b> Re: [Pw_forum] Problem in average.x<br>
</font><br>
</div>
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<div>Try to relaunch it on just one processor, usually it is very fast and it does not require parallelization.
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<div class="">Giovanni</div>
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<blockquote type="cite" class="">
<div class="">On 23 Sep 2015, at 00:06, Huang, Xu <<a href="mailto:xu-huang@uiowa.edu" class="" target="_blank">xu-huang@uiowa.edu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="" 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; direction:ltr; font-family:Tahoma; font-size:10pt">
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="" target="_blank">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="" target="_blank">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>
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</blockquote>
</div>
<br class="">
<div class="">-- <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="" target="_blank">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="" target="_blank">
http://www.researcherid.com/rid/A-1951-2009</a><br class="">
Web page: <a href="http://people.na.infn.it/~cantele" class="" target="_blank">http://people.na.infn.it/~cantele</a><br class="">
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