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<p>Dear Guido,</p>
<p>I think I found out some issues with molecularpdos.x.</p>
<p>I recompile molecularpdos.x for both v5.3.0 and v5.4.0 in a
serial configuration.</p>
<p>v5.3.0 input:</p>
<p><a class="moz-txt-link-abbreviated" href="mailto:rolly@rolly-MacBook:~/QE-530/espresso-5.3.0/bin$">rolly@rolly-MacBook:~/QE-530/espresso-5.3.0/bin$</a>
./molecularpdos.x <~/QE_data/MolPDOS/chainH2_onto_H2.in>
~/QE_data/MolPDOS/chainH2_onto_H2.out2<br>
STOP 1<br>
</p>
v5.3.0 output:<br>
<br>
Program MOLECULARPDOS v.5.3.0 (svn rev. 11974) starts on
13Aug2016 at 12: 1:44 <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>
URL <a class="moz-txt-link-freetext" 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 class="moz-txt-link-freetext" href="http://www.quantum-espresso.org/quote">http://www.quantum-espresso.org/quote</a><br>
<br>
Serial version<br>
<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
Error in routine molecularpdos (5010):<br>
reading inputmopdos namelist<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
<br>
stopping ...<br>
<br>
So, v5.3.0 has a bug :)<br>
<br>
Then I repeat the same input for v5.4.0, it works!<br>
<br>
<br>
Program MOLECULARPDOS v.5.4.0 starts on 13Aug2016 at 12:10:58 <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>
URL <a class="moz-txt-link-freetext" 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 class="moz-txt-link-freetext" href="http://www.quantum-espresso.org/quote">http://www.quantum-espresso.org/quote</a><br>
<br>
Serial version<br>
<br>
Molecular orbitals used for projection<br>
(data for the full system from file
/home/rolly/QE_data/MolPDOS/chainH2.atomic_proj.xml)<br>
Atomic wavefunctions used: 11 - 12<br>
<br>
Projecting onto eigenvectors number: 1 - 2<br>
(of the subsytem described in file
/home/rolly/QE_data/MolPDOS/H2.atomic_proj.xml)<br>
Atomic wavefunctions used: 1 - 2<br>
<br>
...<br>
<br>
JOB DONE.<br>
<br>
One thing I noticed that for molecularpdos.x, the input commend
differs from pw.x, dos.x and projwfc.x.<br>
<br>
It DOES NOT work with: molecularpdos.x -inp file.in |tee file.out,<br>
but it DOES work with: molecularpdos.x <file.in> file.out<br>
<br>
What a surprise and I was taken for granted a consistent input
commend for all QE executables.<br>
<br>
Hope it may help someone.<br>
<br>
Regards,<br>
Rolly<br>
<br>
<div class="moz-cite-prefix">On 08/12/2016 08:46 PM, Guido Fratesi
wrote:<br>
</div>
<blockquote cite="mid:57ADC50F.4060807@unimi.it" type="cite">
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
Can you send me the results you get by running <i>the example</i>
up to the point where it hangs?<br>
Have you tried running on a different PC?<br>
Have you tried running it on top of the files I sent you?<br>
GF<br>
<br>
<div class="moz-cite-prefix">On 12/08/2016 14:42, Rolly Ng wrote:<br>
</div>
<blockquote
cite="mid:b10a7bdb-afbe-f6d5-514d-61105824cd69@gmail.com"
type="cite">
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
<p>Dear Guido,</p>
<p>I am using QE ver 5.3.0 and I am running it on an OpenSUSE
13.2 server.</p>
<p>I also have Intel Parallel Studio 2015 installed so I
configure my QE as,</p>
<p>./configure CC=icc CXX=icpc F90=ifort F77=ifort
MPIF90=mpiifort --with-scalapack=intel</p>
<p>Then, I simply make all to obtain the executables. Please
take a look at my bin files as attached.<br>
</p>
<p>I can run pw.x, dos.x and projwfc.x with 24 threads, no
problem so far.</p>
<p>These are how I run QE,</p>
<p>mpirun -np 24 ./pw.x -inp ~/rolly/Graphene/G_scf.in |tee
~/rolly/Graphene/G_scf.out<br>
mpirun -np 24 ./dos.x -inp ~/rolly/Graphene/G_dos.in |tee
~/rolly/Graphene/G_dos.out <br>
mpirun -np 24 ./projwfc.x -inp ~/rolly/Graphene/G_pdos.in |tee
~/rolly/Graphene/G_pdos.out</p>
<p>But, once I do the same for molecularpdos.x, it keeps all
threads occupied but no output was produced.</p>
<p>The .out file seems frozen with either 24 threads or 1 thread
as attached.<br>
</p>
<p>Any idea of what is going out?<br>
</p>
<p>Thank you,</p>
<p>Rolly<br>
</p>
<br>
<div class="moz-cite-prefix">On 08/12/2016 04:14 PM, Guido
Fratesi wrote:<br>
</div>
<blockquote cite="mid:57AD855C.5080005@unimi.it" type="cite">
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
Dear Rolly,<br>
<br>
I attach the results of MolDos example on my PC (it runs in
few seconds).<br>
You can try rerun molecularpdos.x on top of .xml files
therein.<br>
<br>
Can you send me the results you get by running the example up
to the point where it hangs?<br>
<br>
Which version are you using?<br>
<br>
Have you tried running on a different machine? Molecularpdos.x
is by itself a small code, and the atomic_proj.xml files are
ascii files, so you can in any case export them to other
computers and even the laptop may be fine for analysis.<br>
<br>
Best,<br>
Guido<br>
<br>
PS just to let you know I'll be unavailable next week, so
please expect some possible delay in my answers.<br>
<div class="moz-signature">-- <br>
<br>
<a moz-do-not-send="true"
href="http://wdps17.fisica.unimi.it">17th Workshop on
Dynamical Phenomena at Surfaces<br>
<img alt="19-21 Sept. 2016"
src="cid:part1.ED50A817.57D087D2@gmail.com"></a> <br>
<pre>Guido Fratesi
Dipartimento di Fisica
Universita` degli Studi di Milano
Via Celoria 16, 20133 Milano, Italy
Phone: +39 02 503 17348
email: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:guido.fratesi@unimi.it">guido.fratesi@unimi.it</a>
web: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="https://sites.google.com/site/guidofratesi/">https://sites.google.com/site/guidofratesi/</a>
</pre>
</div>
<p><img src="cid:part5.3246194A.EF5B1155@gmail.com"
alt="MailScanner Signature Unimi"></p>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
PhD. Research Fellow,
Dept. of Physics & Materials Science,
City University of Hong Kong
Tel: +852 3442 4000
Fax: +852 3442 0538</pre>
</blockquote>
<br>
<div class="moz-signature">-- <br>
<br>
<a moz-do-not-send="true" href="http://wdps17.fisica.unimi.it">17th
Workshop on Dynamical Phenomena at Surfaces<br>
<img alt="19-21 Sept. 2016"
src="cid:part6.6B6C1DC1.22B40EC6@gmail.com"></a> <br>
<pre>Guido Fratesi
Dipartimento di Fisica
Universita` degli Studi di Milano
Via Celoria 16, 20133 Milano, Italy
Phone: +39 02 503 17348
email: <a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:guido.fratesi@unimi.it">guido.fratesi@unimi.it</a>
web: <a moz-do-not-send="true" class="moz-txt-link-freetext" href="https://sites.google.com/site/guidofratesi/">https://sites.google.com/site/guidofratesi/</a>
</pre>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
PhD. Research Fellow,
Dept. of Physics & Materials Science,
City University of Hong Kong
Tel: +852 3442 4000
Fax: +852 3442 0538</pre>
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