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<p><font size="-1">by removing the % I mean something like <br>
</font></p>
<p><font size="-1">1) cd </font><span class="s1">/global/cscratch1/sd/mh5213/scanmode/
<br>
</span></p>
<p><span class="s1">2) mv 2% pippo <br>
</span></p>
<p><span class="s1">3) set outdir=</span><span class="s1"><span
class="s1">'/global/cscratch1/sd/mh5213/scanmode/pippo/10x10/test/test_proc'</span></span></p>
<p><span class="s1"><span class="s1"><br>
</span></span></p>
<p><span class="s1"><span class="s1"><br>
</span></span></p>
<div class="moz-cite-prefix">On 18/07/19 15:37, Hildebrand, Mariana
wrote:<br>
</div>
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<p class="MsoNormal"><span style="font-size:11.0pt">Hi Pietro,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Thanks. I
should’ve realised that before…! Now it tells me:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">
Program PHONON v.6.3MaX starts on 18Jul2019 at 6:33: 8<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">
This program is part of the open-source Quantum ESPRESSO
suite<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">
for quantum simulation of materials; please cite<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502
(2009);<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">
"P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901
(2017);<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">
URL <a class="moz-txt-link-freetext" href="http://www.quantum-espresso.org">http://www.quantum-espresso.org</a>",<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">
in publications or presentations arising from this work.
More details at<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">
<a class="moz-txt-link-freetext" href="http://www.quantum-espresso.org/quote">http://www.quantum-espresso.org/quote</a><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black"> ***
WARNING: using old-style file format, will disappear from
next version ***<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">
Parallel version (MPI & OpenMP), running on 288
processor cores<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">
Number of MPI processes: 288<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">
Threads/MPI process: 1<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">
MPI processes distributed on 9 nodes<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">
K-points division: npool = 4<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black"> R
& G space division: proc/nbgrp/npool/nimage = 72<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">mkdir
fail: [2] No such file or directory<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black"> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">
Error in routine check_tempdir (1):<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">
tmp_dir cannot be opened<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black"> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black">
stopping ...<o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span
style="font-size:8.5pt;font-family:Menlo;color:black"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I assume
that might be related to insufficient memory.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Best, M.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="color:black">From: </span></b><span
style="color:black">users
<a class="moz-txt-link-rfc2396E" href="mailto:users-bounces@lists.quantum-espresso.org"><users-bounces@lists.quantum-espresso.org></a> on behalf
of Pietro Delugas <a class="moz-txt-link-rfc2396E" href="mailto:pdelugas@sissa.it"><pdelugas@sissa.it></a><br>
<b>Reply-To: </b>Quantum ESPRESSO users Forum
<a class="moz-txt-link-rfc2396E" href="mailto:users@lists.quantum-espresso.org"><users@lists.quantum-espresso.org></a><br>
<b>Date: </b>Thursday, 18 July 2019 at 14:32<br>
<b>To: </b><a class="moz-txt-link-rfc2396E" href="mailto:users@lists.quantum-espresso.org">"users@lists.quantum-espresso.org"</a>
<a class="moz-txt-link-rfc2396E" href="mailto:users@lists.quantum-espresso.org"><users@lists.quantum-espresso.org></a><br>
<b>Subject: </b>Re: [QE-users] Problem with large phonon
calculation in the gamma point for all 6.x versions:
ERROR(FoX) Could not open file
/global/cscratch1/sd/mh5213/scanmode/2%/10x10/test/test_proc/test.save/data-file-schema.xml
- not a valid URI<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
</div>
<p><span style="font-size:10.0pt">Hi </span><o:p></o:p></p>
<p><span style="font-size:10.0pt">try to remove the % from the
path. </span><o:p></o:p></p>
<p><span style="font-size:10.0pt">Pietro </span><o:p></o:p></p>
<div>
<p class="MsoNormal">On 18/07/19 15:21, Hildebrand, Mariana
wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"><span style="font-size:11.0pt">Dear all,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I have
been facing issues with a phonon calculation in the gamma
point on a 10x10 graphene supercell for two weeks now and
am running out of ideas.
</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">For
varioys reasons, I am obliged to run a phonon calculation
in the gamma point on this large 10x10 supercell.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I compiled
quantum espresso version 6.3 on a crayXC40 machine and
both the pw.x and ph.x executables work perfectly well for
a smaller test system (a 5x5 graphene supercell).</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">For my
10x10 supercell, the pw.x executable works, however, for
the ph.x executable I keep getting the following error:</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">ERROR(FoX)</span><o:p></o:p></p>
<p class="p1"><span class="s1">Could not open file
/global/cscratch1/sd/mh5213/scanmode/2%/10x10/test/test_proc/test.save/data-file-schema.xml
- not a valid URI</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Even
though, the xml file is where it is supposed to be and in
the correct format.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I also
tried version 6.2.1 and obtain the same error. Then I
compiled version 6.3. configured with - - no xml as
previously discussed in the forum but it does not change
anything.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Furthermore,
I tried to increase the RAM and played with the level of
parallelisation (the number of requested nodes and cpus
per node).</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">My input
file for the ph.x executable is:</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="p1"><span class="s1">Normal modes for graphene</span><o:p></o:p></p>
<p class="p1"><span class="s1">&inputph</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">tr2_ph=1.0d-12,</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">prefix='test',</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">recover=.true.,</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">amass(1)=12.010,</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">outdir='/global/cscratch1/sd/mh5213/scanmode/2%/10x10/test/test_proc'</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">epsil=.false.,</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">fildyn='dmat.5x5'</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">/</span><o:p></o:p></p>
<p class="p1"><span class="apple-converted-space"> </span><span
class="s1">0.0 0.0 0.0</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">As I said,
it works perfectly well for my smaller test system (the
5x5 graphene supercell).
</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">I also
tried to remove the recover=.true. keyword but it does not
change anything.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Any help
would be much appreciated.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Best
wishes, </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Mariana.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><br>
<br>
<o:p></o:p></span></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" moz-do-not-send="true">www.max-centre.eu/quantum-espresso</a>)<o:p></o:p></pre>
<pre>users mailing list <a href="mailto:users@lists.quantum-espresso.org" moz-do-not-send="true">users@lists.quantum-espresso.org</a><o:p></o:p></pre>
<pre><a href="https://lists.quantum-espresso.org/mailman/listinfo/users" moz-do-not-send="true">https://lists.quantum-espresso.org/mailman/listinfo/users</a><o:p></o:p></pre>
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<br>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
Quantum ESPRESSO is supported by MaX (<a class="moz-txt-link-abbreviated" href="http://www.max-centre.eu/quantum-espresso">www.max-centre.eu/quantum-espresso</a>)
users mailing list <a class="moz-txt-link-abbreviated" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a>
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