<div dir="ltr"><div dir="ltr">No, it's related to the non-existence of the scratch directory. QE can create a scratch directory, but only if the file system permissions allow that, and, I think, only one level above an existing directory.<br></div><div><br></div><div>Paolo</div><div><br></div><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, Jul 18, 2019 at 3:38 PM Hildebrand, Mariana <<a href="mailto:mariana.hildebrand13@imperial.ac.uk">mariana.hildebrand13@imperial.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
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<p class="MsoNormal"><span style="font-size:11pt">Hi Pietro,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">Thanks. I should’ve realised that before…! Now it tells me:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> Program PHONON v.6.3MaX starts on 18Jul2019 at 6:33: 8<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"><u></u> <u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> This program is part of the open-source Quantum ESPRESSO suite<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> for quantum simulation of materials; please cite<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> URL <a href="http://www.quantum-espresso.org" target="_blank">http://www.quantum-espresso.org</a>",<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> in publications or presentations arising from this work. More details at<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> <a href="http://www.quantum-espresso.org/quote" target="_blank">http://www.quantum-espresso.org/quote</a><u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"><u></u> <u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> *** WARNING: using old-style file format, will disappear from next version ***<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"><u></u> <u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> Parallel version (MPI & OpenMP), running on 288 processor cores<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> Number of MPI processes: 288<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> Threads/MPI process: 1<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"><u></u> <u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> MPI processes distributed on 9 nodes<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> K-points division: npool = 4<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> R & G space division: proc/nbgrp/npool/nimage = 72<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"><u></u> <u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black">mkdir fail: [2] No such file or directory<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"><u></u> <u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> Error in routine check_tempdir (1):<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> tmp_dir cannot be opened<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"><u></u> <u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"> stopping ...<u></u><u></u></span></p>
<p class="MsoNormal" style="background:white none repeat scroll 0% 0%"><span style="font-size:8.5pt;font-family:Menlo;color:black"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">I assume that might be related to insufficient memory.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt">Best, M.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p class="MsoNormal"><b><span style="color:black">From: </span></b><span style="color:black">users <<a href="mailto:users-bounces@lists.quantum-espresso.org" target="_blank">users-bounces@lists.quantum-espresso.org</a>> on behalf of Pietro Delugas <<a href="mailto:pdelugas@sissa.it" target="_blank">pdelugas@sissa.it</a>><br>
<b>Reply-To: </b>Quantum ESPRESSO users Forum <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>><br>
<b>Date: </b>Thursday, 18 July 2019 at 14:32<br>
<b>To: </b>"<a href="mailto:users@lists.quantum-espresso.org" target="_blank">users@lists.quantum-espresso.org</a>" <<a href="mailto:users@lists.quantum-espresso.org" target="_blank">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<u></u><u></u></span></p>
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<p class="MsoNormal"><span style="font-size:11pt"><u></u> <u></u></span></p>
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<p><span style="font-size:10pt">Hi </span><u></u><u></u></p>
<p><span style="font-size:10pt">try to remove the % from the path. </span><u></u><u></u></p>
<p><span style="font-size:10pt">Pietro </span><u></u><u></u></p>
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<p class="MsoNormal">On 18/07/19 15:21, Hildebrand, Mariana wrote:<u></u><u></u></p>
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<p class="MsoNormal"><span style="font-size:11pt">Dear all,</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt">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><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt">For varioys reasons, I am obliged to run a phonon calculation in the gamma point on this large 10x10 supercell.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt">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><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt">For my 10x10 supercell, the pw.x executable works, however, for the ph.x executable I keep getting the following error:</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt"> </span><u></u><u></u></p>
<p class="gmail-m_385067447580077631p1"><span class="gmail-m_385067447580077631s1">ERROR(FoX)</span><u></u><u></u></p>
<p class="gmail-m_385067447580077631p1"><span class="gmail-m_385067447580077631s1">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><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt">Even though, the xml file is where it is supposed to be and in the correct format.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt">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><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt">Furthermore, I tried to increase the RAM and played with the level of parallelisation (the number of requested nodes and cpus per node).</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt">My input file for the ph.x executable is:</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt"> </span><u></u><u></u></p>
<p class="gmail-m_385067447580077631p1"><span class="gmail-m_385067447580077631s1">Normal modes for graphene</span><u></u><u></u></p>
<p class="gmail-m_385067447580077631p1"><span class="gmail-m_385067447580077631s1">&inputph</span><u></u><u></u></p>
<p class="gmail-m_385067447580077631p1"><span class="gmail-m_385067447580077631apple-converted-space"> </span><span class="gmail-m_385067447580077631s1">tr2_ph=1.0d-12,</span><u></u><u></u></p>
<p class="gmail-m_385067447580077631p1"><span class="gmail-m_385067447580077631apple-converted-space"> </span><span class="gmail-m_385067447580077631s1">prefix='test',</span><u></u><u></u></p>
<p class="gmail-m_385067447580077631p1"><span class="gmail-m_385067447580077631apple-converted-space"> </span><span class="gmail-m_385067447580077631s1">recover=.true.,</span><u></u><u></u></p>
<p class="gmail-m_385067447580077631p1"><span class="gmail-m_385067447580077631apple-converted-space"> </span><span class="gmail-m_385067447580077631s1">amass(1)=12.010,</span><u></u><u></u></p>
<p class="gmail-m_385067447580077631p1"><span class="gmail-m_385067447580077631apple-converted-space"> </span><span class="gmail-m_385067447580077631s1">outdir='/global/cscratch1/sd/mh5213/scanmode/2%/10x10/test/test_proc'</span><u></u><u></u></p>
<p class="gmail-m_385067447580077631p1"><span class="gmail-m_385067447580077631apple-converted-space"> </span><span class="gmail-m_385067447580077631s1">epsil=.false.,</span><u></u><u></u></p>
<p class="gmail-m_385067447580077631p1"><span class="gmail-m_385067447580077631apple-converted-space"> </span><span class="gmail-m_385067447580077631s1">fildyn='dmat.5x5'</span><u></u><u></u></p>
<p class="gmail-m_385067447580077631p1"><span class="gmail-m_385067447580077631apple-converted-space"> </span><span class="gmail-m_385067447580077631s1">/</span><u></u><u></u></p>
<p class="gmail-m_385067447580077631p1"><span class="gmail-m_385067447580077631apple-converted-space"> </span><span class="gmail-m_385067447580077631s1">0.0 0.0 0.0</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt">As I said, it works perfectly well for my smaller test system (the 5x5 graphene supercell).
</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt">I also tried to remove the recover=.true. keyword but it does not change anything.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt">Any help would be much appreciated.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt"> </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt">Best wishes, </span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt">Mariana.</span><u></u><u></u></p>
<p class="MsoNormal"><span style="font-size:11pt"><br>
<br>
<u></u><u></u></span></p>
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</blockquote>
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Quantum ESPRESSO is supported by MaX (<a href="http://www.max-centre.eu/quantum-espresso" rel="noreferrer" target="_blank">www.max-centre.eu/quantum-espresso</a>)<br>
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<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso.org/mailman/listinfo/users</a></blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div>Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,<br>Univ. Udine, via delle Scienze 208, 33100 Udine, Italy<br>Phone +39-0432-558216, fax +39-0432-558222<br><br></div></div></div></div></div></div>