<div dir="ltr">Dear Paolo,<div><br></div><div>Thanks so much for your response and for testing my input file on your machine with the latest version of Quantum Espresso. I should compile the latest version on my machine.</div><div><br></div><div>Regarding the memory: that number is quite close to my memory limit (60 GB) and such large memory requirement probably explains why my calculations are so slow. I will consider using a smaller unit cell and using pseudopotentials with less valence electrons to reduce the memory requirement. I have actually been searching for a norm conserving fully relativistic pseudopotential for tellurium with only s and p valence electrons (this would reduce the number of valence electrons from 16 to 6) but I have not been able to find it. I would appreciate any suggestion regarding this aspect.</div><div><br></div><div>Thank you so much,</div><div>Martina <br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, May 24, 2018 at 4:30 AM, Paolo Giannozzi <span dir="ltr"><<a href="mailto:p.giannozzi@gmail.com" target="_blank">p.giannozzi@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div>On 16 processors with the latest QE version, I get<br><br> Estimated max dynamical RAM per process > 3.18 GB<br> Estimated total dynamical RAM > 50.87 GB<br><br></div>Do you have that much memory? <br><span class="HOEnZb"><font color="#888888"><br></font></span></div><span class="HOEnZb"><font color="#888888">Paolo<br><div><div><br></div></div></font></span></div><div class="gmail_extra"><br><div class="gmail_quote"><span class="">On Tue, May 22, 2018 at 1:14 AM, Martina Lessio <span dir="ltr"><<a href="mailto:ml4132@columbia.edu" target="_blank">ml4132@columbia.edu</a>></span> wrote:<br></span><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div dir="ltr">Dear Quantum Espresso community,<div><br></div><div>I recently started running the parallel version of QE 5.4.0 and I am getting the following error message in my output file (the error never appeared when I run the code serial on one processor):</div><div><div><br>[compute-0-6.local:31540] 23 more processes have sent help message help-mpi-btl-base.txt / btl:no-nics<br><br>[compute-0-6.local:31540] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages<br><br>where "compute-0-1" is the name of the node I run my calculation on. </div><div>After the message is printed in the output the calculation typically continues normally and in same cases gets successfully to the end. I other cases, usually when I had large supercell with about 100 atoms, the calculation becomes extremely slow and does not get to the end in a reasonable time. Therefore, I suspect that the error being printed also signals that the calculation will start running only on one processor. However, upon checking, I noticed that all the processors I requested are still busy with the calculation after the error message shows up. <br></div><div><br></div><div>I tried to search the forum and the FAQs for this type of issue but did not find much. I would really appreciate if anybody could share their experience with this type of error. </div><div>I am providing below my submission script and input file (for a large calculation that runs very slowly after the error message is printed).</div><div><br></div><div>Thanks so much,</div><div>Martina</div><div><br></div>-- <br>Martina Lessio, Ph.D.<br>Frontiers of Science Lecturer in Discipline<br>Postdoctoral Research Scientist<br>Department of Chemistry<br>Columbia University<div class="m_6370437949741125441m_8909327228492698gmail_signature"><div dir="ltr"><div dir="ltr"><div><br></div><b>Submission script:</b><br>#!/bin/bash<br>#SBATCH --job-name=QErun<br>#SBATCH -n 24 # node count<br>#SBATCH -p New # node count<br>#SBATCH -o MoTe2ml_super551OPT.out<br>#SBATCH --mem=60000<br>module load openmpi<br>module load mkl<br>module load compilers<br>mpirun -np 24 pw.x < MoTe2ml_super551OPT.in</div><div dir="ltr"><br></div><b>Input file:</b><br> &control<br> calculation = 'relax'<br> restart_mode='from_scratch',<br> prefix='MoTe2ml_super5x5relax'<wbr>,<br> pseudo_dir = '/home/mlessio/espresso-5.4.0/<wbr>pseudo/',<br> outdir='/home/mlessio/espresso<wbr>-5.4.0/tempdir/'<br> /<br><br> &system<br> ibrav= 4, A=17.65, B=17.65, C=16.882, cosAB=-0.5, cosAC=0, cosBC=0,<br> nat= 75, ntyp= 2,<br> ecutwfc =60.<br> lspinorb =.true., noncolin=.true.<br> /<br><br> &electrons<br> mixing_mode = 'plain'<br> mixing_beta = 0.7<br> conv_thr = 1.0d-10<br> diago_david_ndim=2<br> diagonalization='cg'<br> /<br><br> &ions<br> /<br><br>ATOMIC_SPECIES<br> Te 127.6 Te_ONCV_PBE_FR-1.1.upf<br> Mo 95.96 Mo_ONCV_PBE_FR-1.0.upf<br><br>ATOMIC_POSITIONS {crystal}<br>Te 0.133333330 0.066666657 0.313489588<br>Te 0.133333336 0.266666661 0.313489588<br>Te 0.133333334 0.466666672 0.313489588<br>Te 0.133333325 0.666666683 0.313489588<br>Te 0.133333336 0.866666694 0.313489588<br>Te 0.333333312 0.066666657 0.313489588<br>Te 0.333333306 0.266666661 0.313489588<br>Te 0.333333310 0.466666672 0.313489588<br>Te 0.333333304 0.666666683 0.313489588<br>Te 0.333333319 0.866666694 0.313489588<br>Te 0.533333329 0.066666657 0.313489588<br>Te 0.533333336 0.266666661 0.313489588<br>Te 0.533333320 0.466666672 0.313489588<br>Te 0.533333317 0.666666683 0.313489588<br>Te 0.533333335 0.866666694 0.313489588<br>Te 0.733333372 0.066666657 0.313489588<br>Te 0.733333352 0.266666661 0.313489588<br>Te 0.733333390 0.466666672 0.313489588<br>Te 0.733333374 0.666666683 0.313489588<br>Te 0.733333385 0.866666694 0.313489588<br>Te 0.933333361 0.066666657 0.313489588<br>Te 0.933333341 0.266666661 0.313489588<br>Te 0.933333379 0.466666672 0.313489588<br>Te 0.933333363 0.666666683 0.313489588<br>Te 0.933333347 0.866666694 0.313489588<br>Te 0.133333330 0.066666657 0.097661430<br>Te 0.133333336 0.266666661 0.097661430<br>Te 0.133333334 0.466666672 0.097661430<br>Te 0.133333325 0.666666683 0.097661430<br>Te 0.133333336 0.866666694 0.097661430<br>Te 0.333333312 0.066666657 0.097661430<br>Te 0.333333306 0.266666661 0.097661430<br>Te 0.333333310 0.466666672 0.097661430<br>Te 0.333333304 0.666666683 0.097661430<br>Te 0.333333319 0.866666694 0.097661430<br>Te 0.533333329 0.066666657 0.097661430<br>Te 0.533333336 0.266666661 0.097661430<br>Te 0.533333320 0.466666672 0.097661430<br>Te 0.533333317 0.666666683 0.097661430<br>Te 0.533333335 0.866666694 0.097661430<br>Te 0.733333372 0.066666657 0.097661430<br>Te 0.733333352 0.266666661 0.097661430<br>Te 0.733333390 0.466666672 0.097661430<br>Te 0.733333374 0.666666683 0.097661430<br>Te 0.733333385 0.866666694 0.097661430<br>Te 0.933333361 0.066666657 0.097661430<br>Te 0.933333341 0.266666661 0.097661430<br>Te 0.933333379 0.466666672 0.097661430<br>Te 0.933333363 0.666666683 0.097661430<br>Te 0.933333347 0.866666694 0.097661430<br>Mo 0.066666675 0.133333330 0.205570934<br>Mo 0.066666667 0.333333310 0.205570934<br>Mo 0.066666685 0.533333321 0.205570934<br>Mo 0.066666655 0.733333332 0.205570934<br>Mo 0.066666666 0.933333343 0.205570934<br>Mo 0.266666695 0.133333330 0.205570934<br>Mo 0.266666683 0.333333310 0.205570934<br>Mo 0.266666698 0.533333321 0.205570934<br>Mo 0.266666678 0.733333332 0.205570934<br>Mo 0.266666696 0.933333343 0.205570934<br>Mo 0.466666671 0.133333330 0.205570934<br>Mo 0.466666666 0.333333310 0.205570934<br>Mo 0.466666690 0.533333321 0.205570934<br>Mo 0.466666668 0.733333332 0.205570934<br>Mo 0.466666681 0.933333343 0.205570934<br>Mo 0.666666687 0.133333330 0.205570934<br>Mo 0.666666655 0.333333310 0.205570934<br>Mo 0.666666666 0.533333321 0.205570934<br>Mo 0.666666650 0.733333332 0.205570934<br>Mo 0.666666674 0.933333343 0.205570934<br>Mo 0.866666676 0.133333330 0.205570934<br>Mo 0.866666644 0.333333310 0.205570934<br>Mo 0.866666682 0.533333321 0.205570934<br>Mo 0.866666666 0.733333332 0.205570934<br>Mo 0.866666650 0.933333343 0.205570934<br><br>K_POINTS {automatic}<br> 2 2 1 0 0 0</div></div>
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<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-espresso<wbr>.org/mailman/listinfo/users</a><br></span></blockquote></div><span class=""><br><br clear="all"><br>-- <br><div class="m_6370437949741125441gmail_signature" data-smartmail="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>
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users mailing list<br>
<a href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.<wbr>org</a><br>
<a href="https://lists.quantum-espresso.org/mailman/listinfo/users" rel="noreferrer" target="_blank">https://lists.quantum-<wbr>espresso.org/mailman/listinfo/<wbr>users</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr">Martina Lessio, Ph.D.<div>Frontiers of Science Lecturer in Discipline</div><div>Postdoctoral Research Scientist</div><div>Department of Chemistry</div><div>Columbia University</div></div></div></div></div>
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