<div dir="ltr">Thank you so much, Paolo. I will report your feedback to the IT staff in charge of maintaining the cluster I use and see of they have any suggestion.<div><br></div><div>All the best,</div><div>Martina</div></div><br><div class="gmail_quote"><div dir="ltr">On Thu, Aug 30, 2018 at 1:20 PM Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com">p.giannozzi@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">In my opinion, if everything works on less than 16 processors and nothing on more than 16, there is something wrong with your MPI environment<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Aug 30, 2018 at 6:49 PM, Martina Lessio <span dir="ltr"><<a href="mailto:ml4132@columbia.edu" target="_blank">ml4132@columbia.edu</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>Dear Paolo,</div><div><br></div><div>Thanks for testing my input file. I guess this means there is something wrong with how I compiled the code, although it's hard to understand why the error only occurs when I submit my job on more than 16 processors.</div><div><br></div><div>Thanks again for your time.</div><div><br></div><div>All the best,</div><div>Martina<br></div></div><br><div class="gmail_quote"><div dir="ltr">On Thu, Aug 30, 2018 at 12:43 PM Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" target="_blank">p.giannozzi@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>It works for me, on 18, 24, 32 processors, at least for the development version. I ran it on a 16-processor machine, but it doesn't matter how many physical cores one has (the code knows nothing about the actual number of cores, only about the number of MPI processes)<br><br></div>Paolo<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Aug 30, 2018 at 6:23 PM, Martina Lessio <span dir="ltr"><<a href="mailto:ml4132@columbia.edu" target="_blank">ml4132@columbia.edu</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 dir="ltr"><div>Dear Paolo,</div><div><br></div><div>Apologies for not including those details. The sample error message reported in my previous email was the result of a calculation run on 18 cpu (but I get similar messages when running on other cpu numbers larger than 16) using the following submission command:</div><div>mpirun -np 18 pw.x < MoTe2_opt.in</div><div><br></div><div>Thank you in advance for your help.</div><div><br></div><div>All the best,</div><div>Martina<br></div></div></div><div><div class="m_3943993084980698397m_905512270013352176m_-352347250382600804h5"><br><div class="gmail_quote"><div dir="ltr">On Thu, Aug 30, 2018 at 12:09 PM Paolo Giannozzi <<a href="mailto:p.giannozzi@gmail.com" target="_blank">p.giannozzi@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div>Please report the exact conditions under which you are running the 24-processor case: something like <br></div> mpirun -np 24 pw.x -nk .. -nd .. -whatever_option<br><div><br></div><div>Paolo<br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Aug 29, 2018 at 11:49 PM, Martina Lessio <span dir="ltr"><<a href="mailto:ml4132@columbia.edu" target="_blank">ml4132@columbia.edu</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 dir="ltr"><div dir="ltr"><div dir="ltr"><div>Dear all,</div><div><br></div><div>I have been successfully using QE 5.4 for a while now but recently decided to install the newest version hoping that some issues I have been experiencing with 5.4 would be resolved. However, I now have some issues when running version 6.3 in parallel. In particular, if I run a sample calculation (input file provided below) on more than 16 processors the calculation crashes after printing this line "Starting wfcs are random" and the following error message is printed in the output file:</div><div>[compute-0-5.local:5241] *** An error occurred in MPI_Bcast<br>[compute-0-5.local:5241] *** on communicator MPI COMMUNICATOR 20 SPLIT FROM 18<br>[compute-0-5.local:5241] *** MPI_ERR_TRUNCATE: message truncated<br>[compute-0-5.local:5241] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort<br>--------------------------------------------------------------------------<br>mpirun has exited due to process rank 16 with PID 5243 on<br>node compute-0-5.local exiting improperly. There are two reasons this could occur:<br><br>1. this process did not call "init" before exiting, but others in<br>the job did. This can cause a job to hang indefinitely while it waits<br>for all processes to call "init". By rule, if one process calls "init",<br>then ALL processes must call "init" prior to termination.<br><br>2. this process called "init", but exited without calling "finalize".<br>By rule, all processes that call "init" MUST call "finalize" prior to<br>exiting or it will be considered an "abnormal termination"<br><br>This may have caused other processes in the application to be<br>terminated by signals sent by mpirun (as reported here).<br>--------------------------------------------------------------------------<br>[compute-0-5.local:05226] 1 more process has sent help message help-mpi-errors.txt / mpi_errors_are_fatal<br>[compute-0-5.local:05226] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages</div><div><br></div><div><br></div><div>Note that I have been running QE 5.4 on 24 cpu on this same computer cluster without any issue. I am copying my input file at the end of this email.<br></div><div><br></div><div>Any help with this would be greatly appreciated.</div><div>Thank you in advance.</div><div><br></div><div>All the best,</div><div>Martina<br></div><div><br><div dir="ltr" class="m_3943993084980698397m_905512270013352176m_-352347250382600804m_-1157169850918253387m_-4623061823196112426m_-961522314054628027gmail_signature"><div dir="ltr"><div><div dir="ltr">Martina Lessio<br><div>Department of Chemistry</div><div>Columbia University</div><div><br></div><div><b>Input file:</b></div><div>&control<br> calculation = 'relax'<br> restart_mode='from_scratch',<br> prefix='MoTe2_bulk_opt_1',<br> pseudo_dir = '/home/mlessio/espresso-5.4.0/pseudo/',<br> outdir='/home/mlessio/espresso-5.4.0/tempdir/'<br> /<br> &system<br> ibrav= 4, A=3.530, B=3.530, C=13.882, cosAB=-0.5, cosAC=0, cosBC=0,<br> nat= 6, ntyp= 2,<br> ecutwfc =60.<br> occupations='smearing', smearing='gaussian', degauss=0.01<br> nspin =1<br> /<br> &electrons<br> mixing_mode = 'plain'<br> mixing_beta = 0.7<br> conv_thr = 1.0d-10<br> /<br> &ions<br> /<br>ATOMIC_SPECIES<br> Mo 95.96 Mo_ONCV_PBE_FR-1.0.upf<br> Te 127.6 Te_ONCV_PBE_FR-1.1.upf<br>ATOMIC_POSITIONS {crystal}<br>Te 0.333333334 0.666666643 0.625000034<br>Te 0.666666641 0.333333282 0.375000000<br>Te 0.666666641 0.333333282 0.125000000<br>Te 0.333333334 0.666666643 0.874999966<br>Mo 0.333333334 0.666666643 0.250000000<br>Mo 0.666666641 0.333333282 0.750000000<br><br>K_POINTS {automatic}<br> 8 8 2 0 0 0<br><br></div></div></div></div></div></div></div></div></div></div>
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