<div dir="ltr"><div><div><div><div>The check that "max_seconds" have elapsed is done at the end of each
single diagonalization, so if the latter takes "many_seconds", the check
may be triggered in the worst case when "max_seconds + some_seconds" have
elapsed. Since it may take "some_more_seconds" to write data to disk, if you are out of luck, "max_seconds + some_seconds + some_more_seconds" will exceed the maximum allowed time by the batch queue (or, more exactly, the time after which the batch queue realizes that you are out of time: in your run, 86427s, or 27s more than the wall time limit, 86400).<br></div></div><br></div>Unfortunately there is no way you can recover your data. And no, there is no reliable way to ask the operating system "how much time do I have" before starting a new diagonalization ...<br><br></div>Paolo<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Feb 15, 2016 at 6:11 PM, Joshua Davis <span dir="ltr"><<a href="mailto:davis101@chemistry.msu.edu" target="_blank">davis101@chemistry.msu.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">Continued... (Sent before I meant to)<div class="gmail_extra"><br></div><div class="gmail_extra"><span style="font-size:12.8px">I did try to use disk_io = "high", but I ran into "davcio (10)" read and write errors so I just used the default "low" option. There were wfc file written in my outdir too.</span><br></div><div class="gmail_extra"><span style="font-size:12.8px"><br></span></div><div class="gmail_extra"><span style="font-size:12.8px">Below contains much of the control options I used:</span></div><div class="gmail_extra"><span style="font-size:12.8px"><br></span></div><div class="gmail_extra"><div class="gmail_extra"><span style="font-size:12.8px">&CONTROL</span></div><div class="gmail_extra"><span style="font-size:12.8px"> title = 'MgB5C2PP_NORMCON_HSE_ec140_5kp_115bnd_1Q',</span></div><div class="gmail_extra"><span style="font-size:12.8px"> calculation = 'scf',</span></div><div class="gmail_extra"><span style="font-size:12.8px"> pseudo_dir = './pot',</span></div><div class="gmail_extra"><span style="font-size:12.8px"> outdir = './scratch',</span></div><div class="gmail_extra"><span style="font-size:12.8px"> prefix = 'MgB5CPP_NC_PBE_ec140_5kp_115bnd',</span></div><div class="gmail_extra"><span style="font-size:12.8px"> etot_conv_thr = 1.0D-5,</span></div><div class="gmail_extra"><span style="font-size:12.8px"> forc_conv_thr = 1.0D-4,</span></div><div class="gmail_extra"><span style="font-size:12.8px"> verbosity = 'high',</span></div><div class="gmail_extra"><span style="font-size:12.8px"> wf_collect = .true.,</span></div><div class="gmail_extra"><span style="font-size:12.8px"> max_seconds = 84600</span></div><div class="gmail_extra"><span style="font-size:12.8px"> /</span></div><div class="gmail_extra"><span style="font-size:12.8px"><br></span></div><div class="gmail_extra"><span style="font-size:12.8px"> &SYSTEM</span></div><div class="gmail_extra"><span style="font-size:12.8px"> ibrav = 0,</span></div><div class="gmail_extra"><span style="font-size:12.8px"> nat = 52,</span></div><div class="gmail_extra"><span style="font-size:12.8px"> ntyp = 3,</span></div><div class="gmail_extra"><span style="font-size:12.8px"> ecutwfc = 140,</span></div><div class="gmail_extra"><span style="font-size:12.8px"> nspin = 1,</span></div><div class="gmail_extra"><span style="font-size:12.8px"> occupations = 'fixed',</span></div><div class="gmail_extra"><span style="font-size:12.8px"> nbnd = 115,</span></div><div class="gmail_extra"><span style="font-size:12.8px"> input_dft = 'hse',</span></div><div class="gmail_extra"><span style="font-size:12.8px"> screening_parameter = 0.106,</span></div><div class="gmail_extra"><span style="font-size:12.8px"> nqx1 = 1, nqx2 = 1, nqx3 = 1</span></div><div class="gmail_extra"><span style="font-size:12.8px"> /</span></div><div class="gmail_extra"><span style="font-size:12.8px"><br></span></div><div class="gmail_extra"><span style="font-size:12.8px"> &ELECTRONS</span></div><div class="gmail_extra"><span style="font-size:12.8px"> mixing_beta = 0.7,</span></div><div class="gmail_extra"><span style="font-size:12.8px"> conv_thr = 1.D-8,</span></div><div class="gmail_extra"><span style="font-size:12.8px"> electron_maxstep = 200</span></div><div class="gmail_extra"><span style="font-size:12.8px"> /</span></div><div class="gmail_extra"><span style="font-size:12.8px"><br></span></div><div class="gmail_extra"><span style="font-size:12.8px"><br></span></div><div class="gmail_extra"><span style="font-size:12.8px">ATOMIC_SPECIES</span></div><div class="gmail_extra"><span style="font-size:12.8px"> Mg 24.305 Mg.pbe-hgh.UPF</span></div><div class="gmail_extra"><span style="font-size:12.8px"> B 10.81 B.pbe-hgh.UPF</span></div><div class="gmail_extra"><span style="font-size:12.8px"> C 12.011 C.pbe-hgh.UPF</span></div><div style="font-size:12.8px"><br></div></div><div class="gmail_extra"><div class="gmail_extra"><br></div><div class="gmail_extra">K_POINTS (automatic)</div><div class="gmail_extra"> 5 5 5 0 0 0</div><div><br></div><div>The calculation ended with: </div><div><br></div><div><div> 100 total processes killed (some possibly by mpirun during cleanup)</div></div><div><br></div><div>in the out file, and the following was in the scheduler output file:</div><div><div><br></div><div> mpirun: killing job...</div><div><br></div><div> --------------------------------------------------------------------------</div><div> mpirun noticed that process rank 0 with PID 26679 on node scw-003 exited on signal 0 (Unknown signal 0).</div><div> --------------------------------------------------------------------------</div><div> =>> PBS: job killed: walltime 86427 exceeded limit 86400</div><div> mpirun: abort is already in progress...hit ctrl-c again to forcibly terminate</div></div><div><br></div><div><br></div><div><br></div><div>Other info: The system runs CentOS 6.6, and I am running QE5.3 compiled with ifort 13.01</div><div><br></div><div>Any help would be much appreciated. </div><div><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><span class=""><div dir="ltr"><font face="arial, helvetica, sans-serif" size="2">----------------------------------------------------------------------------------------------------------------</font></div><div dir="ltr"><font face="arial, helvetica, sans-serif" size="2">Joshua D. Davis</font></div><div dir="ltr"><font face="arial, helvetica, sans-serif" size="2"><br>Graduate Assistant</font></div></span><div dir="ltr"><div><span style="background-color:transparent"><font face="arial, helvetica, sans-serif" size="2">Department of Chemistry</font></span></div><div><span style="background-color:transparent"><font face="arial, helvetica, sans-serif" size="2">Michigan State University</font></span></div><div><span style="background-color:transparent"><font face="arial, helvetica, sans-serif" size="2">-----------------------------------------------------------------------------------------------------------------</font></span></div></div></div></div></div></div></div></div><div><div class="h5">
<br><div class="gmail_quote">On Mon, Feb 15, 2016 at 11:55 AM, Joshua Davis <span dir="ltr"><<a href="mailto:davis101@chemistry.msu.edu" target="_blank">davis101@chemistry.msu.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex"><div dir="ltr">Dear pwscf fourm,<div><br></div><div>I am currently trying to run an HSE calculation on my university's high performance cluster. To make sure the density and wave-functions are written properly before scheduled session ends I usually use max_seconds to stop the calculation. The max_seconds function did stop the calculation and was ended by the scheduler. Can I still use the wave-function files even though the calculation did not end right?</div><div><br></div><div>The default disk_io is set to the default "low". I did try to use disk_io = "high", but I ran into "davcio (10)"</div><div><br clear="all"><div><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><font face="arial, helvetica, sans-serif" size="2">----------------------------------------------------------------------------------------------------------------</font></div><div dir="ltr"><font face="arial, helvetica, sans-serif" size="2">Joshua D. Davis</font></div><div dir="ltr"><font face="arial, helvetica, sans-serif" size="2"><br>Graduate Assistant</font></div><div dir="ltr"><div><span style="font-family:arial,helvetica,sans-serif;background-color:transparent">Michigan State University</span><br></div><div><span style="background-color:transparent"><p style="margin:0in 0in 0pt"><span style="font-family:arial,helvetica,sans-serif;background-color:transparent">-----------------------------------------------------------------------------------------------------------------</span><br></p></span></div></div></div></div></div></div></div>
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