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<p>Hi<br>
</p>
<p>Does it runs at Gamma only or with very small ecutwfc? It looks
like you simply don't have enough resources for the system of such
size (most likely RAM).</p>
<p>Oleksandr<br>
</p>
<br>
<div class="moz-cite-prefix">On 09/05/19 22:40, Hud Wahab wrote:<br>
</div>
<blockquote type="cite"
cite="mid:f8d00e8a-0edb-4f5d-a133-b12badc941cc@getmailbird.com">
<meta http-equiv="content-type" content="text/html; charset=utf-8">
<div id="__MailbirdStyleContent" style="font-size:
10pt;font-family: Arial;color: #000000"> Hi
<div><br>
</div>
<div>ok, even if I try with ibrav == 0, specify cell_parameters,
and use cartesian coordinates for all as such:</div>
<div><br>
</div>
<div>
<div>&control</div>
<div> calculation = 'scf'</div>
<div> prefix = 'graphene'</div>
<div> pseudo_dir = '/gscratch/hwahab/DFT-code/psp/' </div>
<div> outdir = './'</div>
<div> restart_mode = 'from_scratch'</div>
<div> etot_conv_thr = 1.d-6</div>
<div> forc_conv_thr = 1.d-5</div>
<div>/</div>
<div><br>
</div>
<div>&system</div>
<div> ibrav = 0</div>
<div> nat = 48</div>
<div> ntyp = 1</div>
<div> ecutwfc = 80</div>
<div> occupations = 'smearing'</div>
<div> smearing = 'gaussian'</div>
<div> degauss = 0.1</div>
<div> vdw_corr='grimme-d2'</div>
<div>/</div>
<div><br>
</div>
<div>&electrons</div>
<div> diagonalization = 'david'</div>
<div> diago_thr_init = 1.d-4</div>
<div> mixing_mode = 'local-TF'</div>
<div> mixing_beta = 0.7</div>
<div> conv_thr = 1.d-8</div>
<div>/<span class="Apple-tab-span" style="white-space:pre"> </span></div>
<div><br>
</div>
<div>&ions</div>
<div> </div>
<div>/</div>
<div><br>
</div>
<div>ATOMIC_SPECIES</div>
<div>C 12.0107 C.pbe-n-kjpaw_psl.1.0.0.UPF </div>
<div><br>
</div>
<div>ATOMIC_POSITIONS angstrom</div>
<div>C -0.005594637 0.710607728 17.606217811</div>
<div>C -0.007113039 2.128152101 17.584272182</div>
<div>C 1.224800757 0.002792887 17.613037723</div>
<div>C 1.220781849 2.833821539 17.553802163</div>
<div>C 2.453370565 0.710361709 17.588200291</div>
<div>C 2.452466724 2.129238290 17.551425829</div>
<div>C 3.684434744 0.001530538 17.594476170</div>
<div>C 3.684438920 2.839550201 17.533796214</div>
<div>C 4.915544062 0.711333118 17.590036280</div>
<div>C 4.915853909 2.129726547 17.558981625</div>
<div>C 6.143486600 0.002227196 17.614492659</div>
<div>C 6.144397239 2.838931198 17.567937591</div>
<div>C -0.009386173 4.969207674 17.562655171</div>
<div>C -0.007017413 6.394548846 17.533586100</div>
<div>C 1.221221723 4.253471766 17.548052411</div>
<div>C 1.198574699 7.115165393 17.592468497</div>
<div>C 2.446729939 4.945634289 17.560357556</div>
<div>C 2.429014083 6.377364466 17.843730988</div>
<div>C 3.679896901 4.258356417 17.551643715</div>
<div>C 3.704632453 7.115561848 17.867361404</div>
<div>C 4.916336515 4.974358812 17.564482071</div>
<div>C 4.935632583 6.385210475 17.597930230</div>
<div>C 6.145763199 4.260558789 17.557531939</div>
<div>C 6.139436097 7.104085900 17.546822753</div>
<div>C -0.008057730 9.237466939 17.548881513</div>
<div>C -0.005309676 10.658828114 17.540319093</div>
<div>C 1.220546640 8.524488204 17.583337938</div>
<div>C 1.225791434 11.368226350 17.566890173</div>
<div>C 2.458810059 9.240431880 17.612862514</div>
<div>C 2.454941023 10.659162890 17.592221246</div>
<div>C 3.688725076 8.555854012 17.643635937</div>
<div>C 3.683918063 11.368771580 17.603925777</div>
<div>C 4.910904632 9.244786635 17.581661741</div>
<div>C 4.913395819 10.664333371 17.573847419</div>
<div>C 6.143923926 8.528771033 17.556446236</div>
<div>C 6.142987294 11.370161820 17.555480374</div>
<div>C -0.004309434 13.496944454 17.583281339</div>
<div>C -0.004505934 14.915030012 17.613620426</div>
<div>C 1.226582522 12.786684076 17.587667221</div>
<div>C 1.224762481 15.623384029 17.618836753</div>
<div>C 2.455170254 13.495545076 17.620810601</div>
<div>C 2.455394258 14.913895553 17.626574694</div>
<div>C 3.684071873 12.787455574 17.618041427</div>
<div>C 3.684499812 15.622198165 17.627916140</div>
<div>C 4.913552069 13.495405863 17.614905357</div>
<div>C 4.913417489 14.913710743 17.621452935</div>
<div>C 6.142676777 12.788081224 17.582175333</div>
<div>C 6.143988489 15.623015254 17.616347215</div>
<div><br>
</div>
<div><br>
</div>
<div>K_POINTS automatic</div>
<div>4 2 1 0 0 0</div>
<div><br>
</div>
<div>CELL_PARAMETERS angstrom</div>
<div>7.378073983 0.000000000 0.0000000000</div>
<div>0.000000000 17.038932 0.0000000000</div>
<div>0.000000000 0.000000000 25.00</div>
</div>
<div><br>
</div>
<div>I still get it stuck here in output: </div>
<div><br>
</div>
<div>
<div>Estimated max dynamical RAM per process > 9360.31MB</div>
<div><br>
</div>
<div> Check: negative/imaginary core charge= -0.000003
0.000000</div>
<div><br>
</div>
<div> Initial potential from superposition of free atoms</div>
<div> Check: negative starting charge= -0.001323</div>
<div><br>
</div>
<div> starting charge 191.99800, renormalised to
192.00000</div>
<div><br>
</div>
<div> negative rho (up, down): 1.323E-03 0.000E+00</div>
<div> Starting wfc are 192 randomized atomic wfcs</div>
<div><br>
</div>
<div> total cpu time spent up to now is 1474.4 secs</div>
<div><br>
</div>
<div> per-process dynamical memory: 1195.0 Mb</div>
<div><br>
</div>
<div> Self-consistent Calculation</div>
<div><br>
</div>
<div> iteration # 1 ecut= 80.00 Ry beta=0.70</div>
<div> Davidson diagonalization with overlap</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>This code has worked previously with qe/5.4.0, but gets
stuck with 6.1 serial.</div>
<div><br>
</div>
<div>-Hud</div>
<blockquote class="history_container" type="cite"
style="border-left-style:solid;border-width:1px;
margin-top:20px; margin-left:0px;padding-left:10px;">
<p style="color: #AAAAAA; margin-top: 10px;">On 5/9/2019
1:23:39 PM, Giuseppe Mattioli
<a class="moz-txt-link-rfc2396E" href="mailto:giuseppe.mattioli@ism.cnr.it"><giuseppe.mattioli@ism.cnr.it></a> wrote:</p>
<div style="font-family:Arial,Helvetica,sans-serif"><br>
You are mixing two different ways to indicate cell
parameters<br>
<br>
///---<br>
EITHER:<br>
<br>
+--------------------------------------------------------------------<br>
Variable: celldm(i), i=1,6<br>
<br>
Type: REAL<br>
See: ibrav<br>
Description: Crystallographic constants - see the "ibrav"
variable.<br>
Specify either these OR <br>
"A","B","C","cosAB","cosBC","cosAC" NOT both.<br>
Only needed values (depending on "ibrav") must <br>
be specified<br>
alat = "celldm"(1) is the lattice parameter "a" <br>
(in BOHR)<br>
If "ibrav"==0, only "celldm"(1) is used if present;<br>
cell vectors are read from card "CELL_PARAMETERS"<br>
+--------------------------------------------------------------------<br>
<br>
OR:<br>
<br>
+--------------------------------------------------------------------<br>
Variables: A, B, C, cosAB, cosAC, cosBC<br>
<br>
Type: REAL<br>
See: ibrav<br>
Description: Traditional crystallographic constants:<br>
<br>
a,b,c in ANGSTROM<br>
cosAB = cosine of the angle between axis a <br>
and b (gamma)<br>
cosAC = cosine of the angle between axis a <br>
and c (beta)<br>
cosBC = cosine of the angle between axis b <br>
and c (alpha)<br>
<br>
The axis are chosen according to the value of <br>
@ref ibrav.<br>
Specify either these OR @ref celldm but NOT both.<br>
Only needed values (depending on @ref ibrav) <br>
must be specified.<br>
<br>
The lattice parameter alat = A (in ANGSTROM ).<br>
<br>
If @ref ibrav == 0, only A is used if present, and<br>
cell vectors are read from card @ref CELL_PARAMETERS.<br>
+--------------------------------------------------------------------<br>
<br>
\\\---<br>
<br>
This might be the cause of the strange behavior, supposing
that your <br>
machine has the ~4GB of free RAM to perform the calculation
indicated <br>
in the output. However, in the case of a regular hcp
supercell you <br>
should not need at all to indicate the cosAB and cosAC
values.<br>
HTH<br>
Giuseppe<br>
<br>
<br>
Quoting "H1@GMAIL" <hudwahab@gmail.com>:<br>
<br>
> Hi Giuseppe<br>
><br>
> apologies. My input file:<br>
><br>
> &control<br>
> calculation = 'scf'<br>
> prefix = 'graphene'<br>
> pseudo_dir = '/gscratch/hwahab/DFT-code/psp/'<br>
> outdir = './'<br>
> restart_mode = 'from_scratch'<br>
> etot_conv_thr = 1.d-6<br>
> forc_conv_thr = 1.d-5<br>
> /<br>
> &system<br>
> ibrav = 4<br>
> celldm(1) = 9.84<br>
> celldm(3) = 10<br>
> cosAB = -0.5<br>
> cosAC = 1<br>
> nat = 32<br>
> ntyp = 1<br>
> ecutwfc = 80<br>
> occupations = 'smearing'<br>
> smearing = 'gaussian'<br>
> degauss = 0.1<br>
> vdw_corr='grimme-d2'<br>
> /<br>
><br>
> &electrons<br>
> diagonalization = 'david'<br>
> diago_thr_init = 1.d-4<br>
> mixing_mode = 'local-TF'<br>
> mixing_beta = 0.7<br>
> conv_thr = 1.d-10<br>
> / <br>
><br>
> &ions<br>
> /<br>
><br>
> ATOMIC_SPECIES<br>
> C 12.0107 C.pbe-mt_gipaw.UPF <br>
><br>
> ATOMIC_POSITIONS crystal<br>
> C 0.16667 0.08333 0.00000<br>
> C 0.41667 0.08333 0.00000<br>
> C 0.66667 0.08333 0.00000<br>
> C 0.91667 0.08333 0.00000<br>
> C 0.08333 0.16667 0.00000<br>
> C 0.33333 0.16667 0.00000<br>
> C 0.58333 0.16667 0.00000<br>
> C 0.83333 0.16667 0.00000<br>
> C 0.16667 0.33333 0.00000<br>
> C 0.41667 0.33333 0.00000<br>
> C 0.66667 0.33333 0.00000<br>
> C 0.91667 0.33333 0.00000<br>
> C 0.08333 0.41667 0.00000<br>
> C 0.33333 0.41667 0.00000<br>
> C 0.58333 0.41667 0.00000<br>
> C 0.83333 0.41667 0.00000<br>
> C 0.16667 0.58333 0.00000<br>
> C 0.41667 0.58333 0.00000<br>
> C 0.66667 0.58333 0.00000<br>
> C 0.91667 0.58333 0.00000<br>
> C 0.08333 0.66667 0.00000<br>
> C 0.33333 0.66667 0.00000<br>
> C 0.58333 0.66667 0.00000<br>
> C 0.83333 0.66667 0.00000<br>
> C 0.16667 0.83333 0.00000<br>
> C 0.41667 0.83333 0.00000<br>
> C 0.66667 0.83333 0.00000<br>
> C 0.91667 0.83333 0.00000<br>
> C 0.08333 0.91667 0.00000<br>
> C 0.33333 0.91667 0.00000<br>
> C 0.58333 0.91667 0.00000<br>
> C 0.83333 0.91667 0.00000<br>
> <br>
><br>
> K_POINTS automatic<br>
> 8 8 1 0 0 0<br>
><br>
> And the end snippet of the output:<br>
><br>
> Estimated max dynamical RAM per process >
3558.76MB<br>
><br>
> Initial potential from superposition of free
atoms<br>
><br>
> starting charge 111.99996, renormalised to
128.00000<br>
><br>
> negative rho (up, down): 5.479E-05 0.000E+00<br>
> Starting wfc are 256 randomized atomic wfcs<br>
><br>
> There is no error outputs, it just gets stuck there..<br>
><br>
> Hope this makes sense.<br>
><br>
> Hud Wahab<br>
> University of Wyoming<br>
> 1000 E University Ave<br>
> Laramie WY, 82072<br>
> Email: <a class="moz-txt-link-abbreviated" href="mailto:hwahab@uwyo.edu">hwahab@uwyo.edu</a><br>
> On 5/9/2019 12:50:50 PM, Giuseppe Mattioli <br>
> <giuseppe.mattioli@ism.cnr.it> wrote:<br>
><br>
> Dear Hud (please sign always with full name and
scientific affiliation<br>
> the posts to this forum, we appreciate it)<br>
> It is impossible to help you if you don't post the
input of your<br>
> calculation and the relevant part of your output
(where does the code<br>
> stop?). Is there any system error like a segfault
printed, e.g., in a<br>
> nohup.out file? It is primarily important to look
into such kind of<br>
> information, in order to see if the error is
reproducible on different<br>
> machines/architectures or by using different
compilers/libraries.<br>
> HTH<br>
> Giuseppe<br>
><br>
> Quoting "H1@GMAIL" :<br>
><br>
>> Hello<br>
>> I run on 6.1-serial. My pw.x scf runs ok with
small size systems 2<br>
>> atoms, but nothing happens when scaled to 4x4
or 32 atoms. I let it<br>
>> run for more than an hour and don't expect that
the calculation<br>
>> takes that long.<br>
>><br>
>> From the troubleshooting in User Guide I see it
might be a<br>
>> floating-point error causing endless NaNs - how
to handle for such<br>
>> exceptions?<br>
>><br>
>> As I can't provide the error output, I am not
sure what details you<br>
>> need to troubleshoot, but let me know if
something is missing<br>
>><br>
>> Cheers, Hud<br>
>> Dept. Chemical Engineering<br>
>> University of Wyoming<br>
><br>
><br>
><br>
> GIUSEPPE MATTIOLI<br>
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
> Via Salaria Km 29,300 - C.P. 10<br>
> I-00015 - Monterotondo Scalo (RM)<br>
> Mob (*preferred*) +39 373 7305625<br>
> Tel + 39 06 90672342 - Fax +39 06 90672316<br>
> E-mail:<br>
><br>
> _______________________________________________<br>
> 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>)<br>
> users mailing list <a class="moz-txt-link-abbreviated" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><br>
>
<a class="moz-txt-link-freetext" href="https://lists.quantum-espresso.org/mailman/listinfo/users">https://lists.quantum-espresso.org/mailman/listinfo/users</a><br>
<br>
<br>
<br>
GIUSEPPE MATTIOLI<br>
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA<br>
Via Salaria Km 29,300 - C.P. 10<br>
I-00015 - Monterotondo Scalo (RM)<br>
Mob (*preferred*) +39 373 7305625<br>
Tel + 39 06 90672342 - Fax +39 06 90672316<br>
E-mail: <giuseppe.mattioli@ism.cnr.it><br>
<br>
_______________________________________________<br>
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>)<br>
users mailing list <a class="moz-txt-link-abbreviated" href="mailto:users@lists.quantum-espresso.org">users@lists.quantum-espresso.org</a><br>
<a class="moz-txt-link-freetext" href="https://lists.quantum-espresso.org/mailman/listinfo/users">https://lists.quantum-espresso.org/mailman/listinfo/users</a></giuseppe.mattioli@ism.cnr.it></giuseppe.mattioli@ism.cnr.it></hudwahab@gmail.com></div>
</blockquote>
</div>
<br>
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<br>
<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>)
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Oleksandr Motornyi
PhD candidate
Laboratoire de Solides Irradies
Ecole Polytechnique (Palaiseau, France)</pre>
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