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I am using a single node with 64 gb memory with 32 cpus per task <div><br></div><div>I tried running the 32 atom calc again with 1x1x1 k-points and it got stuck as well.</div><div>But 2 atoms with 8x8x1 works.</div><div><br></div><div>$ top, I dont see the pw.x written explicitly.</div><div><br></div><div>Should I try letting pw.x run longer than an hour?</div><div class="mb_sig"></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 2:59:56 PM, Giuseppe Mattioli <giuseppe.mattioli@ism.cnr.it> wrote:</p><div style="font-family:Arial,Helvetica,sans-serif"><br>Hi<br>I don't know exactly why, because nothing seems clearly wrong in your <br>input file, but I see<br><br>> K_POINTS automatic<br>> 4 2 1 0 0 0<br><br>> total cpu time spent up to now is 1474.4 secs<br><br>Your calculation seems to be very slow, more than 20 minutes for the <br>first scf step, and the second step is often slower... And in your <br>previous calculation I saw<br><br>> K_POINTS automatic<br>> 8 8 1 0 0 0<br><br>that is going to be even slower. Are you sure pw.x hangs? If you type <br>$ top in a console (I suppose you use linux) do you see one active <br>pw.x process?<br>HTH<br>Giuseppe<br><br>Quoting Hud Wahab <hudwahab@gmail.com>:<br><br>> Hi<br>><br>> ok, even if I try with ibrav == 0, specify cell_parameters, and use <br>> cartesian coordinates for all as such:<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>><br>> &system<br>>   ibrav = 0<br>>   nat = 48<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-8<br>> /<br>><br>> &ions<br>>    <br>> /<br>><br>> ATOMIC_SPECIES<br>> C 12.0107 C.pbe-n-kjpaw_psl.1.0.0.UPF <br>><br>> ATOMIC_POSITIONS angstrom<br>> C    -0.005594637  0.710607728  17.606217811<br>> C    -0.007113039  2.128152101  17.584272182<br>> C     1.224800757  0.002792887  17.613037723<br>> C     1.220781849  2.833821539  17.553802163<br>> C     2.453370565  0.710361709  17.588200291<br>> C     2.452466724  2.129238290  17.551425829<br>> C     3.684434744  0.001530538  17.594476170<br>> C     3.684438920  2.839550201  17.533796214<br>> C     4.915544062  0.711333118  17.590036280<br>> C     4.915853909  2.129726547  17.558981625<br>> C     6.143486600  0.002227196  17.614492659<br>> C     6.144397239  2.838931198  17.567937591<br>> C    -0.009386173  4.969207674  17.562655171<br>> C    -0.007017413  6.394548846  17.533586100<br>> C     1.221221723  4.253471766  17.548052411<br>> C     1.198574699  7.115165393  17.592468497<br>> C     2.446729939  4.945634289  17.560357556<br>> C     2.429014083  6.377364466  17.843730988<br>> C     3.679896901  4.258356417  17.551643715<br>> C     3.704632453  7.115561848  17.867361404<br>> C     4.916336515  4.974358812  17.564482071<br>> C     4.935632583  6.385210475  17.597930230<br>> C     6.145763199  4.260558789  17.557531939<br>> C     6.139436097  7.104085900  17.546822753<br>> C    -0.008057730  9.237466939  17.548881513<br>> C    -0.005309676  10.658828114  17.540319093<br>> C     1.220546640  8.524488204  17.583337938<br>> C     1.225791434  11.368226350  17.566890173<br>> C     2.458810059  9.240431880  17.612862514<br>> C     2.454941023  10.659162890  17.592221246<br>> C     3.688725076  8.555854012  17.643635937<br>> C     3.683918063  11.368771580  17.603925777<br>> C     4.910904632  9.244786635  17.581661741<br>> C     4.913395819  10.664333371  17.573847419<br>> C     6.143923926  8.528771033  17.556446236<br>> C     6.142987294  11.370161820  17.555480374<br>> C    -0.004309434  13.496944454  17.583281339<br>> C    -0.004505934  14.915030012  17.613620426<br>> C     1.226582522  12.786684076  17.587667221<br>> C     1.224762481  15.623384029  17.618836753<br>> C     2.455170254  13.495545076  17.620810601<br>> C     2.455394258  14.913895553  17.626574694<br>> C     3.684071873  12.787455574  17.618041427<br>> C     3.684499812  15.622198165  17.627916140<br>> C     4.913552069  13.495405863  17.614905357<br>> C     4.913417489  14.913710743  17.621452935<br>> C     6.142676777  12.788081224  17.582175333<br>> C     6.143988489  15.623015254  17.616347215<br>><br>><br>> K_POINTS automatic<br>> 4 2 1  0 0 0<br>><br>> CELL_PARAMETERS angstrom<br>> 7.378073983 0.000000000 0.0000000000<br>> 0.000000000 17.038932 0.0000000000<br>> 0.000000000 0.000000000 25.00<br>><br>> I still get it stuck here in output: <br>><br>> Estimated max dynamical RAM per process >   9360.31MB<br>><br>>    Check: negative/imaginary core charge=  -0.000003   0.000000<br>><br>>    Initial potential from superposition of free atoms<br>>    Check: negative starting charge=  -0.001323<br>><br>>    starting charge  191.99800, renormalised to  192.00000<br>><br>>    negative rho (up, down):  1.323E-03 0.000E+00<br>>    Starting wfc are  192 randomized atomic wfcs<br>><br>>    total cpu time spent up to now is   1474.4 secs<br>><br>>    per-process dynamical memory:  1195.0 Mb<br>><br>>    Self-consistent Calculation<br>><br>>    iteration #  1   ecut=   80.00 Ry   beta=0.70<br>>    Davidson diagonalization with overlap<br>><br>><br>> This code has worked previously with qe/5.4.0, but gets stuck with <br>> 6.1 serial.<br>><br>> -Hud<br>> On 5/9/2019 1:23:39 PM, Giuseppe Mattioli <br>> <giuseppe.mattioli@ism.cnr.it> wrote:<br>><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" :<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: hwahab@uwyo.edu<br>>> On 5/9/2019 12:50:50 PM, Giuseppe Mattioli<br>>> 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 (www.max-centre.eu/quantum-espresso)<br>>> users mailing list users@lists.quantum-espresso.org<br>>> https://lists.quantum-espresso.org/mailman/listinfo/users<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 (www.max-centre.eu/quantum-espresso)<br>> users mailing list users@lists.quantum-espresso.org<br>> https://lists.quantum-espresso.org/mailman/listinfo/users<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 (www.max-centre.eu/quantum-espresso)<br>users mailing list users@lists.quantum-espresso.org<br>https://lists.quantum-espresso.org/mailman/listinfo/users</giuseppe.mattioli@ism.cnr.it></giuseppe.mattioli@ism.cnr.it></hudwahab@gmail.com></div></blockquote>
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