[QE-users] pw.x stuck.

Giuseppe Mattioli giuseppe.mattioli at ism.cnr.it
Thu May 9 22:59:23 CEST 2019


Hi
I don't know exactly why, because nothing seems clearly wrong in your  
input file, but I see

> K_POINTS automatic
> 4 2 1  0 0 0

>      total cpu time spent up to now is     1474.4 secs

Your calculation seems to be very slow, more than 20 minutes for the  
first scf step, and the second step is often slower... And in your  
previous calculation I saw

> K_POINTS automatic
> 8 8 1 0 0 0

that is going to be even slower. Are you sure pw.x hangs? If you type  
$ top in a console (I suppose you use linux) do you see one active  
pw.x process?
HTH
Giuseppe

Quoting Hud Wahab <hudwahab at gmail.com>:

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



GIUSEPPE MATTIOLI
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
Via Salaria Km 29,300 - C.P. 10
I-00015 - Monterotondo Scalo (RM)
Mob (*preferred*) +39 373 7305625
Tel + 39 06 90672342 - Fax +39 06 90672316
E-mail: <giuseppe.mattioli at ism.cnr.it>



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