[QE-users] (no subject)
Paolo Giannozzi
p.giannozzi at gmail.com
Mon Aug 27 20:52:22 CEST 2018
Reducing mixing_ndim should actually reduce a bit (but not much) the needed
memory. in the very likely case of slow scf convergence, use
mixing_mode='local-TF' and increase the initial scf threshold to 10^-6 or
so.
Paolo
On Tue, Aug 28, 2018 at 12:34 AM, Dan Gil <dan.gil9973 at gmail.com> wrote:
> Thank you Paolo,
>
> I wasn't initially sure that it was really a RAM problem, because I tried
> reducing mixing_ndim but this didn't have any impact on the "Estimated
> total dynamical RAM." I am sorry that this seemed thoughtless.
>
> I tried again with K_POINTS gamma - it is running now without any problems
> so far!
>
> Thanks as always,
>
> Dan
>
> On Mon, Aug 27, 2018 at 11:21 AM Paolo Giannozzi <p.giannozzi at gmail.com>
> wrote:
>
>> On Sat, Aug 25, 2018 at 2:00 AM, Dan Gil <dan.gil9973 at gmail.com> wrote:
>>
>> [...] With the input format shown below, I get the following error from
>>> the HPC.
>>>
>>> - - - - -
>>> /tmp/slurm/job8327489/slurm_script: line 11: 111713
>>> Killed pw.x < sapphire.pw.in > sapphire.pw.out
>>> slurmstepd: error: Exceeded step memory limit at some point.
>>> - - - - -
>>>
>>> When I run it on my personal computer
>>>
>>
>> let me understand: your HPC says "exceeded memory", and you try to run it
>> on your PC?
>> In your output, there should be a line saying something like
>>
>> Estimated total dynamical RAM > 67.08 GB
>>
>> By setting
>> K_POINTS gamma
>> instead of
>> K_POINTS automatic
>> 1 1 1 1 1 1
>> you can cut the RAM into half (results are the same), by the way. You
>> should also consider reducing the cell length along c (95 A!) and starting
>> with smaller cutoffs.
>>
>> Paolo
>>
>> I get this error:
>>>
>>> - - - - -
>>> task # 0
>>> from diropn : error # 10
>>> error opening sapphire/pwscf.wfc1
>>> - - - - -
>>>
>>> And indeed, there is no pwscf.wfc1 to be seen.
>>>
>>> Here is the input:
>>>
>>> - - - - -
>>> &control
>>> calculation='relax',
>>> wf_collect = .true. ,
>>> outdir = 'sapphire' ,
>>> restart_mode = 'from_scratch' ,
>>> pseudo_dir = 'pseudo' ,
>>> disk_io = 'low' ,
>>> verbosity = 'low' ,
>>> max_seconds = 72000 ,
>>> /
>>> &system
>>> ibrav = 4 ,
>>> celldm(1)=17.99085377,
>>> celldm(3)=10,
>>> nat = 168 ,
>>> ntyp = 3 ,
>>> ecutwfc =50,
>>> ecutrho =400,
>>> smearing='mp',
>>> occupations='smearing',
>>> degauss=0.03,
>>> /
>>> &electrons
>>> diagonalization='david',
>>> conv_thr = 1.d-9,
>>> mixing_mode = 'plain',
>>> /
>>> &ions
>>> /
>>> ATOMIC_SPECIES
>>> Al 26.981539 Al.pbe-n-rrkjus_psl.0.1.UPF
>>> O 15.999000 O.pbe-n-rrkjus_psl.0.1.UPF
>>> H 1.000800 H.pbe-rrkjus_psl.0.1.UPF
>>> ATOMIC_POSITIONS crystal
>>> Al 0.000000000 0.000000000 0.095697893
>>> Al 0.000000000 0.000000000 0.177259148
>>> Al 0.000000000 0.000000000 0.040053860
>>> Al 0.000000000 0.000000000 0.232903158
>>> Al 0.333333311 0.166666621 0.187801968
>>> Al 0.333333311 0.166666621 0.270721823
>>> Al 0.333333311 0.166666621 0.131337383
>>> Al 0.333333311 0.166666621 0.045832216
>>> Al 0.166666682 0.333333364 0.002235215
>>> Al 0.166666682 0.333333364 0.085155073
>>> Al 0.166666682 0.333333364 0.227124825
>>> Al 0.166666682 0.333333364 0.141619636
>>> Al 0.500000000 0.000000000 0.095697893
>>> Al 0.500000000 0.000000000 0.177259148
>>> Al 0.500000000 0.000000000 0.040053860
>>> Al 0.500000000 0.000000000 0.232903158
>>> Al 0.833333311 0.166666621 0.187801968
>>> Al 0.833333311 0.166666621 0.270721823
>>> Al 0.833333311 0.166666621 0.131337383
>>> Al 0.833333311 0.166666621 0.045832216
>>> Al 0.666666682 0.333333364 0.002235215
>>> Al 0.666666682 0.333333364 0.085155073
>>> Al 0.666666682 0.333333364 0.227124825
>>> Al 0.666666682 0.333333364 0.141619636
>>> Al 0.500000000 0.500000000 0.095697893
>>> Al 0.500000000 0.500000000 0.177259148
>>> Al 0.500000000 0.500000000 0.040053860
>>> Al 0.500000000 0.500000000 0.232903158
>>> Al 0.833333311 0.666666621 0.187801968
>>> Al 0.833333311 0.666666621 0.270721823
>>> Al 0.833333311 0.666666621 0.131337383
>>> Al 0.833333311 0.666666621 0.045832216
>>> Al 0.666666682 0.833333364 0.002235215
>>> Al 0.666666682 0.833333364 0.085155073
>>> Al 0.666666682 0.833333364 0.227124825
>>> Al 0.666666682 0.833333364 0.141619636
>>> Al 0.000000000 0.500000000 0.095697893
>>> Al 0.000000000 0.500000000 0.177259148
>>> Al 0.000000000 0.500000000 0.040053860
>>> Al 0.000000000 0.500000000 0.232903158
>>> Al 0.333333311 0.666666621 0.187801968
>>> Al 0.333333311 0.666666621 0.270721823
>>> Al 0.333333311 0.666666621 0.131337383
>>> Al 0.333333311 0.666666621 0.045832216
>>> Al 0.166666682 0.833333364 0.002235215
>>> Al 0.166666682 0.833333364 0.085155073
>>> Al 0.166666682 0.833333364 0.227124825
>>> Al 0.166666682 0.833333364 0.141619636
>>> O 0.155404208 0.001886947 0.067662578
>>> O 0.344595898 -0.001886947 0.205294440
>>> O -0.001886987 0.153517181 0.067662578
>>> O 0.001886979 0.346482804 0.205294440
>>> O 0.346482772 0.344595857 0.067662578
>>> O 0.153517221 0.155404128 0.205294440
>>> O 0.171949672 0.170609214 0.023055667
>>> O 0.333498557 0.320107131 0.159438914
>>> O 0.329390758 0.001340470 0.023055667
>>> O 0.179892883 0.013391458 0.159438914
>>> O 0.328050321 0.329390771 0.249901352
>>> O 0.013391439 0.333498589 0.113518146
>>> O 0.166501497 0.179892975 0.113518146
>>> O 0.001340490 0.171949804 0.249901352
>>> O 0.320107118 -0.013391458 0.113518146
>>> O -0.013391447 0.166501396 0.159438914
>>> O -0.001340437 0.328050302 0.023055667
>>> O 0.170609242 -0.001340470 0.249901352
>>> O 0.181666250 0.166682692 0.300333049
>>> O 0.333317280 0.014983569 0.300333049
>>> O 0.485016464 0.318333724 0.300333049
>>> O 0.014983590 0.181666382 -0.027376009
>>> O 0.318333743 0.333317293 -0.027376009
>>> O 0.166682713 0.485016416 -0.027376009
>>> O 0.655404208 0.001886947 0.067662578
>>> O 0.844595898 -0.001886947 0.205294440
>>> O 0.498113014 0.153517181 0.067662578
>>> O 0.501886979 0.346482804 0.205294440
>>> O 0.846482772 0.344595857 0.067662578
>>> O 0.653517221 0.155404128 0.205294440
>>> O 0.671949672 0.170609214 0.023055667
>>> O 0.833498557 0.320107131 0.159438914
>>> O 0.829390758 0.001340470 0.023055667
>>> O 0.679892883 0.013391458 0.159438914
>>> O 0.828050321 0.329390771 0.249901352
>>> O 0.513391439 0.333498589 0.113518146
>>> O 0.666501497 0.179892975 0.113518146
>>> O 0.501340490 0.171949804 0.249901352
>>> O 0.820107118 -0.013391458 0.113518146
>>> O 0.486608554 0.166501396 0.159438914
>>> O 0.498659563 0.328050302 0.023055667
>>> O 0.670609242 -0.001340470 0.249901352
>>> O 0.681666250 0.166682692 0.300333049
>>> O 0.833317280 0.014983569 0.300333049
>>> O 0.985016464 0.318333724 0.300333049
>>> O 0.514983590 0.181666382 -0.027376009
>>> O 0.818333743 0.333317293 -0.027376009
>>> O 0.666682713 0.485016416 -0.027376009
>>> O 0.655404208 0.501886947 0.067662578
>>> O 0.844595898 0.498113054 0.205294440
>>> O 0.498113014 0.653517181 0.067662578
>>> O 0.501886979 0.846482804 0.205294440
>>> O 0.846482772 0.844595857 0.067662578
>>> O 0.653517221 0.655404128 0.205294440
>>> O 0.671949672 0.670609214 0.023055667
>>> O 0.833498557 0.820107131 0.159438914
>>> O 0.829390758 0.501340470 0.023055667
>>> O 0.679892883 0.513391458 0.159438914
>>> O 0.828050321 0.829390771 0.249901352
>>> O 0.513391439 0.833498589 0.113518146
>>> O 0.666501497 0.679892975 0.113518146
>>> O 0.501340490 0.671949804 0.249901352
>>> O 0.820107118 0.486608542 0.113518146
>>> O 0.486608554 0.666501396 0.159438914
>>> O 0.498659563 0.828050302 0.023055667
>>> O 0.670609242 0.498659531 0.249901352
>>> O 0.681666250 0.666682692 0.300333049
>>> O 0.833317280 0.514983569 0.300333049
>>> O 0.985016464 0.818333724 0.300333049
>>> O 0.514983590 0.681666382 -0.027376009
>>> O 0.818333743 0.833317293 -0.027376009
>>> O 0.666682713 0.985016416 -0.027376009
>>> O 0.155404208 0.501886947 0.067662578
>>> O 0.344595898 0.498113054 0.205294440
>>> O -0.001886987 0.653517181 0.067662578
>>> O 0.001886979 0.846482804 0.205294440
>>> O 0.346482772 0.844595857 0.067662578
>>> O 0.153517221 0.655404128 0.205294440
>>> O 0.171949672 0.670609214 0.023055667
>>> O 0.333498557 0.820107131 0.159438914
>>> O 0.329390758 0.501340470 0.023055667
>>> O 0.179892883 0.513391458 0.159438914
>>> O 0.328050321 0.829390771 0.249901352
>>> O 0.013391439 0.833498589 0.113518146
>>> O 0.166501497 0.679892975 0.113518146
>>> O 0.001340490 0.671949804 0.249901352
>>> O 0.320107118 0.486608542 0.113518146
>>> O -0.013391447 0.666501396 0.159438914
>>> O -0.001340437 0.828050302 0.023055667
>>> O 0.170609242 0.498659531 0.249901352
>>> O 0.181666250 0.666682692 0.300333049
>>> O 0.333317280 0.514983569 0.300333049
>>> O 0.485016464 0.818333724 0.300333049
>>> O 0.014983590 0.681666382 -0.027376009
>>> O 0.318333743 0.833317293 -0.027376009
>>> O 0.166682713 0.985016416 -0.027376009
>>> H 0.000000000 0.000000000 0.301962321
>>> H 0.333333311 0.166666621 0.311183904
>>> H 0.166666682 0.333333364 0.301819835
>>> H 0.000000000 0.000000000 -0.029005281
>>> H 0.333333311 0.166666621 -0.028862795
>>> H 0.166666682 0.333333364 -0.038226863
>>> H 0.500000000 0.000000000 0.301962321
>>> H 0.833333311 0.166666621 0.311183904
>>> H 0.666666682 0.333333364 0.301819835
>>> H 0.500000000 0.000000000 -0.029005281
>>> H 0.833333311 0.166666621 -0.028862795
>>> H 0.666666682 0.333333364 -0.038226863
>>> H 0.500000000 0.500000000 0.301962321
>>> H 0.833333311 0.666666621 0.311183904
>>> H 0.666666682 0.833333364 0.301819835
>>> H 0.500000000 0.500000000 -0.029005281
>>> H 0.833333311 0.666666621 -0.028862795
>>> H 0.666666682 0.833333364 -0.038226863
>>> H 0.000000000 0.500000000 0.301962321
>>> H 0.333333311 0.666666621 0.311183904
>>> H 0.166666682 0.833333364 0.301819835
>>> H 0.000000000 0.500000000 -0.029005281
>>> H 0.333333311 0.666666621 -0.028862795
>>> H 0.166666682 0.833333364 -0.038226863
>>> K_POINTS automatic
>>> 1 1 1 1 1 1
>>> - - - - -
>>>
>>> Best Regards,
>>>
>>> Dan Gil
>>> PhD Candidate
>>> Department of Chemical and Biomolecular Engineering
>>> Case Western Reserve University
>>>
>>> _______________________________________________
>>> users mailing list
>>> users at lists.quantum-espresso.org
>>> https://lists.quantum-espresso.org/mailman/listinfo/users
>>>
>>
>>
>>
>> --
>> Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
>> Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
>> Phone +39-0432-558216, fax +39-0432-558222
>>
>> _______________________________________________
>> users mailing list
>> users at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>
>
> _______________________________________________
> users mailing list
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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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