[QE-users] (no subject)
Dan Gil
dan.gil9973 at gmail.com
Tue Aug 28 01:04:08 CEST 2018
Thanks, I'll make sure to try those options out!
Dan
On Mon, Aug 27, 2018 at 2:53 PM Paolo Giannozzi <p.giannozzi at gmail.com>
wrote:
> 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
>> 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
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