[QE-users] (no subject)

Dan Gil dan.gil9973 at gmail.com
Tue Aug 28 00:34:21 CEST 2018


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
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