[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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