[Pw_forum] Geometry optimization on QE530-GPU with memory allocation error?
Filippo Spiga
filippo.spiga at quantum-espresso.org
Tue Feb 16 05:20:11 CET 2016
Dear Rolly,
sorry to hear about your problem, I imagine the frustration of losing so much time and being unable to recover because of an error happened in the middle of a SCF step. It is hard to guess what went wrong at that point, especially after the calculation run continuously on multiple GPU for almost 7 days without stop.
Just a consideration, valid with or without GPU: unless not possible, _never_ run continuously for so long. It is a bad idea for multiple reasons. Always safely checkpoit/restart your calculation more often.
Cheers
--
Filippo SPIGA
* Sent from my iPhone, sorry for typos *
> On 16 Feb 2016, at 04:01, Rolly Ng <rollyng at gmail.com> wrote:
>
> Dear Filippo and QE-GPU users,
>
> I am running a geometry optimization and the system contains 128 atoms. It runs fine but until the time spent reaches 590,000 seconds it stops with the error, and the job fails to complete L and I have this error 3 times for 3 different cases.
>
> “Error in memory allocation, program will be terminated (2) !!! Bye…”
>
> I can confirm the error only appear after running for more than 560,000 seconds, so all the previous effort was wasted L if I cannot restart the optimization L.
>
> I have not seen such problem with QE520-GPU or may be my previous runs did not last for so long.
>
> Could you please check my input file? Thank you!
>
> &CONTROL
> calculation = 'relax' ,
> outdir = '/home/zgdeng/Rolly/TiNSurf200',
> pseudo_dir = '/home/zgdeng/SSSP_acc_PBE' ,
> prefix = 'TiNSurf200+Biotin',
> verbosity = 'low' ,
> etot_conv_thr = 1.0D-3 ,
> forc_conv_thr = 1.0D-2 ,
> nstep = 100 ,
> tstress = .false. ,
> tprnfor = .false. ,
> /
> &SYSTEM
> ibrav = 14,
> celldm(1) = 22.9288029598d0, celldm(2)=1.2990423130d0, celldm(3)=5.2512156527d0,
> celldm(4) = 0.0000000000d0, celldm(5)=0.0000000000d0, celldm(6)=0.0000000000d0,
> nat = 128,
> ntyp = 6,
> ecutwfc = 30d0 ,
> ecutrho = 240d0 ,
> nosym = .true. ,
> nbnd = 600,
> input_dft = 'PBE' ,
> occupations = 'smearing' ,
> degauss = 0.015d0 ,
> smearing = 'gaussian' ,
> /
> &ELECTRONS
> electron_maxstep = 1000,
> conv_thr = 1d-06 ,
> mixing_mode = 'local-TF' ,
> mixing_beta = 0.300d0 ,
> diagonalization = 'david' ,
> /
> &IONS
> ion_dynamics = 'bfgs' ,
> upscale = 100.D0 ,
> bfgs_ndim = 3 ,
> /
> ATOMIC_SPECIES
> C 12.010700d0 C_pbe_v1.2.uspp.F.UPF
> H 1.007940d0 H.pbe-rrkjus_psl.0.1.UPF
> N 14.006700d0 N.pbe.theos.UPF
> O 15.999400d0 O.pbe-n-kjpaw_psl.0.1.UPF
> S 32.065000d0 S_pbe_v1.2.uspp.F.UPF
> Ti 47.867000d0 ti_pbe_v1.4.uspp.F.UPF
> ATOMIC_POSITIONS {alat}
> Ti 0.0000000000d0 0.0000000000d0 0.1021361444d0 0 0 0
> Ti 0.1250000000d0 0.2165113823d0 0.1021361444d0 0 0 0
> Ti 0.0000000000d0 0.1443365914d0 0.3062508969d0 1 1 1
> Ti 0.1250000000d0 0.3608479737d0 0.3062508969d0 1 1 1
> N 0.0000000000d0 0.1443365914d0 0.0001050243d0 0 0 0
> N 0.1250000000d0 0.3608479737d0 0.0001050243d0 0 0 0
> N 0.1250000000d0 0.0721747909d0 0.2042197767d0 1 1 1
> N 0.0000000000d0 0.2886731828d0 0.2042197767d0 1 1 1
> Ti 0.2500000000d0 0.0000000000d0 0.1021361444d0 0 0 0
> Ti 0.3750000000d0 0.2165113823d0 0.1021361444d0 0 0 0
> Ti 0.2500000000d0 0.1443365914d0 0.3062508969d0 1 1 1
> Ti 0.3750000000d0 0.3608479737d0 0.3062508969d0 1 1 1
> N 0.2500000000d0 0.1443365914d0 0.0001050243d0 0 0 0
> N 0.3750000000d0 0.3608479737d0 0.0001050243d0 0 0 0
> N 0.3750000000d0 0.0721747909d0 0.2042197767d0 1 1 1
> N 0.2500000000d0 0.2886731828d0 0.2042197767d0 1 1 1
> Ti 0.5000000000d0 0.0000000000d0 0.1021361444d0 0 0 0
> Ti 0.6250000000d0 0.2165113823d0 0.1021361444d0 0 0 0
> Ti 0.5000000000d0 0.1443365914d0 0.3062508969d0 1 1 1
> Ti 0.6250000000d0 0.3608479737d0 0.3062508969d0 1 1 1
> N 0.5000000000d0 0.1443365914d0 0.0001050243d0 0 0 0
> N 0.6250000000d0 0.3608479737d0 0.0001050243d0 0 0 0
> N 0.6250000000d0 0.0721747909d0 0.2042197767d0 1 1 1
> N 0.5000000000d0 0.2886731828d0 0.2042197767d0 1 1 1
> Ti 0.7500000000d0 0.0000000000d0 0.1021361444d0 0 0 0
> Ti 0.8750000000d0 0.2165113823d0 0.1021361444d0 0 0 0
> Ti 0.7500000000d0 0.1443365914d0 0.3062508969d0 1 1 1
> Ti 0.8750000000d0 0.3608479737d0 0.3062508969d0 1 1 1
> N 0.7500000000d0 0.1443365914d0 0.0001050243d0 0 0 0
> N 0.8750000000d0 0.3608479737d0 0.0001050243d0 0 0 0
> N 0.8750000000d0 0.0721747909d0 0.2042197767d0 1 1 1
> N 0.7500000000d0 0.2886731828d0 0.2042197767d0 1 1 1
> Ti 0.0000000000d0 0.4330097742d0 0.1021361444d0 0 0 0
> Ti 0.1250000000d0 0.6495211565d0 0.1021361444d0 0 0 0
> Ti 0.0000000000d0 0.5773463656d0 0.3062508969d0 1 1 1
> Ti 0.1250000000d0 0.7938577479d0 0.3062508969d0 1 1 1
> N 0.0000000000d0 0.5773463656d0 0.0001050243d0 0 0 0
> N 0.1250000000d0 0.7938577479d0 0.0001050243d0 0 0 0
> N 0.1250000000d0 0.5051845651d0 0.2042197767d0 1 1 1
> N 0.0000000000d0 0.7216959474d0 0.2042197767d0 1 1 1
> Ti 0.2500000000d0 0.4330097742d0 0.1021361444d0 0 0 0
> Ti 0.3750000000d0 0.6495211565d0 0.1021361444d0 0 0 0
> Ti 0.2500000000d0 0.5773463656d0 0.3062508969d0 1 1 1
> Ti 0.3750000000d0 0.7938577479d0 0.3062508969d0 1 1 1
> N 0.2500000000d0 0.5773463656d0 0.0001050243d0 0 0 0
> N 0.3750000000d0 0.7938577479d0 0.0001050243d0 0 0 0
> N 0.3750000000d0 0.5051845651d0 0.2042197767d0 1 1 1
> N 0.2500000000d0 0.7216959474d0 0.2042197767d0 1 1 1
> Ti 0.5000000000d0 0.4330097742d0 0.1021361444d0 0 0 0
> Ti 0.6250000000d0 0.6495211565d0 0.1021361444d0 0 0 0
> Ti 0.5000000000d0 0.5773463656d0 0.3062508969d0 1 1 1
> Ti 0.6250000000d0 0.7938577479d0 0.3062508969d0 1 1 1
> N 0.5000000000d0 0.5773463656d0 0.0001050243d0 0 0 0
> N 0.6250000000d0 0.7938577479d0 0.0001050243d0 0 0 0
> N 0.6250000000d0 0.5051845651d0 0.2042197767d0 1 1 1
> N 0.5000000000d0 0.7216959474d0 0.2042197767d0 1 1 1
> Ti 0.7500000000d0 0.4330097742d0 0.1021361444d0 0 0 0
> Ti 0.8750000000d0 0.6495211565d0 0.1021361444d0 0 0 0
> Ti 0.7500000000d0 0.5773463656d0 0.3062508969d0 1 1 1
> Ti 0.8750000000d0 0.7938577479d0 0.3062508969d0 1 1 1
> N 0.7500000000d0 0.5773463656d0 0.0001050243d0 0 0 0
> N 0.8750000000d0 0.7938577479d0 0.0001050243d0 0 0 0
> N 0.8750000000d0 0.5051845651d0 0.2042197767d0 1 1 1
> N 0.7500000000d0 0.7216959474d0 0.2042197767d0 1 1 1
> Ti 0.0000000000d0 0.8660325388d0 0.1021361444d0 0 0 0
> Ti 0.1250000000d0 1.0825309307d0 0.1021361444d0 0 0 0
> Ti 0.0000000000d0 1.0103691302d0 0.3062508969d0 1 1 1
> Ti 0.1250000000d0 1.2268675220d0 0.3062508969d0 1 1 1
> N 0.0000000000d0 1.0103691302d0 0.0001050243d0 0 0 0
> N 0.1250000000d0 1.2268675220d0 0.0001050243d0 0 0 0
> N 0.1250000000d0 0.9381943393d0 0.2042197767d0 1 1 1
> N 0.0000000000d0 1.1547057216d0 0.2042197767d0 1 1 1
> Ti 0.2500000000d0 0.8660325388d0 0.1021361444d0 0 0 0
> Ti 0.3750000000d0 1.0825309307d0 0.1021361444d0 0 0 0
> Ti 0.2500000000d0 1.0103691302d0 0.3062508969d0 1 1 1
> Ti 0.3750000000d0 1.2268675220d0 0.3062508969d0 1 1 1
> N 0.2500000000d0 1.0103691302d0 0.0001050243d0 0 0 0
> N 0.3750000000d0 1.2268675220d0 0.0001050243d0 0 0 0
> N 0.3750000000d0 0.9381943393d0 0.2042197767d0 1 1 1
> N 0.2500000000d0 1.1547057216d0 0.2042197767d0 1 1 1
> Ti 0.5000000000d0 0.8660325388d0 0.1021361444d0 0 0 0
> Ti 0.6250000000d0 1.0825309307d0 0.1021361444d0 0 0 0
> Ti 0.5000000000d0 1.0103691302d0 0.3062508969d0 1 1 1
> Ti 0.6250000000d0 1.2268675220d0 0.3062508969d0 1 1 1
> N 0.5000000000d0 1.0103691302d0 0.0001050243d0 0 0 0
> N 0.6250000000d0 1.2268675220d0 0.0001050243d0 0 0 0
> N 0.6250000000d0 0.9381943393d0 0.2042197767d0 1 1 1
> N 0.5000000000d0 1.1547057216d0 0.2042197767d0 1 1 1
> Ti 0.7500000000d0 0.8660325388d0 0.1021361444d0 0 0 0
> Ti 0.8750000000d0 1.0825309307d0 0.1021361444d0 0 0 0
> Ti 0.7500000000d0 1.0103691302d0 0.3062508969d0 1 1 1
> Ti 0.8750000000d0 1.2268675220d0 0.3062508969d0 1 1 1
> N 0.7500000000d0 1.0103691302d0 0.0001050243d0 0 0 0
> N 0.8750000000d0 1.2268675220d0 0.0001050243d0 0 0 0
> N 0.8750000000d0 0.9381943393d0 0.2042197767d0 1 1 1
> N 0.7500000000d0 1.1547057216d0 0.2042197767d0 1 1 1
> N 0.4062600000d0 0.9896104340d0 0.6937906120d0 1 1 1
> C 0.4092000000d0 0.9020160108d0 0.6045199459d0 1 1 1
> C 0.4577300000d0 0.7953906178d0 0.6618107087d0 1 1 1
> N 0.4939900000d0 0.8337513373d0 0.7754470154d0 1 1 1
> C 0.4605200000d0 0.9497168446d0 0.7956116835d0 1 1 1
> C 0.5499000000d0 0.7467544736d0 0.5886612747d0 1 1 1
> S 0.5127800000d0 0.7970274111d0 0.4537050324d0 1 1 1
> C 0.4869600000d0 0.9325824765d0 0.5090003332d0 1 1 1
> C 0.5593700000d0 0.6202537332d0 0.5940700268d0 1 1 1
> C 0.5857900000d0 0.5794118428d0 0.7112246480d0 1 1 1
> C 0.5913300000d0 0.4526253131d0 0.7064460418d0 1 1 1
> C 0.6159700000d0 0.4036254371d0 0.8208700308d0 1 1 1
> C 0.6181100000d0 0.2770987158d0 0.8104726238d0 1 1 1
> O 0.6709500000d0 0.2080416264d0 0.8994807291d0 1 1 1
> O 0.5738500000d0 0.2226038907d0 0.7076538214d0 1 1 1
> O 0.4792600000d0 1.0152795101d0 0.8997958021d0 1 1 1
> H 0.3676800000d0 1.0720216783d0 0.6843909360d0 1 1 1
> H 0.3244700000d0 0.8813742285d0 0.5695993618d0 1 1 1
> H 0.3864400000d0 0.7347123514d0 0.6695825079d0 1 1 1
> H 0.5416000000d0 0.7826340223d0 0.8344706794d0 1 1 1
> H 0.6311400000d0 0.7881549521d0 0.6112940141d0 1 1 1
> H 0.4487000000d0 0.9936374652d0 0.4486113532d0 1 1 1
> H 0.5677800000d0 0.9656950650d0 0.5436058444d0 1 1 1
> H 0.6272000000d0 0.5918826491d0 0.5355189723d0 1 1 1
> H 0.4775600000d0 0.5827503816d0 0.5669737540d0 1 1 1
> H 0.5177200000d0 0.6062890283d0 0.7701432876d0 1 1 1
> H 0.6681700000d0 0.6144340236d0 0.7398437733d0 1 1 1
> H 0.6588100000d0 0.4267094190d0 0.6464771590d0 1 1 1
> H 0.5087600000d0 0.4194737533d0 0.6762515517d0 1 1 1
> H 0.5487800000d0 0.4294374078d0 0.8812590108d0 1 1 1
> H 0.6993600000d0 0.4344257303d0 0.8513270816d0 1 1 1
> H 0.5063400000d0 0.2734743877d0 0.6728382616d0 1 1 1
> K_POINTS {automatic}
> 4 4 1 0 0 0
>
> <QE530-GPU memory error.png>
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