[Pw_forum] GIPAW memory problem?
Aleksander Jaworski
aleksander.jaworski at mmk.su.se
Mon May 12 17:18:32 CEST 2014
Dear QE users and developers,
I'm experiencing issues with running gipaw.x on the glass structures which
have been created from the classical MD simulations trajectories.
On the glass pw.x is running smoothly and converging properly. Gipaw.x is
starting, but showing very strange behavior in terms of memory handling and
never terminating the job.
I'm testing very small clusters (35 atoms) so I don't think that hardware
resources are the limiting factors here.
Both pw.x and gipaw.x are runnig properly on the crystalline samples, so I
think I can exclude code compilation problems or pseudopotetnials bugs.
Problem is same when running on one core, so I don't think it is related
to parallelization.
System is well converged with respect to e_cut and k_points.
I went across the mailing list archive and the manuals, and I cannot
conclude what is causing this problem.
I would really appreciate if more experienced users could take a look on
the input and share with me hints and suggestions how to solve this
problem.
Below are the examples of the calculations done on 4 cores for quartz
(where pw.x and gipaw.x are working perfectly) and for 35 atoms glass
cluster (where pw.x is working properly and gipaw.x is never terminating
the job).
Gipaw.x output from the glass is there and both pw.x and gipaw.x inputs.
best regards,
Aleksander Jaworski
PhD student
Physical Chemistry Division
Stockholm University
pw.x on quartz:
VIRT RES SHR S %CPU %MEM TIME+ COMMAND
227m 34m 8032 R 99.9 0.9 0:18.07 pw.x
227m 34m 7324 R 99.9 0.9 0:18.08 pw.x
227m 34m 7792 R 99.5 0.9 0:18.08 pw.x
227m 35m 8536 R 92.5 0.9 0:17.39 pw.x
gipaw.x on quartz:
VIRT RES SHR S %CPU %MEM TIME+ COMMAND
233m 39m 7560 R 99.9 1.0 0:22.84 gipaw.x
233m 39m 7176 R 99.9 1.0 0:22.97 gipaw.x
233m 39m 7072 R 99.5 1.0 0:22.98 gipaw.x
233m 38m 6316 R 99.5 1.0 0:23.19 gipaw.x
pw.x on glass fragment 35 atoms:
VIRT RES SHR S %CPU %MEM TIME+ COMMAND
386m 179m 6972 R 99.9 4.6 27:04.91 pw.x
390m 189m 6164 R 99.9 4.8 27:05.81 pw.x
390m 190m 6740 R 99.5 4.8 27:03.19 pw.x
393m 194m 7428 R 99.2 4.9 26:50.74 pw.x
gipaw.x on glass fragment 35 atoms:
VIRT RES SHR S %CPU %MEM TIME+ COMMAND
294m 23m 5976 R 99.9 0.6 88:09.55 gipaw.x
12.3g 22m 6280 R 99.5 0.6 88:08.72 gipaw.x <--- ???????
294m 23m 6080 R 99.5 0.6 88:09.16 gipaw.x
294m 22m 4936 R 99.5 0.6 88:06.15 gipaw.x
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
gipaw.x output from my glass structure
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Program GIPAW v.5.0.2 (svn rev. 9656) starts on 9May2014 at 21:41:13
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details
at
http://www.quantum-espresso.org/quote.php
Parallel version (MPI), running on 4 processors
R & G space division: proc/nbgrp/npool/nimage = 4
Info: using nr1, nr2, nr3 values from input
Info: using nr1s, nr2s, nr3s values from input
IMPORTANT: XC functional enforced from input :
Exchange-correlation = SLA PW PBX PBC ( 1 4 3 4 0)
EXX-fraction = 0.00
Any further DFT definition will be discarded
Please, verify this is what you really want
file Sc.pbe-spn-kjpaw_psl.0.2.3.UPF: wavefunction(s) 3P 3D
renormalized
WARNING: atomic wfc # 3 for atom type 2 has zero norm
WARNING: atomic wfc # 4 for atom type 2 has zero norm
WARNING: atomic wfc # 3 for atom type 3 has zero norm
WARNING: atomic wfc # 4 for atom type 3 has zero norm
Parallelization info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Min 2027 812 221 137553 34740 5083
Max 2028 813 222 137556 34751 5088
Sum 8109 3249 885 550217 138985 20341
........ and then nothing is going to happen, for days! Program is
printing this in the first seconds of the calculation and is not adding
anything until I will kill it, because of the lack of any progress.
Below are my inputs:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
pw.x input
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
&control
calculation = 'scf'
restart_mode = 'from_scratch'
prefix = 'Sc_glass'
pseudo_dir = './pseudo/'
outdir = './scratch/'
tstress = .true.
tprnfor = .true.
verbosity = 'high'
/
&system
ibrav = 0
a = 7.5593007081
nat = 35
ntyp = 4
ecutwfc = 50
ecutrho = 500
spline_ps = .true.
/
&electrons
diagonalization = 'david'
diago_thr_init = 1e-4
mixing_mode = 'plain'
mixing_beta = 0.7
conv_thr = 1e-10
/
CELL_PARAMETERS
1.0000000000 0.0000000000 0.0000000000
0.0000000000 1.0000000000 0.0000000000
0.0000000000 0.0000000000 1.0000000000
ATOMIC_SPECIES
Sc 44.955 Sc.pbe-spn-kjpaw_psl.0.2.3.UPF
Al 26.982 Al.pbe-tm-gipaw-dc.UPF
Si 28.086 Si.pbe-tm-new-gipaw-dc.UPF
O 15.999 O.pbe-rrkjus-gipaw-dc.UPF
K_POINTS automatic
6 6 6 0 0 0
ATOMIC_POSITIONS angstrom
Sc 3.653986436 -1.770430962 0.453388732
Sc 3.115400121 3.753142894 -2.621880013
Sc -0.228578192 -1.909939933 -0.359045349
Al 1.515612487 0.598794798 1.286089223
Al -2.142042574 0.099970299 -0.997825300
Al 1.457968354 3.343960195 -0.198592654
Al 0.142221475 -3.333943822 2.848542149
Al 2.430118347 -1.305929173 3.548774459
Si 2.140107709 0.526648186 -1.553243084
Si -1.992462971 -1.301007123 -3.529125238
Si -1.326216011 1.426125017 2.723247807
Si -1.199730215 2.921918032 -2.063671047
Si 3.709225042 2.726202959 1.981252239
O -1.902529337 -1.048857347 0.365493973
O -3.664872460 -3.291948284 1.583056465
O 1.746530467 -0.105355750 -2.961930628
O 2.528356530 -0.694635328 1.893182099
O -2.594445490 3.673588810 -1.938872319
O 1.128159783 -0.101570707 -0.346499313
O -2.072151028 0.288350136 3.590230330
O -1.332709251 -1.175862060 -2.030826061
O 3.366250358 2.407365161 3.508386106
O -0.020611539 -3.717768926 -1.386394664
O 2.436173048 -2.829506418 -0.778460058
O 2.397436184 2.158266175 1.045311973
O -1.202022794 1.486908837 -1.356904320
O -0.781158682 2.726208527 3.761115686
O -3.545735497 -1.823195853 -3.420669188
O 0.019501994 0.960865019 2.017730151
O -2.410455796 1.966814312 1.616179899
O 0.422084553 -3.393089790 1.091238287
O 3.644536355 0.062847310 -1.003892882
O -1.083072338 -2.149152584 3.048286539
O 2.016382220 2.165204491 -1.521542899
O 1.598040318 -2.865100753 3.709659988
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
gipaw.x input
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
&inputgipaw
job = 'nmr'
prefix = 'Sc_glass'
tmp_dir = './scratch/'
isolve = 0
iverbosity = 1
q_gipaw = 0.01
spline_ps = .true.
use_nmr_macroscopic_shape = .true.
/
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