HELP: how to reduce the memory needs
Posted: Thu Aug 26, 2010 5:56 pm
I am running abinit 6.0.4 on an x86_64_gnu_4.1 eight-core 16gb machine, compiled with mpirun, and everything works well for small systems, and recently I am following the tutorial to calculate the linear and non-linear optic properties of GaAs crystal.
When I set ngkpt to be 24*24*24, ecut 30, the job quit because no enough memory.
then I set mkmem=0, but the job still quit after the WF files occupy all my free disk space (about 80G ). In the log file I can find that the required memory is about 158M, but during the computation I use "top " command. I can see that almost all the memory is used. What is the matter?
Another question is that how to reduce the memory needs at the expense of (some) CPU time ?
Best,
Ma ZJ
The job stopped in DATASET3 during the calculation.
Part of the log file: mkmem=0
Input files
When I set ngkpt to be 24*24*24, ecut 30, the job quit because no enough memory.
then I set mkmem=0, but the job still quit after the WF files occupy all my free disk space (about 80G ). In the log file I can find that the required memory is about 158M, but during the computation I use "top " command. I can see that almost all the memory is used. What is the matter?
Another question is that how to reduce the memory needs at the expense of (some) CPU time ?
Best,
Ma ZJ
The job stopped in DATASET3 during the calculation.
Part of the log file: mkmem=0
DATASET 3 : space group F-4 3 m (#216); Bravais cF (face-center cubic)
================================================================================
Values of the parameters that define the memory need for DATASET 3.
intxc = 0 ionmov = 0 iscf = -2 xclevel = 1
lmnmax = 1 lnmax = 1 mband = 30 mffmem = 1
P mgfft = 40 mkmem = 0 mpssoang= 2 mpw = 2357
mqgrid = 3001 natom = 2 nfft = 64000 nkpt = 32000
nloalg = 4 nspden = 1 nspinor = 1 nsppol = 1
nsym = 24 n1xccc = 2501 ntypat = 2 occopt = 1
================================================================================
P This job should need less than 158.885 Mbytes of memory.
Rough estimation (10% accuracy) of disk space for files :
WF disk file : 1758.369 Mbytes ; DEN or POT disk file : 0.490 Mbytes.
mkmem==0 => use of 2 WF temporary disk files
================================================================================
Input files
#GaA
#Prepare the computation of linear and non-linear optic properties
#of GaAs crystal : ground-state with few bands,
#then non-SCF with a larger number of bands, then ddk for different directions
#Note that the k point sampling shoud be finer for significant results. The cut-off energy is also too low.
ndtset 6
#First dataset : SC run with kpoints in the IBZ
iscf1 3
nband1 5
nstep1 100
kptopt1 1
nbdbuf1 0
prtden1 1 getden1 0 getwfk1 0 ! Usual file handling data
#Second dataset : NSC run with large number of bands, and points in the IBZ
iscf2 -2
nband2 30 ! This number of bands might be too low for non-linear optics and real part of linear optics
nstep2 100
kptopt2 1
getwfk2 1
getden2 1
#Third dataset : NSC run with large number of bands, and points in the the full BZ
iscf3 -2
nband3 30
nstep3 100
kptopt3 3
getwfk3 2
getden3 1
mkmem3 0
mkqmem3 0
mk1mem3 0
#Fourth dataset : ddk response function along axis 1
iscf4 -3
nband4 30
nstep4 1
nline4 0
kptopt4 3
nqpt4 1
qpt4 0.0d0 0.0d0 0.0d0
rfdir4 1 0 0
rfelfd4 2
getwfk4 3
mkmem4 0
mkqmem4 0
mk1mem4 0
#Fifth dataset : ddk response function along axis 2
iscf5 -3
nband5 30
nstep5 1
nline5 0
kptopt5 3
nqpt5 1
qpt5 0.0d0 0.0d0 0.0d0
rfdir5 0 1 0
rfelfd5 2
getwfk5 3
mkmem5 0
mkqmem5 0
mk1mem5 0
#Sixth dataset : ddk response function along axis 3
iscf6 -3
nband6 30
nstep6 1
nline6 0
kptopt6 3
nqpt6 1
qpt6 0.0d0 0.0d0 0.0d0
rfdir6 0 0 1
rfelfd6 2
getwfk6 3
mkmem6 0
mkqmem6 0
mk1mem6 0
#Data common to all datasets
nshiftk 4
shiftk 0.5 0.5 0.5
0.5 0.0 0.0
0.0 0.5 0.0
0.0 0.0 0.5
ngkpt 20 20 20
acell 3*10.60
amu 69.72 74.9216
diemac 10.0
ecut 30
iscf 3
ixc 1
natom 2
nbdbuf 2
ntypat 2
rprim 0 .5 .5 .5 0 .5 .5 .5 0
xred 3*0.00d0 3*0.25d0
tnons 72*0.0
typat 1 2
tolwfr 1.e-20
znucl 31 33