ABINIT Discussion Forums

Dear colleagues,

I'm trying to calculate the Raman spectra of rutile TiO2. Strain part of the perturbation finished without problems, however, the calc. stops for the non-linear perturbation when starting the 5th dataset (in all previous datasets calc. converged nicely). There is no message at the end of the log file, except:

MPI process terminated unexpectedly
Exit code -5 signaled from node007.srce.cro-ngi.hr
Killing remote processes...DONE

.out says nothing, also, just stops during the reading of the t11o_DS4_1WF22 from the disc. Cluster .err file says:

cannot stat `t11o_DS5_DDB': No such file or directory

while cluster log file says:

012 (151437.000.000) 12/07 14:58:34 Job was held.
Globus error 155: the job manager could not stage out a file
Code 2 Subcode 155

I contacted first the cluster admin, who replied that it is an abinits' error, sending me the log:

/var/log/messages.2:Nov 22 00:43:35 node007 kernel: abinip[25838]:
segfault at 00002aaeaa9d96e8 rip 00000000004e2f39 rsp 00007fff5fefd290
error 4
/var/log/messages.2:Nov 22 00:43:35 node007 kernel: abinip[25836]:
segfault at 0000000011046000 rip 0000000000e2f268 rsp 00007fff40aa0cf8
error 4
/var/log/messages.2:Nov 22 00:43:35 node007 kernel: abinip[25837]:
segfault at 0000000018c9b000 rip 00000000004e2dee rsp 00007fff40cb4840
error 4
/var/log/messages.2:Nov 22 14:14:13 node003 kernel: abinip[11272]:
segfault at 000000000cfbc000 rip 00000000004e2dee rsp 00007fff01edc480
error 4
/var/log/messages.2:Nov 22 14:14:13 node003 kernel: abinip[11271]:
segfault at 00000000168a3000 rip 00000000004e2dee rsp 00007fff97b028d0
error 4
/var/log/messages.2:Nov 22 14:14:13 node003 kernel: abinip[11270]:
segfault at 0000000013ba8000 rip 00000000004e2dee rsp 00007fff5e1458e0
error 4
/var/log/messages.2:Nov 25 03:05:41 node003 kernel: abinip[29518]:
segfault at 000000000f5f7000 rip 00000000004e2dee rsp 00007fff0b85a0f0
error 4
/var/log/messages.2:Nov 25 03:05:41 node003 kernel: abinip[29519]:
segfault at 000000000c245000 rip 00000000004e2dee rsp 00007fff3f13e2b0
error 4
/var/log/messages.2:Nov 25 03:05:41 node003 kernel: abinip[29520]:
segfault at 0000000029425000 rip 00000000004e2dee rsp 00007fff2c90d660
error 4
/var/log/messages.3:Nov 19 17:09:11 node007 kernel: abinip[10886]:
segfault at 00002aafbcce3dd8 rip 00000000004e2f39 rsp 00007fff0f560290
error 4


Has anyone encountered the similar problem? I would like to know where is the problem within abinit. I would appreciate any help. My input file is bellow.
I'm using abinit 5.8.4 on a Linux cluster.

Thank You in advance!

Igor Lukacevic



# Linear and nonlinear response calculation for TiO2 - rutile
# Perturbations: electric fields & atomic displacements

#Definition of lattice parameters
#********************************
acell 2*8.5577462433E+00 5.5134124864E+00
angdeg 90 90 90
spgroup 136
brvltt -1

#Definition of atomic positions and types
#****************************************
natom 6
natrd 3
ntypat 3
typat 1 2 2
znucl 22 8 8
xred 0.00 0.00 0.00
0.3033485499 0.3033485499 0.00
0.8033485499 0.1966514501 0.50
ixc 3

#Parameters of the SCF cycles
#****************************
iscf 5
nstep 100

#Plane wave basis and k-point grid
#*********************************
ecut 50
ecutsm 0.5
dilatmx 1.2
ngkpt 5 5 10
nshiftk 1
shiftk 0.5 0.5 0.5

#Perturbation datasets
#*********************
ndtset 5
jdtset 1 2 3 4 5

#DATASET1 : scf calculation: GS WF in the BZ
#*******************************************
prtden1 1
kptopt1 1
tolvrs1 1.0d-18

#DATASET2 : non-scf calculation: GS WF in the whole BZ
#*****************************************************
getden2 1
kptopt2 2
iscf2 -2
getwfk2 1
tolwfr2 1.0d-22
nband2 24

#DATASET3 : d/dk on the MP grid of k-points
#******************************************
getwfk3 2
rfdir3 1 1 1
rfelfd3 2
tolwfr3 1.0d-22
nband3 24
kptopt3 2

#DATASET4 : d/dE on the MP grid of k-points
#******************************************
prtden4 1
getwfk4 2
getddk4 3
rfdir4 1 1 1
rfphon4 1
rfatpol4 1 6
tolvrs4 1.0d-12
rfelfd4 3
nband4 24
kptopt4 2
prepanl4 1

#DATASET5 : 3DTE calculation
#***************************
getden5 1
get1den5 4
getwfk5 2
get1wf5 4
nband5 24
kptopt5 2
optdriver5 5
rf1elfd5 1
rf1phon5 1
rf1atpol5 1 6
rf1dir5 1 1 1
rf2elfd5 1
rf2dir5 1 1 1
rf3elfd5 1
rf3dir5 1 1 1

nbdbuf 0

timopt 2

Dear all,

after all, it appears that it has been a cluster issue. The calcs are running fine now.

Cheers!

Igor Lukacevic