MD crashes: how to restart
Jörg Saßmannshausen
j.sassma... at ucl.ac.uk
Mon Jun 23 22:51:14 UTC 2014
Dear all,
I got a bit of a problem with a MD calculation. It crashes with that error
message:
Trying to move ./WFN_restart.wfn.bak-2 to ./WFN_restart.wfn.bak-3.
rename returned status: 2
Now, that happened twice so far at different stages. The first time it was after
a few cycles and now it crashed after 83 cycles. I guess it is an underlying
hardware problem (I am stress testing the nodes) and/or a problem with the
nfs-mount on that node. As the rest of the cluster is behaving, I doubt it is
the NFS server. The network connections seem to be ok as well.
Unfortunatels, the error code '2' is not helpful for debugging so I would be
very greatful if somebody could point me in the right direction here. The disc
is not full and I don't have a quota (advantages of being an admin).
Also, I would like to restart the calculation here. I have tried that before
but somehow that failed to restart, it was a new start here.
Any ideas?
All the best from a warm London
Jörg
--
*************************************************************
Dr. Jörg Saßmannshausen, MRSC
University College London
Department of Chemistry
Gordon Street
London
WC1H 0AJ
email: j.sassma... at ucl.ac.uk
web: http://sassy.formativ.net
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html
-------------- next part --------------
&SUBSYS
&CELL
ABC [angstrom] 26.2849800 18.6827240 17.8864620
PERIODIC NONE
&END CELL
&TOPOLOGY
CONNECTIVITY OFF
COORDINATE XYZ
COORD_FILE_NAME files/start-A.xyz
&END TOPOLOGY
&KIND B
POTENTIAL GTH
&POTENTIAL
# B GTH-PBE-q3
2 1
0.41899145 2 -5.85946171 0.90375643
2
0.37132046 1 6.29728018
0.36456308 0
&END POTENTIAL
&BASIS
# B DZVP-GTH
2
2 0 1 4 2 2
2.8854072190 0.1420734374 0.0000000000 -0.0759818266 0.0000000000
0.8566811318 -0.0083272998 0.0000000000 -0.2508295957 0.0000000000
0.2712977126 -0.6707128588 0.0000000000 -0.4610302659 0.0000000000
0.0826097889 -0.4241240913 1.0000000000 -0.4419902640 1.0000000000
3 2 2 1 1
0.4000000000 1.0000000000
2
2 0 1 4 2 2
2.8461657736 0.1478743320 0.0000000000 -0.0780482479 0.0000000000
0.8351785230 -0.0200254137 0.0000000000 -0.2557970914 0.0000000000
0.2702560177 -0.6820892853 0.0000000000 -0.4542195946 0.0000000000
0.0805636848 -0.4080927351 1.0000000000 -0.4455266641 1.0000000000
3 2 2 1 1
0.4000000000 1.0000000000
&END BASIS
&END KIND
&KIND C
POTENTIAL GTH
&POTENTIAL
# C GTH-PBE-q4
2 2
0.33847124 2 -8.80367398 1.33921085
2
0.30257575 1 9.62248665
0.29150694 0
&END POTENTIAL
&BASIS
# C DZVP-GTH-PBE
2
2 0 1 4 2 2
4.3657614966 0.1476030280 0.0000000000 -0.0864171061 0.0000000000
1.2749626469 -0.0210014779 0.0000000000 -0.2743211800 0.0000000000
0.4052884311 -0.7098993929 0.0000000000 -0.4772572587 0.0000000000
0.1172717248 -0.3801259461 1.0000000000 -0.4035098365 1.0000000000
3 2 2 1 1
0.6000000000 1.0000000000
&END BASIS
&END KIND
&KIND F
POTENTIAL GTH
&POTENTIAL
# F GTH-PBE-q7
2 5
0.21492959 2 -21.57302836 3.19977615
2
0.19468402 1 23.74354045
0.18615608 0
&END POTENTIAL
&BASIS
# F SZV-GTH
1
2 0 1 4 1 1
10.7079864789 0.1525178335 -0.1028649155
3.1757211287 -0.0450362306 -0.3085266108
0.9750975998 -0.6987425203 -0.4757649137
0.2701247513 -0.3801470840 -0.3724955108
&END BASIS
&END KIND
&KIND H
POTENTIAL GTH
&POTENTIAL
# H GTH-PBE-q1
1
0.20000000 2 -4.17890044 0.72446331
0
&END POTENTIAL
&BASIS
# H DZVP-GTH-PBE
2
1 0 0 4 2
8.4486934208 -0.0290463773 0.0000000000
1.8581649215 -0.1327955318 0.0000000000
0.5076108225 -0.4061407363 0.0000000000
0.1673904511 -0.5490803703 1.0000000000
2 1 1 1 1
0.7000000000 1.0000000000
&END BASIS
&END KIND
&KIND Si
POTENTIAL GTH
&POTENTIAL
# Si GTH-PBE-q4
2 2
0.44000000 1 -6.26928833
2
0.43563383 2 8.95174150 -2.70627082
3.49378060
0.49794218 1 2.43127673
&END POTENTIAL
&BASIS
# Si DZVP-GTH
2
3 0 1 4 2 2
1.2032422345 0.3290350445 0.0000000000 0.0474539126 0.0000000000
0.4688409786 -0.2533118323 0.0000000000 -0.2594473573 0.0000000000
0.1679863234 -0.7870946277 0.0000000000 -0.5440929303 0.0000000000
0.0575619526 -0.1909898479 1.0000000000 -0.3624010364 1.0000000000
3 2 2 1 1
0.4500000000 1.0000000000
2
3 0 1 4 2 2
1.2283393137 0.3224377170 0.0000000000 0.0594606114 0.0000000000
0.5501858147 -0.1360087627 0.0000000000 -0.2102673957 0.0000000000
0.2104840660 -0.7254143349 0.0000000000 -0.5133271944 0.0000000000
0.0912235796 -0.3482519842 1.0000000000 -0.4108824626 1.0000000000
3 2 2 1 1
0.4500000000 1.0000000000
2
3 0 1 4 2 2
1.1607523260 0.3347731757 0.0000000000 0.0434283150 0.0000000000
0.4367408478 -0.3093572718 0.0000000000 -0.2863246710 0.0000000000
0.1596639467 -0.7662114250 0.0000000000 -0.5309372647 0.0000000000
0.0542076476 -0.1654691868 1.0000000000 -0.3502990755 1.0000000000
3 2 2 1 1
0.4500000000 1.0000000000
2
3 0 1 4 2 2
1.1846613412 0.3285317082 0.0000000000 0.0525302034 0.0000000000
0.4966320416 -0.1837395449 0.0000000000 -0.2375844983 0.0000000000
0.2018817867 -0.7175956794 0.0000000000 -0.4934742426 0.0000000000
0.0883185787 -0.3186166920 1.0000000000 -0.3999071137 1.0000000000
3 2 2 1 1
0.4500000000 1.0000000000
2
3 0 1 4 2 2
1.1815290892 0.3214648125 0.0000000000 0.0458533253 0.0000000000
0.4454622072 -0.2454343061 0.0000000000 -0.2633419994 0.0000000000
0.1674585747 -0.7952663455 0.0000000000 -0.5433222352 0.0000000000
0.0564288769 -0.1828967955 1.0000000000 -0.3560783416 1.0000000000
3 2 2 1 1
0.4500000000 1.0000000000
&END BASIS
&END KIND
&KIND Zr
POTENTIAL GTH
&POTENTIAL
# Zr GTH-PBE-q12
4 6 2
0.47000000 2 7.79605677 -1.89321030
3
0.25982885 2 23.38087417 -8.57193933
11.06632609
0.28896899 2 8.59276581 -5.37735808
6.36257589
0.58124504 2 0.02781064 0.27686186
-0.31393184
&END POTENTIAL
&BASIS
# Zr DZV-GTH-PADE
1
4 0 2 6 3 2 2
7.6857477291 0.0921982715 -0.0300916002 0.0000000000 0.0146645208 0.0000000000 -0.0028305635 0.0000000000
2.8983441504 -0.7069142736 0.2663213129 0.0000000000 -0.2102277970 0.0000000000 0.0073835576 0.0000000000
1.2697609208 0.5009909419 -0.2139641740 0.0000000000 0.4771534202 0.0000000000 0.2198586769 0.0000000000
0.5172494858 0.8658642938 -0.6004758231 0.0000000000 0.6141472939 0.0000000000 0.4200820229 1.0000000000
0.1837156188 0.0697098809 0.1712660028 0.0000000000 0.1280872093 1.0000000000 0.4495790932 0.0000000000
0.0544846775 -0.0001210510 1.0314604844 1.0000000000 -0.0061029355 0.0000000000 0.1822139319 0.0000000000
1
4 0 2 6 3 2 2
7.6907307864 0.0918380423 -0.0320131875 0.0000000000 0.0151438658 0.0000000000 -0.0025460744 0.0000000000
2.8994679368 -0.7065066090 0.2831559477 0.0000000000 -0.2148939669 0.0000000000 0.0047430657 0.0000000000
1.3083923278 0.4616304054 -0.2132614049 0.0000000000 0.4535119288 0.0000000000 0.2123619968 0.0000000000
0.5389907155 0.8834077941 -0.6128847036 0.0000000000 0.6213717566 0.0000000000 0.4126795546 1.0000000000
0.1971440852 0.0929467894 0.0453994877 0.0000000000 0.1490106611 1.0000000000 0.4547421602 0.0000000000
0.0656808473 -0.0016305751 1.1255334296 1.0000000000 -0.0064460597 0.0000000000 0.1726337227 0.0000000000
&END BASIS
&END KIND
&END SUBSYS
-------------- next part --------------
! -*- cp2k -*-
@SET BAND_TYPE SM
@SET SCF_CONV 1.0E-8
@SET CUTOFF 680
@SET FUNCTIONAL PBE
@SET DECOUPLING MT
@SET CHARGE 0
&FORCE_EVAL
STRESS_TENSOR ANALYTICAL
&PRINT
&FORCES OFF
&END
&END
METHOD QS
&DFT
CHARGE ${CHARGE}
&MGRID
CUTOFF ${CUTOFF}
NGRIDS 5
&END MGRID
&QS
EPS_DEFAULT 1.0E-16
&END QS
&SCF
SCF_GUESS random
EPS_SCF ${SCF_CONV}
MAX_SCF 30
&PRINT
&RESTART
LOG_PRINT_KEY T
FILENAME =./WFN_restart.wfn
&EACH
QS_SCF 0
&END EACH
ADD_LAST NUMERIC
COMMON_ITERATION_LEVELS 1
&END RESTART
&END PRINT
&OT ON
MINIMIZER DIIS
PRECONDITIONER FULL_SINGLE_INVERSE
N_DIIS 7
&END OT
&OUTER_SCF
EPS_SCF ${SCF_CONV}
MAX_SCF 5
&END OUTER_SCF
&END SCF
&XC
&XC_FUNCTIONAL ${FUNCTIONAL}
&END XC_FUNCTIONAL
&VDW_POTENTIAL
DISPERSION_FUNCTIONAL PAIR_POTENTIAL
&PAIR_POTENTIAL
TYPE DFTD3
REFERENCE_FUNCTIONAL PBE
CALCULATE_C9_TERM .TRUE.
PARAMETER_FILE_NAME ./dftd3.dat
R_CUTOFF 15.0
VERBOSE_OUTPUT TRUE
&END PAIR_POTENTIAL
&END vdW_POTENTIAL
&END XC
@IF ( ${DECOUPLING} == NONE )
&POISSON
&END
@ENDIF
@IF ( ${DECOUPLING} == MT )
&POISSON
POISSON_SOLVER MT
PERIODIC NONE
&MT
&END
&END
@ENDIF
@IF ( ${DECOUPLING} == WAVELET )
&POISSON
POISSON_SOLVER WAVELET
PERIODIC NONE
&WAVELET
SCF_TYPE 60
&END
&END
@ENDIF
&END DFT
! Include subsys
@INCLUDE 'subsys.inc'
&END FORCE_EVAL
-------------- next part --------------
! -*- cp2k -*-
! Possibly restart (if explicitly requested)
@IF 0
&EXT_RESTART ON
RESTART_DEFAULT F
RESTART_FILE_NAME MD-1.restart
RESTART_POS T
RESTART_COUNTERS T
RESTART_VEL T
RESTART_THERMOSTAT T
&END EXT_RESTART
@ENDIF
@SET BAND_TYPE SM
&GLOBAL
PROJECT sm-scan1
RUN_TYPE BAND
PRINT_LEVEL LOW
&END GLOBAL
&MOTION
&PRINT
&VELOCITIES OFF
&END
&END
&BAND
NPROC_REP 8
@IF ( ${BAND_TYPE} == SM )
BAND_TYPE SM
ROTATE_FRAMES F
@ENDIF
@IF ( ${BAND_TYPE} == NEB )
BAND_TYPE CI-NEB
K_SPRING 0.2
ROTATE_FRAMES T
&CI_NEB
NSTEPS_IT 5
&END
@ENDIF
@ENDIF
NUMBER_OF_REPLICA 16
&CONVERGENCE_CONTROL
MAX_FORCE 0.001
RMS_FORCE 0.0005
&END
&OPTIMIZE_BAND
OPTIMIZE_END_POINTS T
OPT_TYPE DIIS
&DIIS
MAX_STEPS 2000
N_DIIS 7
NO_LS
STEPSIZE 0.5
MAX_STEPSIZE 1.0
&END
&END
&REPLICA
COORD_FILE_NAME files/start-A.xyz
&END
&REPLICA
COORD_FILE_NAME files/g.xyz
&END
&REPLICA
COORD_FILE_NAME files/final-B.xyz
&END
&PROGRAM_RUN_INFO
&END
&CONVERGENCE_INFO
&END
&END BAND
&END MOTION
@INCLUDE 'force_eval.inc'
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