[CP2K:3630] NEB: number of replicas, cpus and input files
Jörg Saßmannshausen
j.sassma... at ucl.ac.uk
Thu Nov 24 09:15:49 UTC 2011
Hi Theo,
sure, no problems. I have attached the complete input file minus the
coordinates it as a text file.
I did not post it as the question originally was independent of the input file.
All the best from London
Jörg
On Thursday 24 November 2011 05:39:05 Teodoro Laino wrote:
> Hi Jörg,
>
> both you and Carlo are correct. That's the way replica/nproc_rep are
> working. If the error you get is in : neb_utils:build_replica_coords, then
> your problem is somewhere else.
>
> Posting the motion section online it would help a lot!
> Thanks,
> Teo
>
> On Nov 24, 2011, at 12:48 AM, Jörg Saßmannshausen wrote:
> > Hi Carlo,
> >
> > gosh that was quick!
> >
> > I got 8 cores per box, so that is where the cores come from.
> > I got 17 points I want to run, hence the 17 files.
> >
> > Right now I only got 32 cores alltogether.
> >
> > So my train of thoughts were similar to yours: 8 replicas and each
> > replica is using 4 cores adds up to 32 cores.
> > However, that crashed with that error message:
> > ERRORL2 in neb_utils:build_replica_coords processor
> >
> > So in the end I decided to use 32 replicas and 32 nproc_rep for the 32
> > cores I have. I guess one could do better. ,-)
> >
> > All the best
> >
> > Jörg
> >
> > On Mittwoch 23 November 2011 c.pignedoli wrote:
> >> Ciao Joerg,
> >> why 17 files an 8 replicas?
> >>
> >> If i remember well:
> >> if you have 8 replicas an specify 100 nproc_rep
> >> then if you run with 200 cores
> >>
> >> you will have two replicas done at a time (each with 100 cores), then
> >> other two then other two finally the last two
> >>
> >> and you cicle.
> >>
> >> if you run with 800 cores all replicas will proceed in parallel
> >>
> >> Ciao
> >>
> >> Carlo
> >>
> >> On 24/nov/2011, at 00:05, Jörg Saßmannshausen
> >> <j.sassma... at ucl.ac.uk>
> >
> > wrote:
> >>> Dear all,
> >>>
> >>> I am a bit confused.
> >>> When I am running a frequency calculation or a NEB calculation, I can
> >>> specify the number of replicas (NUMBER_OF_REPLICA) and the number of
> >>> processors (NPROC_REP) in the MOTION section. Now, lets say I got 32
> >>> cores on my hands and I got 17 files which I want to use for the NEB
> >>> calculation. Now, my understanding was that I could run say 8 replicas
> >>> and each replica is using 4 cores. That would add up to the 32 cores I
> >>> have alltogether. However, that does not work out. It appears I got to
> >>> use 32 replicas and 32 cores for all 32 cores I have available. What is
> >>> the relationship between replicas and cores (in the input file) with
> >>> the cores I have available on the machine (an in relation to the
> >>> number of coordinate files I have). A similar observation was made for
> >>> a frequency calculation.
> >>>
> >>> I seem to have somehow a wrong understanding here :-/
> >>>
> >>> All the best from a foggy London
> >>>
> >>> Jörg
> >>>
> >>>
> >>> --
> >>> *************************************************************
> >>> Jörg Saßmannshausen
> >>> 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
> >>>
> >>> --
> >>> You received this message because you are subscribed to the Google
> >>> Groups "cp2k" group. To post to this group, send email to
> >>> cp... at googlegroups.com. To unsubscribe from this group, send email to
> >>> cp2k+uns... at googlegroups.com. For more options, visit this group
> >>> at http://groups.google.com/group/cp2k?hl=en.
--
*************************************************************
Jörg Saßmannshausen
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 --------------
@SET BAND_TYPE SM
@SET SCF_CONV 1.0E-6
@SET CUTOFF 560
@SET FUNCTIONAL PBE
@SET DECOUPLING MT
@SET CHARGE 0
&FORCE_EVAL
STRESS_TENSOR ANALYTICAL
&PRINT
&FORCES OFF
&END
&END
METHOD QS
&DFT
CHARGE 0
&MGRID
CUTOFF ${CUTOFF}
NGRIDS 5
&END MGRID
&QS
METHOD GPW
MAP_CONSISTENT
EXTRAPOLATION ASPC
EXTRAPOLATION_ORDER 3
&END QS
&SCF
MAX_SCF 30
EPS_SCF ${SCF_CONV}
SCF_GUESS random
&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
MINIMIZER DIIS
PRECONDITIONER FULL_SINGLE_INVERSE
N_DIIS 7
&END
&OUTER_SCF
EPS_SCF ${SCF_CONV}
MAX_SCF 5
&END
&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} == MT )
&POISSON
POISSON_SOLVER MT
PERIODIC NONE
&MT
&END
&END
@ENDIF
&END DFT
&SUBSYS
&CELL
ABC [angstrom] 20.18 13.32 13.07
PERIODIC NONE
&END CELL
&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 H
POTENTIAL GTH
&POTENTIAL
# H GTH-PBE-q1
1
0.20000000 2 -4.17890044 0.72446331
0
&END POTENTIAL
&BASIS
# H DZV-GTH-PBE
1
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
&END BASIS
&END KIND
&KIND Li
POTENTIAL GTH
&POTENTIAL
# Li GTH-PBE-q3
3
0.40000000 4 -14.08115455 9.62621962 -1.78361605 0.08515207
0
&END POTENTIAL
&BASIS
# Li DZVP-GTH-PADE
1
1 0 1 6 3 3
9.0645724591 0.1412707699 -0.0257336579 0.0000000000 0.0000000000 0.0000000000 0.0000000000
4.3479418841 0.2767295609 -0.0520596034 0.0000000000 0.0000000000 0.0000000000 0.0000000000
1.4344377059 0.4501408198 -0.1264254986 0.0000000000 0.0000000000 0.0000000000 0.0000000000
0.4969595308 0.2616803664 -0.1023799272 0.0000000000 1.0000000000 0.0000000000 0.0000000000
0.0729934685 0.0116600998 0.5635942604 0.0000000000 0.0000000000 1.0000000000 0.0000000000
0.0264321968 -0.0038582262 0.5289910438 1.0000000000 0.0000000000 0.0000000000 1.0000000000
&END BASIS
&END KIND
&KIND N
POTENTIAL GTH
&POTENTIAL
# N GTH-PBE-q5
2 3
0.28379051 2 -12.41522559 1.86809592
2
0.25540500 1 13.63026257
0.24549453 0
&END POTENTIAL
&BASIS
# N DZVP-GTH-PBE
2
2 0 1 4 2 2
6.1646187898 0.1507499417 0.0000000000 -0.0938164220 0.0000000000
1.8037211883 -0.0339053520 0.0000000000 -0.2912161121 0.0000000000
0.5658506122 -0.7128963473 0.0000000000 -0.4795028541 0.0000000000
0.1603297607 -0.3703029459 1.0000000000 -0.3849298984 1.0000000000
3 2 2 1 1
0.7000000000 1.0000000000
&END BASIS
&END KIND
&KIND Zn
POTENTIAL GTH
&POTENTIAL
# Zn GTH-PBE-q12
2 0 10
0.51000000 0
3
0.40031644 3 11.53004133 -8.79189815 3.14508644
16.46577518 -8.12057827
6.44550918
0.54318233 2 2.59719512 -0.59426275
0.70314117
0.25095885 1 -14.46695795
&END POTENTIAL
&BASIS
# Zn DZV-GTH-PADE
1
3 0 2 6 2 2 2
6.4206423601 -0.0159961492 0.0000000000 -0.0017007517 0.0000000000 0.2738774540 -0.0086808361
3.2164545624 0.0700921695 0.0000000000 0.0057876549 0.0000000000 0.3543101613 -0.0259525057
1.3637346905 -0.2332431465 0.0000000000 -0.0557262454 0.0000000000 0.3285180198 0.0317203087
0.5481563712 -0.1137154667 0.0000000000 0.0463783393 0.0000000000 0.2334531038 -0.3651680612
0.2053011443 0.5909100816 0.0000000000 0.2629520047 1.0000000000 0.1017295445 0.3530864382
0.0662102782 0.6085540919 1.0000000000 0.7908150346 0.0000000000 0.0108701745 0.8289022633
1
3 0 2 6 2 2 2
6.4635610128 -0.0174178283 0.0000000000 0.0014889091 0.0000000000 0.2661076361 -0.0172911104
3.3087913561 0.0729496060 0.0000000000 -0.0053382185 0.0000000000 0.3453918347 -0.0353171901
1.4436868426 -0.2102985944 0.0000000000 0.0544382687 0.0000000000 0.3206623881 0.0094335277
0.6045470598 -0.1788671076 0.0000000000 -0.0164095173 0.0000000000 0.2357873353 -0.3686660487
0.2390582336 0.5149852625 0.0000000000 -0.2811557323 1.0000000000 0.1164010142 0.3573346078
0.0857774784 0.7053938257 1.0000000000 -0.7792591266 0.0000000000 0.0149561710 0.8225277665
&END BASIS
&END KIND
&TOPOLOGY
COORD_FILE_NAME files/107.xyz
COORDINATE XYZ
CONNECTIVITY OFF
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
PRINT_LEVEL LOW
PROJECT neb-testjob
RUN_TYPE BAND
&END GLOBAL
&MOTION
&PRINT
&VELOCITIES OFF
&END
&END
&BAND
NPROC_REP 32
@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
NUMBER_OF_REPLICA 32
&CONVERGENCE_CONTROL
MAX_FORCE 0.001
RMS_FORCE 0.0005
&END
&OPTIMIZE_BAND
OPTIMIZE_END_POINTS F
OPT_TYPE DIIS
&DIIS
MAX_STEPS 100
N_DIIS 7
NO_LS
STEPSIZE 0.5
MAX_STEPSIZE 1.0
&END
&END
&REPLICA
COORD_FILE_NAME files/107.xyz
&END
&REPLICA
COORD_FILE_NAME files/97.xyz
&END
&REPLICA
COORD_FILE_NAME files/87.xyz
&END
&REPLICA
COORD_FILE_NAME files/77.xyz
&END
&REPLICA
COORD_FILE_NAME files/67.xyz
&END
&REPLICA
COORD_FILE_NAME files/57.xyz
&END
&REPLICA
COORD_FILE_NAME files/47.xyz
&END
&REPLICA
COORD_FILE_NAME files/37.xyz
&END
&REPLICA
COORD_FILE_NAME files/27.xyz
&END
&REPLICA
COORD_FILE_NAME files/17.xyz
&END
&REPLICA
COORD_FILE_NAME files/7.xyz
&END
&REPLICA
COORD_FILE_NAME files/1-3.xyz
&END
&REPLICA
COORD_FILE_NAME files/1-13.xyz
&END
&REPLICA
COORD_FILE_NAME files/1-23.xyz
&END
&REPLICA
COORD_FILE_NAME files/1-33.xyz
&END
&REPLICA
COORD_FILE_NAME files/1-43.xyz
&END
&REPLICA
COORD_FILE_NAME files/1-53.xyz
&END
&PROGRAM_RUN_INFO
&END
&CONVERGENCE_INFO
&END
&END BAND
&END MOTION
More information about the CP2K-user
mailing list