Memory Issue QMMM Cray XE6

[marco.stenta]

Hello,
I have a memory issue when running QM/MM-MD on a Cray XE6 machine (our
dear rosa@CSCS, 16-core AMD Opteron 6272 2.1 GHz Interlagos
processors).
I did not do the compilation myself but infer it is gfortran (if you
need I can ask the SA for more info)
Below I attach both input and output (sorry: it is super long but I
cannot attach zip files).
The system used to run smoothly on an IBM-SP6 machine (SP6@CINECA).

On the Cray the job crashes while in the QM/MM module. the last thing
it prints is
QMMM| QM/MM Coupling computed collocating the Gaussian Potential
Functions.

and then:
Application 347501 exit signals: Killed
Application 347501 resources: utime ~8s, stime ~0s

I use 128 MP processes.
Now on the Cray if I create 128 tasks and use 32 tasks per node (fully
packed nodes) the job crashes the very first time it performs the QMMM
operation
If, instead, I use half the tasks per node (16 out of a max of 32),
thus leaving half node empty, but still use 128 tasks, the job goes on
for a couple of cycles and then it crashes at the same time.

With 256 tasks with fully packed nodes It crashes, but when I leave
node half empty (16 tasks per node) it goes on for a while.

Did any one experience something like that? I've seen in the forum
some option to reduce the memory consumption and I used some of them
to no avail.

Would a different compilation solve the problem? Can you tell me which
libraries could be critical for this issue (if all is OK in the
input)? Would in your opinion a MPI-openMP solve the problem?


Thank you very much in advance


################################################################
@SET NSTEPS 500000
@SET SOLNAME MOL69
@SET QMCHARGE -1
@SET QMPOISSON MT

@SET FREQ 1
@INCLUDE ../data/boxes.inc

&GLOBAL
PRINT_LEVEL LOW
PROJECT system
PROGRAM CP2K
RUN_TYPE MD
WALLTIME 82800
SAVE_MEM TRUE
#TRACE TRUE
&END GLOBAL

&MOTION
&MD
ENSEMBLE NVT
STEPS ${NSTEPS}
TIMESTEP 0.50
TEMPERATURE 300.0
&THERMOSTAT
TYPE CSVR
REGION DEFINED
&DEFINE_REGION
MM_SUBSYS ATOMIC
&END DEFINE_REGION
&DEFINE_REGION
QM_SUBSYS ATOMIC
&END DEFINE_REGION
&CSVR
TIMECON 50
&END CSVR
&END THERMOSTAT
&PRINT
FORCE_LAST T
&ENERGY
&EACH
MD 1
&END EACH
FILENAME =system.ene
&END ENERGY
&END PRINT
&END MD
&PRINT
&TRAJECTORY SILENT
&EACH
MD ${FREQ}
&END EACH
FILENAME =system.dcd
FORMAT DCD
&END TRAJECTORY
&VELOCITIES OFF
&EACH
MD ${FREQ}
&END EACH
FILENAME =system.vel
&END VELOCITIES
&FORCES
&EACH
MD ${FREQ}
&END EACH
FILENAME =system.for.DCD
FORMAT DCD
&END FORCES
&RESTART_HISTORY OFF
&END RESTART_HISTORY
&RESTART SILENT
ADD_LAST NUMERIC
&EACH
MD ${FREQ}
&END EACH
FILENAME =system.restart
&END RESTART
&END PRINT
&CONSTRAINT
&G3X3
MOLNAME ${SOLNAME}
DISTANCES 1.7958 1.7958 2.85444
ATOMS 1 2 3
EXCLUDE_QM
&END G3X3
# @INCLUDE ../data/fix_qm_heavy.inc
&END CONSTRAINT
# @INCLUDE ../data/FREE_ENERGY.inc
&END MOTION

&FORCE_EVAL
METHOD QMMM
&DFT
BASIS_SET_FILE_NAME ../data/BASIS_SET
POTENTIAL_FILE_NAME ../data/GTH_POTENTIALS
CHARGE ${QMCHARGE}
&SCF
MAX_SCF 40
EPS_SCF 1.0E-7
SCF_GUESS ATOMIC
&OUTER_SCF
EPS_SCF 1.0E-7
MAX_SCF 10
&END OUTER_SCF
&OT
PRECONDITIONER FULL_ALL
MINIMIZER DIIS
N_DIIS 7
&END OT
&PRINT
&RESTART
ADD_LAST NUMERIC
&EACH
MD ${FREQ}
&END EACH
FILENAME =RESTART
&END RESTART
&RESTART_HISTORY OFF
&END RESTART_HISTORY
&END PRINT
&END SCF
&QS
EPS_DEFAULT 1.0E-12
EXTRAPOLATION ASPC
EXTRAPOLATION_ORDER 3
&END QS
&MGRID
CUTOFF 320
COMMENSURATE
&END MGRID
&POISSON
POISSON_SOLVER ${QMPOISSON}
PERIODIC NONE
&END POISSON
&XC
&XC_FUNCTIONAL BLYP
&END XC_FUNCTIONAL
&END XC
&END DFT

&MM
&FORCEFIELD
PARMTYPE AMBER
PARM_FILE_NAME ../data/molbox.prmtop
EI_SCALE14 0.8333
VDW_SCALE14 0.5
&SPLINE
RCUT_NB 12.0
&END SPLINE

&BOND
KIND AMBER
ATOMS ZN SH
K [angstrom^-2kcalmol] 68.05
R0 [angstrom] 2.311
&END BOND
&BOND
KIND AMBER
ATOMS ZN NB
K [angstrom^-2kcalmol] 45.58
R0 [angstrom] 1.957
&END BOND

&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE SPME
ALPHA .35
GMAX ${EWALDA} ${EWALDB} ${EWALDC}
&END EWALD
&END POISSON
&END MM

&QMMM
NOCENTER T
NOCENTER0 T
USE_GEEP_LIB 7
ECOUPL GAUSS
&CELL
ABC ${QMBOXA} ${QMBOXB} ${QMBOXC}
PERIODIC NONE
&END CELL

@INCLUDE ../data/QM_KIND-LINK.inc

&WALLS
WALL_SKIN [angstrom] 2.0 2.0 2.0
TYPE REFLECTIVE
&END WALLS

&PRINT
&PROGRAM_RUN_INFO SILENT
&END PROGRAM_RUN_INFO
&PERIODIC_INFO SILENT
&END PERIODIC_INFO
&QMMM_LINK_INFO SILENT
&END QMMM_LINK_INFO
&END PRINT
&END QMMM

&SUBSYS
&CELL
ABC ${MMBOXA} ${MMBOXB} ${MMBOXC}
PERIODIC XYZ
&END CELL
&TOPOLOGY
&MOL_SET
&MERGE_MOLECULES
&BONDS
1520 8881
11567 16020
&END BONDS
&END MERGE_MOLECULES
&END MOL_SET

&GENERATE
&BOND ADD
ATOMS 1520 8881
&END BOND
&BOND ADD
ATOMS 1476 8881
&END BOND
&BOND ADD
ATOMS 961 8881
&END BOND
&BOND ADD
ATOMS 905 8881
&END BOND
&BOND ADD
ATOMS 11567 16020
&END BOND
&BOND ADD
ATOMS 11611 16020
&END BOND
&BOND ADD
ATOMS 11052 16020
&END BOND
&BOND ADD
ATOMS 10996 16020
&END BOND
&END GENERATE


# COORD_FILE_NAME ../data/molbox.rst7
# COORD_FILE_FORMAT CRD
CONN_FILE_FORMAT psf
CONN_FILE_NAME ../data/molbox_mod.psf
MOL_CHECK T
&END TOPOLOGY
@INCLUDE ../data/KIND_BASIS_POTENTIAL.inc
&END SUBSYS
&END FORCE_EVAL

&EXT_RESTART
RESTART_FILE_NAME system.restart
RESTART_DEFAULT T
RESTART_POS T
RESTART_QMMM T
RESTART_CELL T
RESTART_VEL T
RESTART_CONSTRAINT F
&END EXT_RESTART

################################################################
128 task 32 task /node

*******************************************************************************
* RESTART
INFORMATION *

*******************************************************************************

*
*
* RESTART FILE NAME:
system.restart *

*
*
* RESTARTED
QUANTITIES: *
*
CELL *
*
COORDINATES *
* RANDOM NUMBER
GENERATOR *
*
VELOCITIES *
* QMMM TRANSLATION
VECTOR *
* MD
COUNTERS *
* MD
AVERAGES *
* PARTICLE
THERMOSTAT *
* REAL TIME
PROPAGATION *
* PINT BEAD
POSITIONS *
* PINT BEAD
VELOCITIES *
* PINT NOSE
THERMOSTAT *
* PINT GLE
THERMOSTAT *
* HELIUM BEAD
POSITIONS *
* HELIUM PERMUTATION
STATE *
* HELIUM FORCES ON
SOLUTE *
* HELIUM RNG
STATE *

*******************************************************************************

DBCSR| Multiplication
driver SMM
DBCSR| Multiplication stack
size 1000
DBCSR| Multiplication size
stacks 0
DBCSR| Use
subcommunicators F
DBCSR| Use MPI combined
types F
DBCSR| Use MPI memory
allocation T
DBCSR| Use Communication
thread T
DBCSR| Communication thread
load 100


**** **** ****** ** PROGRAM STARTED AT 2012-01-26
10:01:28.566
***** ** *** *** ** PROGRAM STARTED
ON nid01132
** **** ****** PROGRAM STARTED
BY root ;-)
***** ** ** ** ** PROGRAM PROCESS
ID 23112
**** ** ******* ** PROGRAM STARTED IN /scratch/rosa/mstenta/
integrase/integ
rase_reac_new/prod_1

CP2K| version string: CP2K version 2.3.29
(Development Version)
CP2K| is freely available from http://cp2k.berlios.de/
CP2K| Program compiled at Mon Nov 21
10:22:36 CET 2011
CP2K| Program compiled
on gele2
CP2K| Program compiled for CRAY-
XE6-gfortran
CP2K| Last CVS
entry
CP2K| Input file name
system_prod_trace.inp

GLOBAL| Force Environment
number 1
GLOBAL| Basis set file name ../data/
BASIS_SET
GLOBAL| Geminal file name
BASIS_GEMINAL
GLOBAL| Potential file name ../data/
GTH_POTENTIALS
GLOBAL| MM Potential file name
MM_POTENTIAL
GLOBAL| Coordinate file name
__STD_INPUT__
GLOBAL| Method
name CP2K
GLOBAL| Project
name system
GLOBAL| Preferred FFT
library FFTW3
GLOBAL| Run
type MD
GLOBAL| All-to-all communication in single
precision F
GLOBAL| FFTs using library dependent
lengths F
GLOBAL| Global print
level LOW
GLOBAL| Total number of message passing
processes 128
GLOBAL| Number of threads for this
process 1
GLOBAL| This output is from
process 0

MEMORY| system memory details [Kb]
MEMORY| rank 0 min
max average
MEMORY| MemTotal 33083456 33083456
33083456 33083456
MEMORY| MemFree 25030868 25030868
25076528 25064135
MEMORY| Buffers 0 0
0 0
MEMORY| Cached 100412 59880
100412 70112
MEMORY| Slab 169372 164880
169372 166280
MEMORY| SReclaimable 3824 3556
3824 3703
MEMORY| MemLikelyFree 25135104 25135104
25140480 25137950



SPLINE_INFO| Generating 73920 splines for the NONBONDED interactions
due to 384 different atomic kinds
000000:000128>> 9 424 init_genpot
start 3671 Mb
000000:000128<< 9 424 init_genpot
0.014 3671 Mb
...7392
...14784
...22176
...29568
...36960
...44352
...51744
...59136
...66528
...73920

....
....
....
....
....
....


SPLINE_INFO| Number of unique splines computed: 211

SPLINE_INFO| Done
000000:000128<< 8 2
spline_nonbond_control 0.047 3671 Mb
000000:000128<< 7 2
force_field_pack_splines 4.011 3671 Mb
000000:000128>> 7 1 force_field_pack_eicut
start 3674 Mb
000000:000128<< 7 1 force_field_pack_eicut
0.151 3677 Mb
000000:000128<< 6 1 force_field_pack 30.658
3677 Mb
000000:000128>> 6 1 force_field_qeff_output
start 3677 Mb
000000:000128<< 6 1 force_field_qeff_output
0.061 3677 Mb
000000:000128>> 6 1 clean_intra_force_kind
start 3677 Mb
000000:000128<< 6 1 clean_intra_force_kind
0.018 3677 Mb
000000:000128<< 5 1 force_field_control 66.176
3677 Mb
000000:000128>> 5 1 fist_init_subsys start 3677
Mb
000000:000128>> 6 1 write_molecule_kind_set
start 3677 Mb
000000:000128<< 6 1 write_molecule_kind_set
0.000 3677 Mb
000000:000128>> 6 1 write_particle_distances
start 3677 Mb
000000:000128<< 6 1 write_particle_distances
0.000 3677 Mb
000000:000128>> 6 1 write_structure_data
start 3677 Mb
000000:000128<< 6 1 write_structure_data
0.000 3677 Mb
000000:000128>> 6 1 write_symmetry start 3677
Mb
000000:000128<< 6 1 write_symmetry 0.000 3677
Mb
000000:000128>> 6 1 distribute_molecules_1d
start 3677 Mb
000000:000128<< 6 1 distribute_molecules_1d
0.056 3677 Mb
000000:000128>> 6 1 ewald_pw_init start 3677
Mb
000000:000128>> 7 1 pw_grid_setup start
3677 Mb
000000:000128>> 8 1 pw_grid_distribute
start 3683 Mb
000000:000128<< 8 1 pw_grid_distribute
0.004 3683 Mb
000000:000128>> 8 1 pw_grid_allocate
start 3683 Mb
000000:000128<< 8 1 pw_grid_allocate
0.001 3683 Mb
000000:000128>> 8 1 pw_grid_assign
start 3683 Mb
000000:000128<< 8 1 pw_grid_assign
0.001 3683 Mb
000000:000128>> 8 1 pw_grid_sort start
3683 Mb
000000:000128>> 9 1 sort_shells
start 3683 Mb
000000:000128<< 9 1 sort_shells
0.002 3683 Mb
000000:000128<< 8 1 pw_grid_sort 0.003
3683 Mb
000000:000128>> 8 1 pw_grid_remap start
3683 Mb
000000:000128<< 8 1 pw_grid_remap 0.006
3691 Mb
000000:000128<< 7 1 pw_grid_setup 0.021
3691 Mb
000000:000128>> 7 1
rs_grid_create_descriptor start 3691 Mb
000000:000128<< 7 1
rs_grid_create_descriptor 0.001 3691 Mb
000000:000128>> 7 1 rs_grid_create start
3691 Mb
000000:000128<< 7 1 rs_grid_create 0.001
3691 Mb
000000:000128<< 6 1 ewald_pw_init 0.373 3691
Mb
000000:000128>> 6 1 ewald_pw_release start
3691 Mb
000000:000128<< 6 1 ewald_pw_release 0.000
3691 Mb
000000:000128>> 6 2 ewald_pw_release start
3691 Mb
000000:000128<< 6 2 ewald_pw_release 0.000
3691 Mb
000000:000128<< 5 1 fist_init_subsys 0.432 3691
Mb
000000:000128<< 4 1 fist_init 95.746 3691 Mb
000000:000128>> 4 2 cp_result_create start 3691 Mb
000000:000128<< 4 2 cp_result_create 0.000 3691 Mb
000000:000128<< 3 1 fist_create_force_env 95.748 3691
Mb
Number of QM atoms: 87
Number of MM atoms: 232348
QM cell ::


-------------------------------------------------------------------------

QM/MM LINKS


-------------------------------------------------------------------------

IMOMM TYPE LINK
TYPE: IMOMM QM INDEX: 12075 MM INDEX: 12073 ALPHA:
1.410000
TYPE: IMOMM QM INDEX: 12952 MM INDEX: 12950 ALPHA:
1.410000
TYPE: IMOMM QM INDEX: 13493 MM INDEX: 13490 ALPHA:
1.410000
TYPE: IMOMM QM INDEX: 20093 MM INDEX: 20090 ALPHA:
1.410000
TYPE: IMOMM QM INDEX: 20096 MM INDEX: 20098 ALPHA:
1.410000
TYPE: IMOMM QM INDEX: 20128 MM INDEX: 20130 ALPHA:
1.410000
TYPE: IMOMM QM INDEX: 20154 MM INDEX: 20157 ALPHA:
1.410000


-------------------------------------------------------------------------

000000:000128>> 3 2 connectivity_control start 3697 Mb
000000:000128>> 4 2
connectivity_control_check_element_name start 3697 Mb
000000:000128<< 4 2
connectivity_control_check_element_name 0.001 3697 Mb
000000:000128>> 4 1 topology_set_atm_mass start
3697 Mb
000000:000128<< 4 1 topology_set_atm_mass 0.000
3697 Mb
000000:000128>> 4 1 topology_generate_bend start
3697 Mb
GENERATE| Number of Bends
generated: 0
000000:000128<< 4 1 topology_generate_bend 0.000
3697 Mb
000000:000128>> 4 1 topology_generate_ub start 3697
Mb
GENERATE| Number of UB
generated: 0
000000:000128<< 4 1 topology_generate_ub 0.000 3697
Mb
000000:000128>> 4 1 topology_generate_dihe start
3697 Mb
GENERATE| Number of Torsions
generated: 0
000000:000128<< 4 1 topology_generate_dihe 0.000
3697 Mb
000000:000128>> 4 1 topology_generate_impr start
3697 Mb
GENERATE| Number of Impropers
generated: 0
000000:000128<< 4 1 topology_generate_impr 0.000
3697 Mb
000000:000128>> 4 1 topology_generate_onfo start
3697 Mb
GENERATE| Number of 1-4 interactions
generated: 0
000000:000128<< 4 1 topology_generate_onfo 0.000
3697 Mb
000000:000128>> 4 2 topology_muc start 3697 Mb
000000:000128<< 4 2 topology_muc 0.000 3697 Mb
000000:000128>> 4 2 topology_generate_molecule
start 3697 Mb
000000:000128>> 5 2
topology_generate_molecule_PARA_RES start 3697 Mb
000000:000128<< 5 2
topology_generate_molecule_PARA_RES 0.000 3697 Mb
000000:000128<< 4 2 topology_generate_molecule
0.001 3697 Mb
000000:000128<< 3 2 connectivity_control 0.004 3697 Mb
000000:000128>> 3 2 topology_connectivity_pack start
3697 Mb
000000:000128>> 4 2 topology_connectivity_pack_1
start 3697 Mb
000000:000128<< 4 2 topology_connectivity_pack_1
0.000 3697 Mb
000000:000128>> 4 2 topology_connectivity_pack_1.1
start 3697 Mb
000000:000128<< 4 2 topology_connectivity_pack_1.1
0.001 3697 Mb
000000:000128>> 4 2 topology_connectivity_pack_2
start 3697 Mb
000000:000128<< 4 2 topology_connectivity_pack_2
0.000 3697 Mb
000000:000128>> 4 2 topology_connectivity_pack_3
start 3697 Mb
000000:000128<< 4 2 topology_connectivity_pack_3
0.000 3697 Mb
000000:000128>> 4 2 topology_connectivity_pack_4
start 3697 Mb
000000:000128<< 4 2 topology_connectivity_pack_4
0.000 3697 Mb
000000:000128>> 4 2 topology_connectivity_pack_5
start 3697 Mb
000000:000128<< 4 2 topology_connectivity_pack_5
0.001 3697 Mb
000000:000128>> 4 2 topology_connectivity_pack_6
start 3697 Mb
000000:000128<< 4 2 topology_connectivity_pack_6
0.000 3697 Mb
000000:000128>> 4 2 topology_connectivity_pack_7
start 3697 Mb
000000:000128<< 4 2 topology_connectivity_pack_7
0.000 3697 Mb
000000:000128>> 4 2 topology_connectivity_pack_8
start 3697 Mb
000000:000128<< 4 2 topology_connectivity_pack_8
0.000 3697 Mb
000000:000128>> 4 2 topology_connectivity_pack_9
start 3697 Mb
000000:000128<< 4 2 topology_connectivity_pack_9
0.000 3697 Mb
000000:000128>> 4 2 topology_connectivity_pack_10
start 3697 Mb
000000:000128<< 4 2 topology_connectivity_pack_10
0.000 3697 Mb
000000:000128>> 4 2
topology_connectivity_pack_11_pre start 3697 Mb
000000:000128<< 4 2
topology_connectivity_pack_11_pre 0.000 3697 Mb
000000:000128>> 4 2 topology_connectivity_pack_11
start 3697 Mb
000000:000128<< 4 2 topology_connectivity_pack_11
0.000 3697 Mb
000000:000128>> 4 2
topology_connectivity_pack_12_pre start 3697 Mb
000000:000128<< 4 2
topology_connectivity_pack_12_pre 0.000 3697 Mb
000000:000128>> 4 2 topology_connectivity_pack_12
start 3697 Mb
000000:000128<< 4 2 topology_connectivity_pack_12
0.000 3697 Mb
000000:000128>> 4 2
topology_connectivity_pack_13_pre start 3697 Mb
000000:000128<< 4 2
topology_connectivity_pack_13_pre 0.000 3697 Mb
000000:000128>> 4 2 topology_connectivity_pack_13
start 3697 Mb
000000:000128<< 4 2 topology_connectivity_pack_13
0.000 3697 Mb
000000:000128>> 4 2
topology_connectivity_pack_14_pre start 3697 Mb
000000:000128<< 4 2
topology_connectivity_pack_14_pre 0.000 3697 Mb
000000:000128>> 4 2 topology_connectivity_pack_14
start 3697 Mb
000000:000128<< 4 2 topology_connectivity_pack_14
0.001 3697 Mb
000000:000128<< 3 2 topology_connectivity_pack 0.004
3697 Mb
000000:000128>> 3 2 topology_coordinate_pack start
3697 Mb
000000:000128>> 4 2 topology_coordinate_pack_1
start 3697 Mb
000000:000128<< 4 2 topology_coordinate_pack_1
0.000 3697 Mb
000000:000128>> 4 2 topology_coordinate_pack_2
start 3697 Mb
000000:000128<< 4 2 topology_coordinate_pack_2
0.000 3697 Mb
000000:000128>> 4 2 topology_coordinate_pack_3
start 3697 Mb
000000:000128<< 4 2 topology_coordinate_pack_3
0.000 3697 Mb
000000:000128>> 4 2 topology_coordinate_pack_4
start 3697 Mb
000000:000128<< 4 2 topology_coordinate_pack_4
0.000 3697 Mb
000000:000128>> 4 2 topology_coordinate_pack_5
start 3697 Mb
000000:000128<< 4 2 topology_coordinate_pack_5
0.000 3697 Mb
000000:000128>> 4 2 topology_coordinate_pack_6
start 3697 Mb
000000:000128<< 4 2 topology_coordinate_pack_6
0.000 3697 Mb
000000:000128>> 4 2 topology_coordinate_pack_7a
start 3697 Mb
000000:000128<< 4 2 topology_coordinate_pack_7a
0.000 3697 Mb
000000:000128>> 4 2 topology_coordinate_pack_7b
start 3697 Mb
000000:000128<< 4 2 topology_coordinate_pack_7b
0.000 3697 Mb
000000:000128>> 4 2 topology_coordinate_pack_89
start 3697 Mb
000000:000128<< 4 2 topology_coordinate_pack_89
0.000 3697 Mb
000000:000128>> 4 2 topology_coordinate_pack_10
start 3697 Mb
000000:000128<< 4 2 topology_coordinate_pack_10
0.000 3697 Mb
000000:000128>> 4 2 topology_coordinate_pack_11
start 3697 Mb
000000:000128<< 4 2 topology_coordinate_pack_11
0.000 3697 Mb
000000:000128<< 3 2 topology_coordinate_pack 0.001
3697 Mb
000000:000128>> 3 1 quickstep_create_force_env start
3697 Mb
000000:000128>> 4 3 cp_result_create start 3697 Mb
000000:000128<< 4 3 cp_result_create 0.000 3697 Mb
000000:000128>> 4 1 read_atomic_kind_set start 3697
Mb
000000:000128>> 5 1 read_atomic_kind start 3697
Mb
000000:000128>> 6 824 parser_read_line_low
start 3701 Mb
000000:000128>> 7 824
broadcast_input_information start 3701 Mb
000000:000128<< 7 824
broadcast_input_information 0.005 3701 Mb
000000:000128<< 6 824 parser_read_line_low
0.030 3701 Mb
000000:000128>> 6 825 parser_read_line_low
start 3701 Mb
000000:000128>> 7 825
broadcast_input_information start 3701 Mb
000000:000128<< 7 825
broadcast_input_information 0.005 3701 Mb
000000:000128<< 6 825 parser_read_line_low
0.011 3701 Mb
000000:000128>> 6 826 parser_read_line_low
start 3701 Mb
000000:000128>> 7 826
broadcast_input_information start 3701 Mb
000000:000128<< 7 826
broadcast_input_information 0.004 3701 Mb
000000:000128<< 6 826 parser_read_line_low
0.010 3701 Mb
000000:000128>> 6 827 parser_read_line_low
start 3701 Mb
000000:000128>> 7 827
broadcast_input_information start 3701 Mb
000000:000128<< 7 827
broadcast_input_information 0.004 3701 Mb
000000:000128<< 6 827 parser_read_line_low
0.009 3701 Mb
000000:000128<< 5 1 read_atomic_kind 0.107 3701
Mb
000000:000128>> 5 2 read_atomic_kind start 3701
Mb
000000:000128>> 6 828 parser_read_line_low
start 3701 Mb
000000:000128>> 7 828
broadcast_input_information start 3701 Mb
000000:000128<< 7 828
broadcast_input_information 0.004 3701 Mb
000000:000128<< 6 828 parser_read_line_low
0.009 3701 Mb
000000:000128>> 6 829 parser_read_line_low
start 3701 Mb
000000:000128>> 7 829
broadcast_input_information start 3701 Mb
000000:000128<< 7 829
broadcast_input_information 0.005 3701 Mb
000000:000128<< 6 829 parser_read_line_low
0.010 3701 Mb
000000:000128>> 6 830 parser_read_line_low
start 3701 Mb
000000:000128>> 7 830
broadcast_input_information start 3701 Mb
000000:000128<< 7 830
broadcast_input_information 0.004 3701 Mb
000000:000128<< 6 830 parser_read_line_low
0.010 3701 Mb
000000:000128>> 6 831 parser_read_line_low
start 3701 Mb
000000:000128>> 7 831
broadcast_input_information start 3701 Mb
000000:000128<< 7 831
broadcast_input_information 0.003 3701 Mb
000000:000128<< 6 831 parser_read_line_low
0.009 3701 Mb
000000:000128<< 5 2 read_atomic_kind 0.069 3701
Mb
000000:000128>> 5 3 read_atomic_kind start 3701
Mb
000000:000128>> 6 832 parser_read_line_low
start 3701 Mb
000000:000128>> 7 832
broadcast_input_information start 3701 Mb
000000:000128<< 7 832
broadcast_input_information 0.003 3701 Mb
000000:000128<< 6 832 parser_read_line_low
0.009 3701 Mb
000000:000128>> 6 833 parser_read_line_low
start 3701 Mb
000000:000128>> 7 833
broadcast_input_information start 3701 Mb
000000:000128<< 7 833
broadcast_input_information 0.005 3701 Mb
000000:000128<< 6 833 parser_read_line_low
0.009 3701 Mb
000000:000128>> 6 834 parser_read_line_low
start 3701 Mb
000000:000128>> 7 834
broadcast_input_information start 3701 Mb
000000:000128<< 7 834
broadcast_input_information 0.004 3701 Mb
000000:000128<< 6 834 parser_read_line_low
0.010 3701 Mb
000000:000128>> 6 835 parser_read_line_low
start 3701 Mb
000000:000128>> 7 835
broadcast_input_information start 3701 Mb
000000:000128<< 7 835
broadcast_input_information 0.003 3701 Mb
000000:000128<< 6 835 parser_read_line_low
0.009 3701 Mb
000000:000128<< 5 3 read_atomic_kind 0.069 3701
Mb
000000:000128>> 5 4 read_atomic_kind start 3701
Mb
000000:000128>> 6 836 parser_read_line_low
start 3701 Mb
000000:000128>> 7 836
broadcast_input_information start 3701 Mb
000000:000128<< 7 836
broadcast_input_information 0.004 3701 Mb
000000:000128<< 6 836 parser_read_line_low
0.008 3701 Mb
000000:000128>> 6 837 parser_read_line_low
start 3701 Mb
000000:000128>> 7 837
broadcast_input_information start 3701 Mb
000000:000128<< 7 837
broadcast_input_information 0.005 3701 Mb
000000:000128<< 6 837 parser_read_line_low
0.010 3701 Mb
000000:000128>> 6 838 parser_read_line_low
start 3701 Mb
000000:000128>> 7 838
broadcast_input_information start 3701 Mb
000000:000128<< 7 838
broadcast_input_information 0.003 3701 Mb
000000:000128<< 6 838 parser_read_line_low
0.009 3701 Mb
000000:000128>> 6 839 parser_read_line_low
start 3701 Mb
000000:000128>> 7 839
broadcast_input_information start 3701 Mb
000000:000128<< 7 839
broadcast_input_information 0.004 3701 Mb
000000:000128<< 6 839 parser_read_line_low
0.009 3701 Mb
000000:000128<< 5 4 read_atomic_kind 0.071 3701
Mb
000000:000128>> 5 5 read_atomic_kind start 3701
Mb
000000:000128>> 6 840 parser_read_line_low
start 3701 Mb
000000:000128>> 7 840
broadcast_input_information start 3701 Mb
000000:000128<< 7 840
broadcast_input_information 0.003 3701 Mb
000000:000128<< 6 840 parser_read_line_low
0.009 3701 Mb
000000:000128>> 6 841 parser_read_line_low
start 3701 Mb
000000:000128>> 7 841
broadcast_input_information start 3701 Mb
000000:000128<< 7 841
broadcast_input_information 0.004 3701 Mb
000000:000128<< 6 841 parser_read_line_low
0.009 3701 Mb
000000:000128>> 6 842 parser_read_line_low
start 3701 Mb
000000:000128>> 7 842
broadcast_input_information start 3701 Mb
000000:000128<< 7 842
broadcast_input_information 0.004 3701 Mb
000000:000128<< 6 842 parser_read_line_low
0.009 3701 Mb
000000:000128>> 6 843 parser_read_line_low
start 3701 Mb
000000:000128>> 7 843
broadcast_input_information start 3701 Mb
000000:000128<< 7 843
broadcast_input_information 0.004 3701 Mb
000000:000128<< 6 843 parser_read_line_low
0.008 3701 Mb
000000:000128>> 6 844 parser_read_line_low
start 3701 Mb
000000:000128>> 7 844
broadcast_input_information start 3701 Mb
000000:000128<< 7 844
broadcast_input_information 0.004 3701 Mb
000000:000128<< 6 844 parser_read_line_low
0.008 3701 Mb
000000:000128<< 5 5 read_atomic_kind 0.083 3701
Mb
000000:000128>> 5 6 read_atomic_kind start 3701
Mb
000000:000128<< 5 6 read_atomic_kind 0.001 3701
Mb
000000:000128<< 4 1 read_atomic_kind_set 0.400 3701
Mb
000000:000128>> 4 1 qs_init_subsys start 3701 Mb


*******************************************************************************

*******************************************************************************

**
**
** ##### ##
## **
** ## ## ## ##
## **
** ## ## ##
###### **
** ## ## ## ## ## ##### ## ## #### ## #####
##### **
** ## ## ## ## ## ## ## ## ## ## ## ##
## ## **
** ## ## ## ## ## ## ## #### ### ## ######
###### **
** ## ### ## ## ## ## ## ## ## ## ##
## **
** ####### ##### ## ##### ## ## #### ## #####
## **
** ##
## **

**
**
** ... make the atoms
dance **

**
**
** Copyright (C) by CP2K Developers Group (2000 -
2011) **

**
**

*******************************************************************************
000000:000128>> 5 1 read_qs_section start 3701
Mb
000000:000128<< 5 1 read_qs_section 0.003 3701
Mb
000000:000128>> 5 1 read_mgrid_section start
3701 Mb
000000:000128<< 5 1 read_mgrid_section 0.000
3701 Mb
000000:000128>> 5 1 check_atomic_kind_set start
3701 Mb
000000:000128<< 5 1 check_atomic_kind_set 0.000
3701 Mb
000000:000128>> 5 1 init_atomic_kind_set start
3701 Mb
000000:000128>> 6 1 init_atomic_kind start
3701 Mb
000000:000128<< 6 1 init_atomic_kind 0.000
3733 Mb
000000:000128>> 6 2 init_atomic_kind start
3733 Mb
000000:000128<< 6 2 init_atomic_kind 0.000
3733 Mb
000000:000128>> 6 3 init_atomic_kind start
3733 Mb
000000:000128<< 6 3 init_atomic_kind 0.000
3733 Mb
000000:000128>> 6 4 init_atomic_kind start
3733 Mb
000000:000128<< 6 4 init_atomic_kind 0.000
3733 Mb
000000:000128>> 6 5 init_atomic_kind start
3733 Mb
000000:000128<< 6 5 init_atomic_kind 0.000
3733 Mb
000000:000128>> 6 6 init_atomic_kind start
3733 Mb
000000:000128<< 6 6 init_atomic_kind 0.000
3733 Mb
000000:000128<< 5 1 init_atomic_kind_set 0.003
3733 Mb
000000:000128>> 5 1 init_interaction_radii start
3733 Mb
000000:000128<< 5 1 init_interaction_radii 0.001
3733 Mb
000000:000128>> 5 2 distribute_molecules_1d
start 3733 Mb
000000:000128<< 5 2 distribute_molecules_1d
0.001 3733 Mb
000000:000128>> 5 1 scf_c_create start 3733 Mb
000000:000128<< 5 1 scf_c_create 0.000 3733 Mb
000000:000128>> 5 1 scf_c_read_parameters start
3733 Mb
000000:000128<< 5 1 scf_c_read_parameters 0.001
3733 Mb
000000:000128>> 5 1 allocate_qs_energy start
3733 Mb
000000:000128<< 5 1 allocate_qs_energy 0.000
3733 Mb
000000:000128>> 5 1 wfi_create start 3733 Mb
000000:000128<< 5 1 wfi_create 0.001 3733 Mb
000000:000128>> 5 1 write_dft_control start 3733
Mb
000000:000128<< 5 1 write_dft_control 0.000 3733
Mb
000000:000128>> 5 1 write_dispersion start 3733
Mb
000000:000128<< 5 1 write_dispersion 0.001 3733
Mb
000000:000128>> 5 1 write_qs_control start 3733
Mb
000000:000128<< 5 1 write_qs_control 0.001 3733
Mb
000000:000128>> 5 1 write_gto_basis_sets start
3733 Mb
000000:000128<< 5 1 write_gto_basis_sets 0.000
3733 Mb
000000:000128>> 5 1 write_atomic_kind_set start
3733 Mb
000000:000128<< 5 1 write_atomic_kind_set 0.000
3733 Mb
000000:000128>> 5 2 write_molecule_kind_set
start 3733 Mb
000000:000128<< 5 2 write_molecule_kind_set
0.001 3733 Mb
000000:000128>> 5 1
write_qs_particle_coordinates start 3733 Mb
000000:000128<< 5 1
write_qs_particle_coordinates 0.000 3733 Mb
000000:000128>> 5 2 write_particle_distances
start 3733 Mb
000000:000128<< 5 2 write_particle_distances
0.000 3733 Mb
000000:000128>> 5 2 write_structure_data start
3733 Mb
000000:000128<< 5 2 write_structure_data 0.000
3733 Mb
000000:000128>> 5 2 write_symmetry start 3733 Mb
000000:000128<< 5 2 write_symmetry 0.000 3733 Mb
000000:000128>> 5 1 scf_c_write_parameters start
3733 Mb


SCF PARAMETERS Density
guess: ATOMIC

--------------------------------------------------------

max_scf: 40

max_scf_history: 0

max_diis: 4

--------------------------------------------------------

eps_scf: 1.00E-07

eps_scf_history: 0.00E+00

eps_diis: 1.00E-01

eps_eigval: 1.00E-05

--------------------------------------------------------
level_shift
[a.u.]: 0.00

--------------------------------------------------------
Outer loop SCF in use
No variables optimised in outer loop

eps_scf 1.00E-07

max_scf 10
No outer loop optimization

step_size 5.00E-01
000000:000128<< 5 1 scf_c_write_parameters 0.004
3733 Mb
000000:000128>> 5 1 qs_env_setup start 3733 Mb
000000:000128>> 6 1 qs_env_rebuild_pw_env
start 3733 Mb
000000:000128>> 7 1 pw_env_rebuild start
3733 Mb
000000:000128>> 8 2 pw_grid_setup start
3733 Mb
000000:000128>> 9 2
pw_grid_distribute start 3743 Mb
000000:000128<< 9 2
pw_grid_distribute 0.026 3743 Mb
000000:000128>> 9 2 pw_grid_allocate
start 3743 Mb
000000:000128<< 9 2 pw_grid_allocate
0.001 3792 Mb
000000:000128>> 9 2 pw_grid_assign
start 3792 Mb
000000:000128<< 9 2 pw_grid_assign
0.203 3792 Mb
000000:000128>> 9 2 pw_grid_sort
start 3792 Mb
000000:000128>> 10 2 sort_shells
start 3796 Mb
000000:000128<< 10 2 sort_shells
0.173 3796 Mb
000000:000128<< 9 2 pw_grid_sort
0.461 3815 Mb
000000:000128>> 9 2 pw_grid_remap
start 3815 Mb
000000:000128<< 9 2 pw_grid_remap
0.039 3825 Mb
000000:000128<< 8 2 pw_grid_setup 0.772
3825 Mb
000000:000128>> 8 3 pw_grid_setup start
3825 Mb
000000:000128>> 9 3
pw_grid_distribute start 3835 Mb
000000:000128<< 9 3
pw_grid_distribute 0.012 3835 Mb
000000:000128>> 9 3 pw_grid_allocate
start 3835 Mb
000000:000128<< 9 3 pw_grid_allocate
0.001 3836 Mb
000000:000128>> 9 3 pw_grid_assign
start 3836 Mb
000000:000128<< 9 3 pw_grid_assign
0.027 3836 Mb
000000:000128>> 9 3 pw_grid_sort
start 3836 Mb
000000:000128>> 10 3 sort_shells
start 3837 Mb
000000:000128<< 10 3 sort_shells
0.076 3837 Mb
000000:000128<< 9 3 pw_grid_sort
0.231 3846 Mb
000000:000128>> 9 3 pw_grid_remap
start 3846 Mb
000000:000128<< 9 3 pw_grid_remap
0.025 3856 Mb
000000:000128<< 8 3 pw_grid_setup 0.318
3856 Mb
000000:000128>> 8 4 pw_grid_setup start
3856 Mb
000000:000128>> 9 4
pw_grid_distribute start 3862 Mb
000000:000128<< 9 4
pw_grid_distribute 0.004 3862 Mb
000000:000128>> 9 4 pw_grid_allocate
start 3862 Mb
000000:000128<< 9 4 pw_grid_allocate
0.001 3862 Mb
000000:000128>> 9 4 pw_grid_assign
start 3862 Mb
000000:000128<< 9 4 pw_grid_assign
0.003 3862 Mb
000000:000128>> 9 4 pw_grid_sort
start 3862 Mb
000000:000128>> 10 4 sort_shells
start 3862 Mb
000000:000128<< 10 4 sort_shells
0.008 3862 Mb
000000:000128<< 9 4 pw_grid_sort
0.025 3862 Mb
000000:000128>> 9 4 pw_grid_remap
start 3862 Mb
000000:000128<< 9 4 pw_grid_remap
0.006 3872 Mb
000000:000128<< 8 4 pw_grid_setup 0.045
3872 Mb
000000:000128>> 8 5 pw_grid_setup start
3872 Mb
000000:000128>> 9 5
pw_grid_distribute start 3874 Mb
000000:000128<< 9 5
pw_grid_distribute 0.003 3874 Mb
000000:000128>> 9 5 pw_grid_allocate
start 3874 Mb
000000:000128<< 9 5 pw_grid_allocate
0.001 3874 Mb
000000:000128>> 9 5 pw_grid_assign
start 3874 Mb
000000:000128<< 9 5 pw_grid_assign
0.001 3874 Mb
000000:000128>> 9 5 pw_grid_sort
start 3874 Mb
000000:000128>> 10 5 sort_shells
start 3874 Mb
000000:000128<< 10 5 sort_shells
0.001 3874 Mb
000000:000128<< 9 5 pw_grid_sort
0.002 3874 Mb
000000:000128>> 9 5 pw_grid_remap
start 3874 Mb
000000:000128<< 9 5 pw_grid_remap
0.003 3876 Mb
000000:000128<< 8 5 pw_grid_setup 0.011
3876 Mb
000000:000128>> 8 6 pw_grid_setup start
3876 Mb
000000:000128>> 9 6
pw_grid_distribute start 3876 Mb
000000:000128<< 9 6
pw_grid_distribute 0.003 3876 Mb
000000:000128>> 9 6 pw_grid_allocate
start 3876 Mb
000000:000128<< 9 6 pw_grid_allocate
0.000 3876 Mb
000000:000128>> 9 6 pw_grid_assign
start 3876 Mb
000000:000128<< 9 6 pw_grid_assign
0.001 3876 Mb
000000:000128>> 9 6 pw_grid_sort
start 3876 Mb
000000:000128>> 10 6 sort_shells
start 3876 Mb
000000:000128<< 10 6 sort_shells
0.001 3876 Mb
000000:000128<< 9 6 pw_grid_sort
0.002 3876 Mb
000000:000128>> 9 6 pw_grid_remap
start 3876 Mb
000000:000128<< 9 6 pw_grid_remap
0.001 3876 Mb
000000:000128<< 8 6 pw_grid_setup 0.008
3876 Mb
000000:000128>> 8 1 compute_max_radius
start 3876 Mb
000000:000128<< 8 1 compute_max_radius
0.203 3876 Mb
000000:000128>> 8 1 init_cube_info
start 3876 Mb
000000:000128<< 8 1 init_cube_info
0.002 3876 Mb
000000:000128>> 8 2
rs_grid_create_descriptor start 3876 Mb
000000:000128<< 8 2
rs_grid_create_descriptor 0.001 3876 Mb
000000:000128>> 8 2 rs_grid_create
start 3876 Mb
000000:000128<< 8 2 rs_grid_create
0.000 3885 Mb
000000:000128>> 8 2 init_cube_info
start 3885 Mb
000000:000128<< 8 2 init_cube_info
0.003 3885 Mb
000000:000128>> 8 3
rs_grid_create_descriptor start 3885 Mb
000000:000128<< 8 3
rs_grid_create_descriptor 0.000 3885 Mb
000000:000128>> 8 3 rs_grid_create
start 3885 Mb
000000:000128<< 8 3 rs_grid_create
0.000 3890 Mb
000000:000128>> 8 3 init_cube_info
start 3890 Mb
000000:000128<< 8 3 init_cube_info
0.002 3890 Mb
000000:000128>> 8 4
rs_grid_create_descriptor start 3890 Mb
000000:000128<< 8 4
rs_grid_create_descriptor 0.000 3890 Mb
000000:000128>> 8 4 rs_grid_create
start 3890 Mb
000000:000128<< 8 4 rs_grid_create
0.000 3896 Mb
000000:000128>> 8 4 init_cube_info
start 3896 Mb
000000:000128<< 8 4 init_cube_info
0.007 3896 Mb
000000:000128>> 8 5
rs_grid_create_descriptor start 3896 Mb
000000:000128<< 8 5
rs_grid_create_descriptor 0.000 3896 Mb
000000:000128>> 8 5 rs_grid_create
start 3896 Mb
000000:000128<< 8 5 rs_grid_create
0.002 3897 Mb
000000:000128<< 7 1 pw_env_rebuild 1.384
3897 Mb
000000:000128>> 7 1 pw_pool_create_pw
start 3897 Mb
000000:000128>> 8 1 pw_create start
3897 Mb
000000:000128<< 8 1 pw_create 0.001
3903 Mb
000000:000128<< 7 1 pw_pool_create_pw
0.001 3903 Mb
000000:000128<< 6 1 qs_env_rebuild_pw_env
1.385 3903 Mb
000000:000128>> 6 1 mpools_rebuild_fm_pools
start 3903 Mb
000000:000128<< 6 1 mpools_rebuild_fm_pools
0.001 3903 Mb
000000:000128>> 6 1 distribute_molecules_2d
start 3903 Mb
000000:000128>> 7 1
make_basic_distribution start 3903 Mb
000000:000128<< 7 1
make_basic_distribution 0.001 3903 Mb
000000:000128<< 6 1 distribute_molecules_2d
0.002 3903 Mb
000000:000128<< 5 1 qs_env_setup 1.388 3903 Mb
000000:000128<< 4 1 qs_init_subsys 1.415 3903 Mb
000000:000128>> 4 4 cp_result_create start 3903 Mb
000000:000128<< 4 4 cp_result_create 0.000 3903 Mb
000000:000128<< 3 1 quickstep_create_force_env 1.824
3903 Mb


*******************************************************************************

*******************************************************************************

**
**
** ####### ## ## ## ## ##
## **
** ## ## ### ### ### ### ###
### **
** ## ## #### #### #### #### ####
#### **
** ## ## ## ### ## ## ### ## ## ###
## **
** ## ## ## ## ## ## ## ##
## **
** ## ## ## ## ## ## ## ## T.Laino and
F.Mohamed **
** ##### ## ## ## ## ## ## ##
2005-2011 **

**
**
** Calculation
Started.. **

*******************************************************************************

*******************************************************************************
000000:000128>> 3 5 cp_result_create start 3905 Mb
000000:000128<< 3 5 cp_result_create 0.000 3905 Mb
000000:000128<< 2 1 qmmm_create_force_env 265.651 3905 Mb
000000:000128>> 2 1 metadyn_read start 3905 Mb
000000:000128<< 2 1 metadyn_read 0.000 3905 Mb
000000:000128>> 2 1 fp_env_create start 3905 Mb
000000:000128<< 2 1 fp_env_create 0.000 3905 Mb
000000:000128>> 2 1 fp_env_read start 3905 Mb
000000:000128<< 2 1 fp_env_read 0.000 3905 Mb
000000:000128>> 2 1 fp_env_write start 3905 Mb
000000:000128<< 2 1 fp_env_write 0.001 3905 Mb
000000:000128>> 2 1 fp_env_release start 3905 Mb
000000:000128<< 2 1 fp_env_release 0.001 3905 Mb
000000:000128>> 2 2 fp_env_release start 3905 Mb
000000:000128<< 2 2 fp_env_release 0.000 3905 Mb
000000:000128>> 2 1 qs_mol_dyn_low start 3905 Mb

MD| Molecular Dynamics Protocol
MD| Ensemble
Type NVT
MD| Number of Time
Steps 500000
MD| Time Step
[fs] 0.50
MD| Temperature
[K] 300.00
MD| Temperature tolerance
[K] 0.00
MD| Constraints activated
MD| Tolerance for shake
0.1000E-05
MD| Print MD information every
1 step(s)
MD| File type Print frequency[steps]
File names
MD| Coordinates 1
system.dcd
MD| Velocities 1
system.vel
MD| Energies 1
system.ene
MD| Dump 1
system.restart

000000:000128>> 3 1 rot_ana start 3905 Mb
000000:000128>> 4 1 diamat_all start 3905 Mb
000000:000128<< 4 1 diamat_all 0.001 3905 Mb
ROT| Rotational Analysis Info
ROT| Principal axes and moments of inertia in atomic units:
ROT| 1
2 3
ROT| EIGENVALUES 0.202294878E+14 0.346096292E+14
0.394887163E+14
ROT| X -0.005663006 0.999954168
-0.007719647
ROT| Y -0.006728067 0.007681496
0.999947863
ROT| Z 0.999961331 0.005714649
0.006684259
ROT| Numer of Rotovibrational vectors: 6
000000:000128<< 3 1 rot_ana 0.270 3935 Mb

Calculation of degrees of freedom
Number of
atoms: 232428
Number of Intramolecular
constraints: 212169
Number of Intermolecular
constraints: 0
Invariants(translation +
rotations): 0
Degrees of
freedom: 485115


Restraints Information
Number of Intramolecular
restraints: 0
Number of Intermolecular
restraints: 0
000000:000128>> 3 1 thermostat_mapping_region start
3935 Mb
000000:000128>> 4 1 mapping_region_evaluate start
3935 Mb
000000:000128<< 4 1 mapping_region_evaluate 0.027
3935 Mb
000000:000128>> 4 1 massive_list_generate start
3935 Mb
000000:000128<< 4 1 massive_list_generate 0.000
3935 Mb
000000:000128>> 4 1 thermostat_mapping_region_low
start 3935 Mb
000000:000128<< 4 1 thermostat_mapping_region_low
0.001 3935 Mb
000000:000128<< 3 1 thermostat_mapping_region 0.030
3935 Mb

THERMOSTAT| Thermostat Info for PARTICLES
THERMOSTAT| Type of thermostat Canonical Sampling/Velocity
Rescaling
THERMOSTAT| CSVR time constant
[ fs] 50.00
THERMOSTAT| Initial Kinetic Energy
-0.412238
THERMOSTAT| End of Thermostat Info for PARTICLES

000000:000128>> 3 1 setup_velocities start 3935 Mb
000000:000128>> 4 1 initialize_velocities start
3935 Mb
************************** Velocities initialization
**************************
000000:000128>> 5 1 read_binary_velocities start
3935 Mb
000000:000128<< 5 1 read_binary_velocities 0.000
3935 Mb
Initial
Temperature 299.69
K
COM velocity: -0.000000013862 0.000000131448
-0.000000639613

*******************************************************************************

000000:000128<< 4 1 initialize_velocities 0.213
3935 Mb
000000:000128<< 3 1 setup_velocities 0.215 3935 Mb
000000:000128>> 3 2 write_qs_particle_coordinates
start 3935 Mb
000000:000128<< 3 2 write_qs_particle_coordinates
0.001 3935 Mb
000000:000128>> 3 1 qs_ks_qmmm_create start 3935 Mb
000000:000128>> 4 2 pw_pool_create_pw start 3935 Mb
000000:000128>> 5 2 pw_create start 3935 Mb
000000:000128<< 5 2 pw_create 0.001 3935 Mb
000000:000128<< 4 2 pw_pool_create_pw 0.001 3935 Mb
000000:000128>> 4 5 init_cube_info start 3935 Mb
000000:000128<< 4 5 init_cube_info 0.000 3935 Mb
000000:000128>> 4 6 init_cube_info start 3935 Mb
000000:000128<< 4 6 init_cube_info 0.000 3935 Mb
000000:000128>> 4 7 init_cube_info start 3935 Mb
000000:000128<< 4 7 init_cube_info 0.009 3935 Mb
000000:000128>> 4 8 init_cube_info start 3935 Mb
000000:000128<< 4 8 init_cube_info 0.009 3935 Mb
000000:000128<< 3 1 qs_ks_qmmm_create 0.020 3935 Mb
000000:000128>> 3 1 qmmm_el_coupling start 3935 Mb
QMMM| Information on the QM/MM Electrostatic Potential:
000000:000128>> 4 1 pw_zero start 3935 Mb
000000:000128<< 4 1 pw_zero 0.002 3935 Mb
QMMM| QM/MM Coupling computed collocating the Gaussian Potential
Functions.
000000:000128>> 4 1 qmmm_elec_with_gaussian start
3935 Mb
000000:000128>> 5 3 pw_pool_create_pw start 3935
Mb
000000:000128>> 6 3 pw_create start 3935 Mb
000000:000128<< 6 3 pw_create 0.000 4294 Mb
000000:000128<< 5 3 pw_pool_create_pw 0.001 4294
Mb
000000:000128>> 5 4 pw_pool_create_pw start 4294
Mb
000000:000128>> 6 4 pw_create start 4294 Mb
000000:000128<< 6 4 pw_create 0.000 4340 Mb
000000:000128<< 5 4 pw_pool_create_pw 0.000 4340
Mb
000000:000128>> 5 5 pw_pool_create_pw start 4340
Mb
000000:000128>> 6 5 pw_create start 4340 Mb
000000:000128<< 6 5 pw_create 0.000 4340 Mb
000000:000128<< 5 5 pw_pool_create_pw 0.000 4340
Mb
000000:000128>> 5 6 pw_pool_create_pw start 4340
Mb
000000:000128>> 6 6 pw_create start 4340 Mb
000000:000128<< 6 6 pw_create 0.000 4340 Mb
000000:000128<< 5 6 pw_pool_create_pw 0.000 4340
Mb
000000:000128>> 5 2 pw_zero start 4340 Mb
000000:000128<< 5 2 pw_zero 0.769 4340 Mb
000000:000128>> 5 3 pw_zero start 4340 Mb
000000:000128<< 5 3 pw_zero 0.047 4340 Mb
000000:000128>> 5 4 pw_zero start 4340 Mb
000000:000128<< 5 4 pw_zero 0.003 4340 Mb
000000:000128>> 5 5 pw_zero start 4340 Mb
000000:000128<< 5 5 pw_zero 0.000 4340 Mb
000000:000128>> 5 1 qmmm_elec_with_gaussian_low
start 4340 Mb
000000:000128>> 6 1 qmmm_elec_gaussian_low_G
start 4340 Mb
000000:000128<< 6 1 qmmm_elec_gaussian_low_G
0.120 4340 Mb
000000:000128>> 6 1 qmmm_elec_gaussian_low_R
start 4340 Mb
000000:000128>> 7 1
qmmm_elec_with_gaussian_LR start 4340 Mb
Application 350059 exit signals: Killed
Application 350059 resources: utime ~4s, stime ~6s

[Teodoro Laino]

I have no experience on the new configuration of Rosa. Nonetheless, from the info I was able to collect, I found that each node has 32 GB of memory.
This means that running 32 mpi tasks per node, each cp2k task has ~ 1GB of memory (maybe something less.. because of OS, IO, etc..).
Depending on your system this is definitely not too much.

You can try to change the parallelization inside QM/MM - switching to grid instead of atomic may help you to avoid an additional memory allocation which may cause the problem you see.

-----

Now the thought of the evening:

a machine with 32 cores per node is not designed to sustain 32 mpi tasks.
Clearly, there will be the need (more and more, looking at the machines of the next years) to move to hybrid parallel schemes on such a platform.
So, I would encourage you to try a mixed omp/mpi for cp2k.

Unfortunately, not all pieces of cp2k support omp, and unfortunately^2 qm/mm is not one of those few parts that supports it.
But you may still take advantage of the few parts that use it and avoid at the same time the memory issues that you observe.

Teo

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