CP2K running slow
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Tanmoy Paul
Oct 28, 2014, 10:10:44 AM10/28/14
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Hello CP2K users,
I am new to this field . I have installed cp2k using "sudo apt-get install cp2k" . I am trying to run a QM/MM minimization for 40000 steps using command "mpirun -np 8 cp2k.popt -i inputfile -o outputfile ". It does not show any error message but the problem is it is terribly slow ( around 100 steps per day ) .My system is quite large (~48000 atoms are there ) and the QM-selection contains 150 atoms .I can understand that something has gone wrong with cp2k installation or my understanding about how it works, but I don't know what's going wrong . This may really be an aw-coward question to ask and I am really sorry about that . Can I have your kind suggestions on this topic.
Regards
Tanmoy
Samuel Andermatt
Oct 28, 2014, 10:14:43 AM10/28/14
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Could you post your input file, knowing which parameters you chose (e.g. for the PW cutoff and the basis set) would help.
Tanmoy Paul
Oct 28, 2014, 10:20:07 AM10/28/14
to cp...@googlegroups.com
Thanks Samuel for a quick reply. Here is the input file.............
&FORCE_EVAL
METHOD QMMM
&DFT
CHARGE 0
BASIS_SET_FILE_NAME ../BASIS_SET
BASIS_SET_FILE_NAME ../BASIS_MOLOPT
POTENTIAL_FILE_NAME ../POTENTIAL
&MGRID
COMMENSURATE
CUTOFF 250
&END MGRID
&QS
EXTRAPOLATION PS
EXTRAPOLATION_ORDER 3
METHOD GPW
PW_GRID NS-FULLSPACE
&END QS
&SCF
SCF_GUESS ATOMIC
MAX_SCF 300
EPS_SCF 1.0E-06
&OUTER_SCF
EPS_SCF 1.0E-06
MAX_SCF 20
&END OUTER_SCF
&OT
PRECONDITIONER FULL_ALL
ENERGY_GAP 0.001
MINIMIZER CG
&END OT
&END SCF
&POISSON
POISSON_SOLVER PERIODIC
PERIODIC XYZ
&END POISSON
&XC
&XC_GRID
XC_SMOOTH_RHO NN10
XC_DERIV SPLINE2_SMOOTH
&END XC_GRID
&XC_FUNCTIONAL BLYP
&END XC_FUNCTIONAL
&END XC
&END DFT
&MM
&FORCEFIELD
PARMTYPE CHM
PARM_FILE_NAME par_all27_prot_lipid.inp
EI_SCALE14 1.0
VDW_SCALE14 1.0
&SPLINE
EMAX_SPLINE 5.00000000E-01
RCUT_NB 15.0
&END SPLINE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE PME
ALPHA 0.20
GMAX 100
RCUT 15.0
&END EWALD
&END POISSON
&END MM
&QMMM
&CELL
ABC 20.0 20.0 20.0
&END CELL
E_COUPL GAUSS
&INTERPOLATOR
EPS_R 1.0e-15
EPS_X 1.0e-15
MAXITER 100
&END INTERPOLATOR
&PERIODIC
GMAX 1.0
&MULTIPOLE ON
ANALYTICAL_GTERM TRUE
NGRIDS 60 60 60
RCUT 50.0
&END MULTIPOLE
&END PERIODIC
&PRINT
&PERIODIC_INFO
&END PERIODIC_INFO
&POTENTIAL
&END POTENTIAL
&END PRINT
&QM_KIND H
MM_INDEX 43 42 46 48 56 58 54 52 73 74 77 79
MM_INDEX 82 84 86 941 942 946 947 967 969
MM_INDEX 971 962 963 1014 1015 1010 1009 1398
MM_INDEX 1399 1393 1394 1427 1428 1436 1430
MM_INDEX 1433 1473 1464 1465 1467 1470 1820
MM_INDEX 1818 1816 1811 1812 3040 3038 3054
MM_INDEX 3052 25438 25437 41848 41847 11184
MM_INDEX 11185 45760 45759 10410 10411 4078
MM_INDEX 4077 4093 4092 4075 4074
&END QM_KIND
&QM_KIND O
MM_INDEX 81 944 1012 1396 3039 3053 11183
MM_INDEX 41846 25436 10409 4076 4091 4073
MM_INDEX 45758
&END QM_KIND
&QM_KIND C
MM_INDEX 41 44 45 49 55 57 53 51 50 72 75 76
MM_INDEX 78 80 85 83 943 940 961 965 970 966
MM_INDEX 1008 1011 1395 1392 1426 1431 1432
MM_INDEX 1435 1472 1468 1469 1815 1819 1814
MM_INDEX 1810 3037 3051 1463
&END QM_KIND
&QM_KIND N
MM_INDEX 47 945 968 964 1013 1397 1434 1429
MM_INDEX 1466 1817 1813 1471
&END QM_KIND
&QM_KIND ZN
MM_INDEX 4072
&END QM_KIND
&LINK
MM_INDEX 39
QM_INDEX 41
QM_KIND H
ALPHA_IMOMM 1.322
&END LINK
&LINK
MM_INDEX 70
QM_INDEX 72
QM_KIND H
ALPHA_IMOMM 1.363
&END LINK
&LINK
MM_INDEX 938
QM_INDEX 940
QM_KIND H
ALPHA_IMOMM 1.369
&END LINK
&LINK
MM_INDEX 959
QM_INDEX 961
QM_KIND H
ALPHA_IMOMM 1.423
&END LINK
&LINK
MM_INDEX 1006
QM_INDEX 1008
QM_KIND H
ALPHA_IMOMM 1.407
&END LINK
&LINK
MM_INDEX 1389
QM_INDEX 1392
QM_KIND H
ALPHA_IMOMM 1.290
&END LINK
&LINK
MM_INDEX 1424
QM_INDEX 1426
QM_KIND H
ALPHA_IMOMM 1.411
&END LINK
&LINK
MM_INDEX 1461
QM_INDEX 1463
QM_KIND H
ALPHA_IMOMM 1.286
&END LINK
&LINK
MM_INDEX 1808
QM_INDEX 1810
QM_KIND H
ALPHA_IMOMM 1.454
&END LINK
&LINK
MM_INDEX 3041
QM_INDEX 3037
QM_KIND H
ALPHA_IMOMM 1.373
&END LINK
&LINK
MM_INDEX 3035
QM_INDEX 3037
QM_KIND H
ALPHA_IMOMM 1.391
&END LINK
&LINK
MM_INDEX 3055
QM_INDEX 3051
QM_KIND H
ALPHA_IMOMM 1.378
&END LINK
&LINK
MM_INDEX 3049
QM_INDEX 3051
QM_KIND H
ALPHA_IMOMM 1.387
&END LINK
&END QMMM
&SUBSYS
&CELL
ABC 77.18 74.44 85.17
PERIODIC XYZ
&END CELL
&KIND H
BASIS_SET DZVP-GTH-BLYP
POTENTIAL GTH-BLYP-q1
&END KIND
&KIND O
BASIS_SET DZVP-GTH-BLYP
POTENTIAL GTH-BLYP-q6
&END KIND
&KIND C
BASIS_SET DZVP-GTH-BLYP
POTENTIAL GTH-BLYP-q4
&END KIND
&KIND N
BASIS_SET DZVP-GTH-BLYP
POTENTIAL GTH-BLYP-q5
&END KIND
&KIND ZN
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-BLYP-q12
&END KIND
&TOPOLOGY
CONN_FILE_FORMAT UPSF
CONN_FILE_NAME HCA_in_final.psf
COORD_FILE_FORMAT PDB
COORD_FILE_NAME HCA_no_co2_cp2k.pdb
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
PROJECT HCA_qmmm_min_cp2k_no_co2
PRINT_LEVEL MEDIUM
RUN_TYPE MD
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVE
STEPS 50000
TIMESTEP 0.5
TEMPERATURE 310
&THERMOSTAT
REGION GLOBAL
TYPE NOSE
&NOSE
LENGTH 4
YOSHIDA 9
TIMECON 1000
&END NOSE
&END THERMOSTAT
&PRINT
&ENERGY
&EACH
MD 1
&END EACH
&END ENERGY
&END PRINT
&END MD
&PRINT
&RESTART
&EACH
MD 10000
&END EACH
&END RESTART
&RESTART_HISTORY OFF
&END RESTART_HISTORY
&TRAJECTORY SILENT
FORMAT DCD
&EACH
MD 100
&END EACH
&END TRAJECTORY
&VELOCITIES OFF
LOG_PRINT_KEY T
FORMAT XYZ
UNIT angstrom
&EACH
MD 100
&END EACH
ADD_LAST NUMERIC
&END VELOCITIES
&FORCES OFF
&END FORCES
&END PRINT
&END MOTION
&FORCE_EVAL
METHOD QMMM
&DFT
CHARGE 0
BASIS_SET_FILE_NAME ../BASIS_SET
BASIS_SET_FILE_NAME ../BASIS_MOLOPT
POTENTIAL_FILE_NAME ../POTENTIAL
&MGRID
COMMENSURATE
CUTOFF 250
&END MGRID
&QS
EXTRAPOLATION PS
EXTRAPOLATION_ORDER 3
METHOD GPW
PW_GRID NS-FULLSPACE
&END QS
&SCF
SCF_GUESS ATOMIC
MAX_SCF 300
EPS_SCF 1.0E-06
&OUTER_SCF
EPS_SCF 1.0E-06
MAX_SCF 20
&END OUTER_SCF
&OT
PRECONDITIONER FULL_ALL
ENERGY_GAP 0.001
MINIMIZER CG
&END OT
&END SCF
&POISSON
POISSON_SOLVER PERIODIC
PERIODIC XYZ
&END POISSON
&XC
&XC_GRID
XC_SMOOTH_RHO NN10
XC_DERIV SPLINE2_SMOOTH
&END XC_GRID
&XC_FUNCTIONAL BLYP
&END XC_FUNCTIONAL
&END XC
&END DFT
&MM
&FORCEFIELD
PARMTYPE CHM
PARM_FILE_NAME par_all27_prot_lipid.inp
EI_SCALE14 1.0
VDW_SCALE14 1.0
&SPLINE
EMAX_SPLINE 5.00000000E-01
RCUT_NB 15.0
&END SPLINE
&END FORCEFIELD
&POISSON
&EWALD
EWALD_TYPE PME
ALPHA 0.20
GMAX 100
RCUT 15.0
&END EWALD
&END POISSON
&END MM
&QMMM
&CELL
ABC 20.0 20.0 20.0
&END CELL
E_COUPL GAUSS
&INTERPOLATOR
EPS_R 1.0e-15
EPS_X 1.0e-15
MAXITER 100
&END INTERPOLATOR
&PERIODIC
GMAX 1.0
&MULTIPOLE ON
ANALYTICAL_GTERM TRUE
NGRIDS 60 60 60
RCUT 50.0
&END MULTIPOLE
&END PERIODIC
&PERIODIC_INFO
&END PERIODIC_INFO
&POTENTIAL
&END POTENTIAL
&END PRINT
&QM_KIND H
MM_INDEX 43 42 46 48 56 58 54 52 73 74 77 79
MM_INDEX 82 84 86 941 942 946 947 967 969
MM_INDEX 971 962 963 1014 1015 1010 1009 1398
MM_INDEX 1399 1393 1394 1427 1428 1436 1430
MM_INDEX 1433 1473 1464 1465 1467 1470 1820
MM_INDEX 1818 1816 1811 1812 3040 3038 3054
MM_INDEX 3052 25438 25437 41848 41847 11184
MM_INDEX 11185 45760 45759 10410 10411 4078
MM_INDEX 4077 4093 4092 4075 4074
&END QM_KIND
&QM_KIND O
MM_INDEX 81 944 1012 1396 3039 3053 11183
MM_INDEX 41846 25436 10409 4076 4091 4073
MM_INDEX 45758
&END QM_KIND
&QM_KIND C
MM_INDEX 41 44 45 49 55 57 53 51 50 72 75 76
MM_INDEX 78 80 85 83 943 940 961 965 970 966
MM_INDEX 1008 1011 1395 1392 1426 1431 1432
MM_INDEX 1435 1472 1468 1469 1815 1819 1814
MM_INDEX 1810 3037 3051 1463
&END QM_KIND
&QM_KIND N
MM_INDEX 47 945 968 964 1013 1397 1434 1429
MM_INDEX 1466 1817 1813 1471
&END QM_KIND
&QM_KIND ZN
MM_INDEX 4072
&END QM_KIND
&LINK
MM_INDEX 39
QM_INDEX 41
QM_KIND H
ALPHA_IMOMM 1.322
&END LINK
&LINK
MM_INDEX 70
QM_INDEX 72
QM_KIND H
ALPHA_IMOMM 1.363
&END LINK
&LINK
MM_INDEX 938
QM_INDEX 940
QM_KIND H
ALPHA_IMOMM 1.369
&END LINK
&LINK
MM_INDEX 959
QM_INDEX 961
QM_KIND H
ALPHA_IMOMM 1.423
&END LINK
&LINK
MM_INDEX 1006
QM_INDEX 1008
QM_KIND H
ALPHA_IMOMM 1.407
&END LINK
&LINK
MM_INDEX 1389
QM_INDEX 1392
QM_KIND H
ALPHA_IMOMM 1.290
&END LINK
&LINK
MM_INDEX 1424
QM_INDEX 1426
QM_KIND H
ALPHA_IMOMM 1.411
&END LINK
&LINK
MM_INDEX 1461
QM_INDEX 1463
QM_KIND H
ALPHA_IMOMM 1.286
&END LINK
&LINK
MM_INDEX 1808
QM_INDEX 1810
QM_KIND H
ALPHA_IMOMM 1.454
&END LINK
&LINK
MM_INDEX 3041
QM_INDEX 3037
QM_KIND H
ALPHA_IMOMM 1.373
&END LINK
&LINK
MM_INDEX 3035
QM_INDEX 3037
QM_KIND H
ALPHA_IMOMM 1.391
&END LINK
&LINK
MM_INDEX 3055
QM_INDEX 3051
QM_KIND H
ALPHA_IMOMM 1.378
&END LINK
&LINK
MM_INDEX 3049
QM_INDEX 3051
QM_KIND H
ALPHA_IMOMM 1.387
&END LINK
&END QMMM
&SUBSYS
&CELL
ABC 77.18 74.44 85.17
PERIODIC XYZ
&END CELL
&KIND H
BASIS_SET DZVP-GTH-BLYP
POTENTIAL GTH-BLYP-q1
&END KIND
&KIND O
BASIS_SET DZVP-GTH-BLYP
POTENTIAL GTH-BLYP-q6
&END KIND
&KIND C
BASIS_SET DZVP-GTH-BLYP
POTENTIAL GTH-BLYP-q4
&END KIND
&KIND N
BASIS_SET DZVP-GTH-BLYP
POTENTIAL GTH-BLYP-q5
&END KIND
&KIND ZN
BASIS_SET DZVP-MOLOPT-SR-GTH
POTENTIAL GTH-BLYP-q12
&END KIND
&TOPOLOGY
CONN_FILE_FORMAT UPSF
CONN_FILE_NAME HCA_in_final.psf
COORD_FILE_FORMAT PDB
COORD_FILE_NAME HCA_no_co2_cp2k.pdb
&END TOPOLOGY
&END SUBSYS
&END FORCE_EVAL
&GLOBAL
PROJECT HCA_qmmm_min_cp2k_no_co2
PRINT_LEVEL MEDIUM
RUN_TYPE MD
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVE
STEPS 50000
TIMESTEP 0.5
TEMPERATURE 310
&THERMOSTAT
REGION GLOBAL
TYPE NOSE
&NOSE
LENGTH 4
YOSHIDA 9
TIMECON 1000
&END NOSE
&END THERMOSTAT
&ENERGY
&EACH
MD 1
&END EACH
&END ENERGY
&END PRINT
&END MD
&RESTART
&EACH
MD 10000
&END EACH
&END RESTART
&RESTART_HISTORY OFF
&END RESTART_HISTORY
&TRAJECTORY SILENT
FORMAT DCD
&EACH
MD 100
&END EACH
&END TRAJECTORY
&VELOCITIES OFF
LOG_PRINT_KEY T
FORMAT XYZ
UNIT angstrom
&EACH
MD 100
&END EACH
ADD_LAST NUMERIC
&END VELOCITIES
&FORCES OFF
&END FORCES
&END PRINT
&END MOTION
Samuel Andermatt
Oct 29, 2014, 5:45:07 AM10/29/14
to cp...@googlegroups.com
Sadly I do not know what exactly the reason for the performance issue is. An additional method to figure out the problem would be to make a short run and at the end of the output you will see the timings. It will give some information about the performance bottlenecks.
hut...@chem.uzh.ch
Oct 29, 2014, 6:02:59 AM10/29/14
to cp...@googlegroups.com
Hi
yes, check the timing information at the end of a short run.
This will give some information on possible problems.
You should also change the EWALD method from PME to SPME.
regards
Juerg
--------------------------------------------------------------
Juerg Hutter Phone : ++41 44 635 4491
Institut für Chemie C FAX : ++41 44 635 6838
Universität Zürich E-mail: hut...@chem.uzh.ch
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
---------------------------------------------------------------
-----cp...@googlegroups.com wrote: -----
To: cp...@googlegroups.com
From: Samuel Andermatt
Sent by: cp...@googlegroups.com
Date: 10/29/2014 10:45AM
Subject: [CP2K:5788] Re: CP2K running slow
Sadly I do not know what exactly the reason for the performance issue is. An additional method to figure out the problem would be to make a short run and at the end of the output you will see the timings. It will give some information about the performance bottlenecks.
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yes, check the timing information at the end of a short run.
This will give some information on possible problems.
You should also change the EWALD method from PME to SPME.
regards
Juerg
--------------------------------------------------------------
Juerg Hutter Phone : ++41 44 635 4491
Institut für Chemie C FAX : ++41 44 635 6838
Universität Zürich E-mail: hut...@chem.uzh.ch
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
---------------------------------------------------------------
-----cp...@googlegroups.com wrote: -----
To: cp...@googlegroups.com
From: Samuel Andermatt
Sent by: cp...@googlegroups.com
Date: 10/29/2014 10:45AM
Subject: [CP2K:5788] Re: CP2K running slow
Sadly I do not know what exactly the reason for the performance issue is. An additional method to figure out the problem would be to make a short run and at the end of the output you will see the timings. It will give some information about the performance bottlenecks.
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Tanmoy Paul
Oct 29, 2014, 6:07:46 AM10/29/14
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Thanks Samuel and Juerg for your inputs .
Tanmoy Paul
Oct 30, 2014, 1:30:20 AM10/30/14
to cp...@googlegroups.com
Dear CP2K users,
I checked the output files and to be frank I have understood a very little about it . Last few lines of the output file says...-------------------------------------------------------------------------------
---- MULTIGRID INFO ----
-------------------------------------------------------------------------------
count for grid 1: 317951 cutoff [a.u.] 125.00
count for grid 2: 302978 cutoff [a.u.] 31.25
count for grid 3: 76551 cutoff [a.u.] 7.81
count for grid 4: 684 cutoff [a.u.] 1.95
total gridlevel count : 698164
-------------------------------------------------------------------------------
- -
- MESSAGE PASSING PERFORMANCE -
- -
-------------------------------------------------------------------------------
ROUTINE CALLS TOT TIME [s] AVE VOLUME [Bytes] PERFORMANCE [MB/s]
MP_Group 6 0.000
MP_Bcast 1834 0.213 5713507. 49195.17
MP_Allreduce 10132 130.663 142451. 11.05
MP_Sync 101392 0.269
MP_Alltoall 9590 652.514 46235404. 679.52
MP_SendRecv 15776 87.207 294912. 53.35
MP_ISendRecv 23730 0.566 4071645. 170706.96
MP_Wait 24093 402.879
MP_ISend 275 0.038 728596. 5272.74
MP_IRecv 264 0.001 746667. 197120.00
MP_Recv 76412 0.793 3234. 311.65
-------------------------------------------------------------------------------
-------------------------------------------------------------------------------
- -
- T I M I N G -
- -
-------------------------------------------------------------------------------
SUBROUTINE CALLS ASD SELF TIME TOTAL TIME
AVERAGE MAXIMUM AVERAGE MAXIMUM
CP2K 1 1.0 1.346 1.804 9476.129 9476.130
qs_mol_dyn_low 1 2.0 0.095 0.314 9465.241 9465.854
qs_forces 11 3.9 0.027 0.040 8706.050 8706.055
qs_energies_scf 11 4.9 0.001 0.002 8569.698 8569.705
scf_env_do_scf 11 5.9 0.004 0.004 8453.922 8453.929
scf_env_do_scf_inner_loop 639 6.5 0.218 0.273 8289.159 8289.172
velocity_verlet 10 3.0 0.894 3.202 5147.091 5147.116
qs_ks_build_kohn_sham_matrix 650 8.5 12.649 13.425 4123.288 4123.607
qs_rho_update_rho 650 7.5 0.026 0.031 4077.287 4077.571
calculate_rho_elec 1300 8.5 592.558 649.730 4077.261 4077.552
qs_ks_update_qs_env 651 7.5 0.014 0.027 3995.187 3995.463
fft_wrap_pw1pw2 9590 11.0 0.464 0.476 3630.990 3654.319
fft_wrap_pw1pw2_130 3630 11.8 366.371 376.203 3397.033 3418.254
density_rs2pw 1300 9.5 0.135 0.159 3331.163 3383.539
fft3d_ps 9590 13.0 1685.880 1712.933 2797.864 2836.568
qs_vxc_create 650 9.5 0.047 0.054 1589.974 1590.199
sum_up_and_integrate 336 9.4 46.390 55.122 1355.401 1368.971
integrate_v_rspace 672 10.4 301.274 329.909 1309.006 1315.670
xc_rho_set_and_dset_create 650 11.5 202.175 205.516 1171.640 1217.797
potential_pw2rs 672 11.4 0.450 0.575 1007.402 1032.221
xc_vxc_pw_create 336 10.4 118.323 123.799 1030.731 1030.957
rs_pw_transfer 7954 11.1 0.263 0.272 886.089 941.457
qs_ks_ddapc 650 9.5 0.014 0.016 682.186 683.086
rs_pw_transfer_RS2PW_130 1311 11.5 529.773 582.666 529.773 582.666
x_to_yz 3696 14.5 561.963 566.914 561.963 566.914
yz_to_x 5894 13.7 549.928 566.657 549.928 566.657
xc_exc_calc 314 10.5 30.516 71.193 559.196 559.200
xc_functional_eval 1300 12.5 0.114 0.123 501.124 543.504
pw_nn_compose_r 7920 12.1 443.318 502.878 443.318 502.878
cp_dbcsr_multiply_d 18824 11.3 0.056 0.060 440.552 455.131
dbcsr_multiply_anytype 18824 13.3 6.863 8.968 438.921 453.471
qmmm_forces 11 3.9 5.057 7.224 418.833 418.835
qmmm_forces_with_gaussian 11 4.9 8.177 8.259 402.521 404.942
qs_scf_loop_do_ot 639 7.5 0.006 0.010 397.926 398.436
cp_ddapc_apply_CD 650 10.5 65.894 68.079 357.733 357.740
ot_scf_mini 639 8.5 0.129 0.142 357.246 357.589
qmmm_force_with_gaussian_low 11 5.9 0.000 0.000 345.037 345.171
lyp_lsd_eval 650 13.5 314.342 343.915 314.342 343.915
qmmm_forces_with_gaussian_LG 11 7.9 340.844 340.922 340.844 340.922
qmmm_forces_gaussian_low_R 11 6.9 0.000 0.000 340.844 340.922
dbcsr_mm_cannon_multiply 18824 14.3 10.537 23.151 264.680 278.647
qmmm_el_coupling 11 3.9 0.005 0.007 272.055 272.925
rs_pw_transfer_PW2RS_130 683 13.3 263.671 264.213 263.671 264.213
qmmm_elec_with_gaussian 11 4.9 10.833 11.870 259.977 262.493
pw_scatter_p 3696 13.5 250.884 255.081 250.884 255.081
pw_axpy 11933 9.6 219.576 219.933 219.576 219.933
fft_wrap_pw1pw2_40 1972 12.2 15.362 15.579 211.444 216.042
cp_dbcsr_mult_NS_NR 2831 11.3 0.015 0.017 202.511 214.845
pw_zero 12765 10.0 211.188 214.613 211.188 214.613
qmmm_elec_with_gaussian_low 11 5.9 0.000 0.000 203.561 204.576
pw_copy 5587 11.3 197.645 200.647 197.645 200.647
qmmm_elec_with_gaussian_LG 11 7.9 199.115 200.356 199.115 200.356
qmmm_elec_gaussian_low_R 11 6.9 0.000 0.000 199.115 200.356
pw_poisson_solve 661 9.4 115.353 117.174 200.327 200.345
pw_gather_p 5894 12.7 197.867 200.180 197.867 200.180
xb88_lsd_eval 650 13.5 186.668 199.483 186.668 199.483
ot_mini 639 9.5 0.017 0.022 198.207 198.562
-------------------------------------------------------------------------------
**** **** ****** ** PROGRAM ENDED AT 2014-10-30 00:27:35.638
***** ** *** *** ** PROGRAM RAN ON user
** **** ****** PROGRAM RAN BY user
***** ** ** ** ** PROGRAM PROCESS ID 16608
**** ** ******* ** PROGRAM STOPPED IN /home/user/cp2k_run/cp2k_input/for_co
2_HCA
Samuel Andermatt
Oct 30, 2014, 5:04:16 AM10/30/14
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The fft's take quite a bit of time. If your computer has an Nvidia GPU you could move the FFT's to it, which might help (-D__PW_CUDA flag and link in -lcufft -lcublas).
Michael Banck
Oct 30, 2014, 5:59:16 AM10/30/14
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On Tue, Oct 28, 2014 at 07:10:43AM -0700, Tanmoy Paul wrote:
> I am new to this field . I have installed cp2k
> using "sudo apt-get install cp2k" .
So you are using a prepackaged version. Which distribution, which
> I am new to this field . I have installed cp2k
> using "sudo apt-get install cp2k" .
version of that distribution and on which architecture?
The packaged versions have to run on as many configurations as possible,
so are not highly optimized. It might make sense to look into compiling
CP2K yourself if the performance is not acceptable.
Michael
Samuel Andermatt
Oct 30, 2014, 6:00:09 AM10/30/14
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Another question, does they Keyword COMMENSURATE in the MGRID impact your performance (positive or negative).
Teodoro Laino
Oct 30, 2014, 9:05:42 AM10/30/14
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COMMENSURATE is mandatory for the type of job he is running.
On 30 Oct 2014, at 11:00, Samuel Andermatt <samuel.a...@student.ethz.ch> wrote:
Another question, does they Keyword COMMENSURATE in the MGRID impact your performance (positive or negative).
Teodoro Laino
Oct 30, 2014, 9:28:13 AM10/30/14
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I cannot see the point..
-) First you are not running a minimization but simply an MD (at least this is what I see from your input and timings)
-) You are running on 8 mpi task.
-) Your system contains 150 QM atoms
-) Your QM cell is 20 Ang cubic
-) The reported timing is for 10 MD steps.
For 10 MD steps you get 9476 seconds overall. A good part of it (approximately > 3000 secs) are for the first step (difficult to be sure without a more extended output).
This means that at regime you can do 1 MD step in 550 seconds.
What is the problem? Does it look too slow?
Why don’t you increase # MPI task? Your system definitely is not made for a workstation. You should run that on more than just 8 tasks.
Criticism:
-) a cutoff of 250 with BLYP… very much on the very low side..
-) This setup:
SCF_GUESS ATOMIC
MAX_SCF 300
EPS_SCF 1.0E-06
&OUTER_SCF
EPS_SCF 1.0E-06
MAX_SCF 20
&END OUTER_SCF
MAX_SCF 300
EPS_SCF 1.0E-06
&OUTER_SCF
EPS_SCF 1.0E-06
MAX_SCF 20
&END OUTER_SCF
The 300 in the MAX_SCF is difficult to understand. The idea is that you do a certain number of steps (few tens) and then you reset with a new PC.
Try to decrease 300 to something more meaningful, like 30. You’ll also definitely notice an improvement in terms of time to solution.
Other things, like the setup of the PERIODIC QMMM section will affect performance, but they will pop up in the timing only when you arrive at the scaling limit. 8 is very far from being the scaling limit for this job.
Final comment:
-) if you are a beginner I would try with something more simple.. You combined, QS, QMMM and the periodic version of it.. Even for experts all this s**t requires some careful tuning, before going in production.
Regards,
Teo
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