<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">I cannot see the point.. </div><div class=""><br class=""></div><div class="">-) First you are not running a minimization but simply an MD (at least this is what I see from your input and timings)</div><div class=""><br class=""></div><div class="">-) You are running on 8 mpi task.</div><div class="">-) Your system contains 150 QM atoms</div><div class="">-) Your QM cell is 20 Ang cubic</div><div class="">-) The reported timing is for 10 MD steps.</div><div class=""><br class=""></div><div class="">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).</div><div class="">This means that at regime you can do 1 MD step in 550 seconds.</div><div class=""><br class=""></div><div class="">What is the problem? Does it look too slow? </div><div class="">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.</div><div class=""><br class=""></div><div class="">Criticism:</div><div class=""><br class=""></div><div class="">-) a cutoff of 250 with BLYP… very much on the very low side..</div><div class=""><br class=""></div><div class="">-) This setup:</div><div class=""><br class=""></div><div class=""> SCF_GUESS ATOMIC<br class=""> MAX_SCF 300<br class=""> EPS_SCF 1.0E-06<br class=""> &OUTER_SCF<br class=""> EPS_SCF 1.0E-06<br class=""> MAX_SCF 20<br class=""> &END OUTER_SCF<br class=""></div><div class=""><br class=""></div><div class="">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.</div><div class="">Try to decrease 300 to something more meaningful, like 30. You’ll also definitely notice an improvement in terms of time to solution.</div><div class=""><br class=""></div><div class="">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.</div><div class=""><br class=""></div><div class="">Final comment:</div><div class=""><br class=""></div><div class="">-) 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.</div><div class=""><br class=""></div><div class="">Regards,</div><div class="">Teo</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div><blockquote type="cite" class=""><div class="">On 30 Oct 2014, at 06:30, Tanmoy Paul <<a href="mailto:tanmo...@gmail.com" class="">tanmo...@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class="">Dear CP2K users,<br class=""></div> 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...<br class=""><br class="">-------------------------------------------------------------------------------<br class=""> ---- MULTIGRID INFO ----<br class=""> -------------------------------------------------------------------------------<br class=""> count for grid 1: 317951 cutoff [a.u.] 125.00<br class=""> count for grid 2: 302978 cutoff [a.u.] 31.25<br class=""> count for grid 3: 76551 cutoff [a.u.] 7.81<br class=""> count for grid 4: 684 cutoff [a.u.] 1.95<br class=""> total gridlevel count : 698164<br class=""><br class=""> -------------------------------------------------------------------------------<br class=""> - -<br class=""> - MESSAGE PASSING PERFORMANCE -<br class=""> - -<br class=""> -------------------------------------------------------------------------------<br class=""><br class=""> ROUTINE CALLS TOT TIME [s] AVE VOLUME [Bytes] PERFORMANCE [MB/s]<br class=""> MP_Group 6 0.000<br class=""> MP_Bcast 1834 0.213 5713507. 49195.17<br class=""> MP_Allreduce 10132 130.663 142451. 11.05<br class=""> MP_Sync 101392 0.269<br class=""> MP_Alltoall 9590 652.514 46235404. 679.52<br class=""> MP_SendRecv 15776 87.207 294912. 53.35<br class=""> MP_ISendRecv 23730 0.566 4071645. 170706.96<br class=""> MP_Wait 24093 402.879<br class=""> MP_ISend 275 0.038 728596. 5272.74<br class=""> MP_IRecv 264 0.001 746667. 197120.00<br class=""> MP_Recv 76412 0.793 3234. 311.65<br class=""> -------------------------------------------------------------------------------<br class=""><br class=""><br class="">-------------------------------------------------------------------------------<br class=""> - -<br class=""> - T I M I N G -<br class=""> - -<br class=""> ------------------------------------------------------------------------------- <br class=""> SUBROUTINE CALLS ASD SELF TIME TOTAL TIME<br class=""> AVERAGE MAXIMUM AVERAGE MAXIMUM<br class=""> CP2K 1 1.0 1.346 1.804 9476.129 9476.130<br class=""> qs_mol_dyn_low 1 2.0 0.095 0.314 9465.241 9465.854<br class=""> qs_forces 11 3.9 0.027 0.040 8706.050 8706.055<br class=""> qs_energies_scf 11 4.9 0.001 0.002 8569.698 8569.705<br class=""> scf_env_do_scf 11 5.9 0.004 0.004 8453.922 8453.929<br class=""> scf_env_do_scf_inner_loop 639 6.5 0.218 0.273 8289.159 8289.172<br class=""> velocity_verlet 10 3.0 0.894 3.202 5147.091 5147.116<br class=""> qs_ks_build_kohn_sham_matrix 650 8.5 12.649 13.425 4123.288 4123.607<br class=""> qs_rho_update_rho 650 7.5 0.026 0.031 4077.287 4077.571<br class=""> calculate_rho_elec 1300 8.5 592.558 649.730 4077.261 4077.552<br class=""> qs_ks_update_qs_env 651 7.5 0.014 0.027 3995.187 3995.463<br class=""> fft_wrap_pw1pw2 9590 11.0 0.464 0.476 3630.990 3654.319<br class=""> fft_wrap_pw1pw2_130 3630 11.8 366.371 376.203 3397.033 3418.254<br class=""> density_rs2pw 1300 9.5 0.135 0.159 3331.163 3383.539<br class=""> fft3d_ps 9590 13.0 1685.880 1712.933 2797.864 2836.568<br class=""> qs_vxc_create 650 9.5 0.047 0.054 1589.974 1590.199<br class=""> sum_up_and_integrate 336 9.4 46.390 55.122 1355.401 1368.971<br class=""> integrate_v_rspace 672 10.4 301.274 329.909 1309.006 1315.670<br class=""> xc_rho_set_and_dset_create 650 11.5 202.175 205.516 1171.640 1217.797<br class=""> potential_pw2rs 672 11.4 0.450 0.575 1007.402 1032.221<br class=""> xc_vxc_pw_create 336 10.4 118.323 123.799 1030.731 1030.957<br class=""> rs_pw_transfer 7954 11.1 0.263 0.272 886.089 941.457<br class=""> qs_ks_ddapc 650 9.5 0.014 0.016 682.186 683.086<br class=""> rs_pw_transfer_RS2PW_130 1311 11.5 529.773 582.666 529.773 582.666<br class=""> x_to_yz 3696 14.5 561.963 566.914 561.963 566.914<br class=""> yz_to_x 5894 13.7 549.928 566.657 549.928 566.657<br class=""> xc_exc_calc 314 10.5 30.516 71.193 559.196 559.200<br class=""> xc_functional_eval 1300 12.5 0.114 0.123 501.124 543.504<br class=""> pw_nn_compose_r 7920 12.1 443.318 502.878 443.318 502.878<br class=""> cp_dbcsr_multiply_d 18824 11.3 0.056 0.060 440.552 455.131<br class=""> dbcsr_multiply_anytype 18824 13.3 6.863 8.968 438.921 453.471<br class=""> qmmm_forces 11 3.9 5.057 7.224 418.833 418.835<br class=""> qmmm_forces_with_gaussian 11 4.9 8.177 8.259 402.521 404.942<br class=""> qs_scf_loop_do_ot 639 7.5 0.006 0.010 397.926 398.436<br class=""> cp_ddapc_apply_CD 650 10.5 65.894 68.079 357.733 357.740<br class=""> ot_scf_mini 639 8.5 0.129 0.142 357.246 357.589<br class=""> qmmm_force_with_gaussian_low 11 5.9 0.000 0.000 345.037 345.171<br class=""> lyp_lsd_eval 650 13.5 314.342 343.915 314.342 343.915<br class=""> qmmm_forces_with_gaussian_LG 11 7.9 340.844 340.922 340.844 340.922<br class=""> qmmm_forces_gaussian_low_R 11 6.9 0.000 0.000 340.844 340.922<br class=""> dbcsr_mm_cannon_multiply 18824 14.3 10.537 23.151 264.680 278.647<br class=""> qmmm_el_coupling 11 3.9 0.005 0.007 272.055 272.925<br class=""> rs_pw_transfer_PW2RS_130 683 13.3 263.671 264.213 263.671 264.213<br class=""> qmmm_elec_with_gaussian 11 4.9 10.833 11.870 259.977 262.493<br class=""> pw_scatter_p 3696 13.5 250.884 255.081 250.884 255.081<br class=""> pw_axpy 11933 9.6 219.576 219.933 219.576 219.933<br class=""> fft_wrap_pw1pw2_40 1972 12.2 15.362 15.579 211.444 216.042<br class=""> cp_dbcsr_mult_NS_NR 2831 11.3 0.015 0.017 202.511 214.845<br class=""> pw_zero 12765 10.0 211.188 214.613 211.188 214.613<br class=""> qmmm_elec_with_gaussian_low 11 5.9 0.000 0.000 203.561 204.576<br class=""> pw_copy 5587 11.3 197.645 200.647 197.645 200.647<br class=""> qmmm_elec_with_gaussian_LG 11 7.9 199.115 200.356 199.115 200.356<br class=""> qmmm_elec_gaussian_low_R 11 6.9 0.000 0.000 199.115 200.356<br class=""> pw_poisson_solve 661 9.4 115.353 117.174 200.327 200.345<br class=""> pw_gather_p 5894 12.7 197.867 200.180 197.867 200.180<br class=""> xb88_lsd_eval 650 13.5 186.668 199.483 186.668 199.483<br class=""> ot_mini 639 9.5 0.017 0.022 198.207 198.562<br class=""> -------------------------------------------------------------------------------<br class=""><br class=""> **** **** ****** ** PROGRAM ENDED AT 2014-10-30 00:27:35.638<br class=""> ***** ** *** *** ** PROGRAM RAN ON user<br class=""> ** **** ****** PROGRAM RAN BY user<br class=""> ***** ** ** ** ** PROGRAM PROCESS ID 16608<br class=""> **** ** ******* ** PROGRAM STOPPED IN /home/user/cp2k_run/cp2k_input/for_co<br class=""> 2_HCA<br class=""><br class=""></div>Any idea ? And one more added question to it........... Where can I find the file formats of the cp2k output files?<br class=""></div> Regards<br class=""></div> Tanmoy <br class=""><div class=""><div class=""><div class=""><div class=""><br class=""></div></div></div></div></div><div class="gmail_extra"><br class=""><div class="gmail_quote">On Wed, Oct 29, 2014 at 3:37 PM, Tanmoy Paul <span dir="ltr" class=""><<a href="mailto:tanmo...@gmail.com" target="_blank" class="">tanmo...@gmail.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr" class="">Thanks Samuel and Juerg for your inputs . <br class=""></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br class=""><div class="gmail_quote">On Wed, Oct 29, 2014 at 3:32 PM, <span dir="ltr" class=""><<a href="mailto:hut...@chem.uzh.ch" target="_blank" class="">hut...@chem.uzh.ch</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi<br class=""> <br class=""> yes, check the timing information at the end of a short run.<br class=""> This will give some information on possible problems.<br class=""> <br class=""> You should also change the EWALD method from PME to SPME.<br class=""> <br class=""> regards<br class=""> <br class=""> Juerg<br class=""> --------------------------------------------------------------<br class=""> Juerg Hutter Phone : ++41 44 635 4491<br class=""> Institut für Chemie C FAX : ++41 44 635 6838<br class=""> Universität Zürich E-mail: <a href="mailto:hut...@chem.uzh.ch" target="_blank" class="">hut...@chem.uzh.ch</a><br class=""> Winterthurerstrasse 190<br class=""> CH-8057 Zürich, Switzerland<br class=""> ---------------------------------------------------------------<br class=""> <br class=""> -----<a href="mailto:cp...@googlegroups.com" target="_blank" class="">cp...@googlegroups.com</a> wrote: -----<br class=""> To: <a href="mailto:cp...@googlegroups.com" target="_blank" class="">cp...@googlegroups.com</a><br class=""> From: Samuel Andermatt<br class=""> Sent by: <a href="mailto:cp...@googlegroups.com" target="_blank" class="">cp...@googlegroups.com</a><br class=""> Date: 10/29/2014 10:45AM<br class=""> Subject: [CP2K:5788] Re: CP2K running slow<br class=""> <div class=""><div class=""><br class=""> 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.<br class=""> <br class=""> --<br class=""> You received this message because you are subscribed to the Google Groups "cp2k" group.<br class=""> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k%2Bun...@googlegroups.com" target="_blank" class="">cp2k+uns...@googlegroups.com</a>.<br class=""> To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank" class="">cp...@googlegroups.com</a>.<br class=""> Visit this group at <a href="http://groups.google.com/group/cp2k" target="_blank" class="">http://groups.google.com/group/cp2k</a>.<br class=""> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank" class="">https://groups.google.com/d/optout</a>.<br class=""> <br class=""> <br class=""> --<br class=""> You received this message because you are subscribed to the Google Groups "cp2k" group.<br class=""> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k%2Bun...@googlegroups.com" target="_blank" class="">cp2k+uns...@googlegroups.com</a>.<br class=""> To post to this group, send email to <a href="mailto:cp...@googlegroups.com" target="_blank" class="">cp...@googlegroups.com</a>.<br class=""> Visit this group at <a href="http://groups.google.com/group/cp2k" target="_blank" class="">http://groups.google.com/group/cp2k</a>.<br class=""> For more options, visit <a href="https://groups.google.com/d/optout" target="_blank" class="">https://groups.google.com/d/optout</a>.<br class=""> </div></div></blockquote></div><br class=""></div> </div></div></blockquote></div><br class=""></div><div class=""><br class="webkit-block-placeholder"></div> -- <br class=""> You received this message because you are subscribed to the Google Groups "cp2k" group.<br class=""> To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp2k+uns...@googlegroups.com" class="">cp2k+uns...@googlegroups.com</a>.<br class=""> To post to this group, send email to <a href="mailto:cp...@googlegroups.com" class="">cp...@googlegroups.com</a>.<br class=""> Visit this group at <a href="http://groups.google.com/group/cp2k" class="">http://groups.google.com/group/cp2k</a>.<br class=""> For more options, visit <a href="https://groups.google.com/d/optout" class="">https://groups.google.com/d/optout</a>.<br class=""> </div></blockquote></div><br class=""></body></html>