[CP2K:3499] Re: CI BAND calculation

Teodoro Laino teodor... at gmail.com
Fri Sep 16 17:46:58 CEST 2011


I cannot do more than posting the error message you have:

[node-57-02:23530] [ 0] /lib64/libpthread.so.0 [0x2b0e21461b00]
[node-57-02:23529] [ 0] /lib64/libpthread.so.0 [0x2ac4c190db00]
[node-57-02:23529] [ 1] /usr/lib/openmpi/lib/libmpi.so.0(ompi_group_increment_proc_count+0x17) [0x2ac4c0424757]
[node-57-02:23529] [ 2] /usr/lib/openmpi/lib/libmpi.so.0(ompi_comm_set+0xdc) [0x2ac4c041b7ec]
[node-57-02:23529] [ 3] /usr/lib/openmpi/lib/libmpi.so.0 [0x2ac4c041c491]
[node-57-02:23529] [ 4] /usr/lib/openmpi/lib/libmpi.so.0(MPI_Comm_create+0xb1) [0x2ac4c0446e51]
[node-57-02:23529] [ 5] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(Cblacs_gridmap+0x13b) [0x18510bb]
[node-57-02:23529] [ 6] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(Cpdgemr2d+0x1e0) [0x1728260]
[node-57-02:23529] [ 7] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__cp_fm_diag_MOD_cp_fm_syevd+0x7c8) [0xe4cb58]
[node-57-02:23529] [ 8] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__cp_dbcsr_diag_MOD_cp_dbcsr_syevd+0x2ba) [0xdefc6a]
[node-57-02:23529] [ 9] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__qs_mo_methods_MOD_subspace_eigenvalues_ks_dbcsr+0x68b) [0x8885fb]
[node-57-02:23529] [10] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__qs_scf_MOD_init_scf_loop+0x445a) [0x93c90a]
[node-57-02:23529] [11] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__qs_scf_MOD_scf_env_do_scf+0xa16) [0x940866]
[node-57-02:23529] [12] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__qs_scf_MOD_scf+0x653) [0x9437c3]
[node-57-02:23529] [13] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__qs_energy_MOD_qs_energies_scf+0x606) [0x7ba016]
[node-57-02:23529] [14] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__qs_energy_MOD_qs_energies+0x521) [0x7bbcb1]
[node-57-02:23529] [15] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__qs_force_MOD_qs_forces+0xb5b) [0x7d267b]
[node-57-02:23529] [16] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__force_env_methods_MOD_force_env_calc_energy_force+0x1900) [0x5042c0]
[node-57-02:23529] [17] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__f77_interface_MOD_calc_energy_force+0x9c) [0x4d033c]
[node-57-02:23529] [18] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__f77_interface_MOD_calc_force+0xa8) [0x4d1e38]
[node-57-02:23529] [19] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__replica_methods_MOD_rep_env_calc_e_f_int+0x4e5) [0x1392a65]
[node-57-02:23529] [20] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__replica_methods_MOD_rep_env_calc_e_f_low+0x8f) [0x139333f]
[node-57-02:23529] [21] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__replica_types_MOD_rep_env_calc_e_f+0x98) [0x9bbb48]
[node-57-02:23529] [22] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__neb_utils_MOD_neb_calc_energy_forces+0x8a5) [0x712825]
[node-57-02:23529] [23] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__neb_methods_MOD_neb_diis+0xb5f) [0x6fda2f]
[node-57-02:23529] [24] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__neb_methods_MOD_neb+0x14b5) [0x701cd5]
[node-57-02:23529] [25] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__cp2k_runs_MOD_cp2k_run+0x2693) [0x4a5bc3]
[node-57-02:23529] [26] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__cp2k_runs_MOD_run_input+0xad) [0x4a939d]
[node-57-02:23529] [27] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt [0x49eb5f]
[node-57-02:23529] [28] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(main+0x1f) [0x49fcbf]
[node-57-02:23529] [29] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2ac4c1b37cf4]

The problem appears to be in your libraries. Maybe somebody else here can help you.
Best,
Teo



on Sep 16, 2011, at 5:36 PM, Nikita Vakula wrote:

> Thank you very much! But when I use 50 procs and 10 procs/replica (in this case numb of replicas = numb of images = 5) I have segmentation fault:
> 
>  *******************************************************************************
>  *******************************************************************************
>  **                                                                           **
>  **  ########     ###    ##    ## ########    Nudged Elastic Band Method      **
>  **  ##     ##   ## ##   ###   ## ##     ##   String Method                   **
>  **  ##     ##  ##   ##  ####  ## ##     ##                                   **
>  **  ########  ##     ## ## ## ## ##     ##   Number of Images :            5 **
>  **  ##     ## ######### ##  #### ##     ##   Number of Replicas:           5 **
>  **  ##     ## ##     ## ##   ### ##     ##   Number of Procs/Rep:         10 **
>  **  ########  ##     ## ##    ## ########                                    **
>  **                                           T. Laino  2009-2010             **
>  *******************************************************************************
>  *******************************************************************************
> 
>  NEB| Building initial set of coordinates. START
>  NEB| Building initial set of coordinates. END
> 
>  NEB| Computing Energies and Forces
> [node-35-05:00410] *** Process received signal ***
> [node-35-05:00410] Signal: Segmentation fault (11)
> [node-35-05:00410] Signal code:  (128)
> 
> The output is attached in the letter. Could you please tell me what's wrong?
> 
> Best regards,
> Nikita
> 
> 
> 2011/9/16 Teodoro Laino <teodor... at gmail.com>
> Ok : then this explains why you have 30 replicas.
> The goal is to tune number of procs/replica and total number of mpi procs, in order to have a number of replicas = (or smaller, NEVER larger!!!) to the number of images.
> 
> Teo
> 
> On Sep 16, 2011, at 11:57 AM, Nikita wrote:
> 
> > Thanks for your reply!
> > I used 120 procs.
> > Best regards,
> > Nikita
> >
> > On Sep 16, 10:06 am, Teodoro Laino <teodor... at gmail.com> wrote:
> >> I'm forwarding this message to the list, I do not reply to single instances in private mode, because at least the time I spent to write this message will be useful not only to you but possibly to other people.
> >>
> >> Let's go back and see your output:
> >>
> >>>  I sent the output on your email (there's no option to attach files in google groups)
> >>>  *******************************************************************************
> >>>  *******************************************************************************
> >>>  **                                                                           **
> >>>  **  ########     ###    ##    ## ########    Nudged Elastic Band Method      **
> >>>  **  ##     ##   ## ##   ###   ## ##     ##   String Method                   **
> >>>  **  ##     ##  ##   ##  ####  ## ##     ##                                   **
> >>>  **  ########  ##     ## ## ## ## ##     ##   Number of Images :            5 **
> >>
> >> That's correct.. you specified 5 images in your input and this is what you get in your output.
> >>
> >>>  **  ##     ## ######### ##  #### ##     ##   Number of Replicas:          30 **
> >>
> >> This depends on the number of your processors: the number of replicas is (tot numb procs) / (number of procs/rep) .
> >>
> >>>  **  ##     ## ##     ## ##   ### ##     ##   Number of Procs/Rep:          4 **
> >>
> >> This should be self-explicative...
> >>
> >>>  **  ########  ##     ## ##    ## ########                                    **
> >>>  **                                           T. Laino  2009-2010             **
> >>>  *******************************************************************************
> >>>  *******************************************************************************
> >>
> >>>> (the number of processors used in calculation was 120).
> >>>> And the second question is how to set coordinates of images correctly?
> >>>> I mean if I have 5 images with xyz files 1.xyz, 2.xyz, 3.xyz, 4.xyz,
> >>>> 5.xyz: where the first and the last xyz correspond to optimized
> >>>> initial and final configurations, consequently, and 2,3,4 correspond
> >>>> to some intermidiate configurations, what should I write in &coord
> >>>> section and in &replica?
> >>> please refer to the regtest: you can find this information in them..
> >>> I looked at this example and that's not clear what to write in coord section and replica section. In this input in coord section I wrote the initial configuration (the file start.xyz), and in replica section I wrote coordinates of all configurations (initial, final and intermediate). Am I right?
> >>
> >> yes.
> >>
> >> p.s.: output files can be attached to the google list, exactly as attachments, sending an email to cp2k .AT. googlegroups.com and putting an attachment.
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>> Best regards,
> >>> Nikita
> >>> <cp2k.popt.out-47248>
> >
> > --
> > 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.
> >
> 
> --
> 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.
> 
> 
> 
> -- 
> 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.
> <cp2k.popt.out-47335>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20110916/bbd361dc/attachment.html>


More information about the CP2K-user mailing list