[CP2K:3500] Re: CI BAND calculation

Nikita Vakula vakul... at gmail.com
Mon Sep 19 10:10:09 CEST 2011


Thanks, Teo! Hope somebody can help me!
Best regards,
Nikita

2011/9/16 Teodoro Laino <teodor... at gmail.com>

> 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>
>> >
>> > --
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>>
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>>
>
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