Thanks, Teo! Hope somebody can help me!<br>Best regards,<br>Nikita<br><br><div class="gmail_quote">2011/9/16 Teodoro Laino <span dir="ltr"><<a href="mailto:teodor...@gmail.com">teodor...@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div style="word-wrap:break-word">I cannot do more than posting the error message you have:<div><br></div><div><div>[node-57-02:23530] [ 0] /lib64/libpthread.so.0 [0x2b0e21461b00]</div>
<div>[node-57-02:23529] [ 0] /lib64/libpthread.so.0 [0x2ac4c190db00]</div><div>[node-57-02:23529] [ 1] /usr/lib/openmpi/lib/libmpi.so.0(ompi_group_increment_proc_count+0x17) [0x2ac4c0424757]</div><div>[node-57-02:23529] [ 2] /usr/lib/openmpi/lib/libmpi.so.0(ompi_comm_set+0xdc) [0x2ac4c041b7ec]</div>
<div>[node-57-02:23529] [ 3] /usr/lib/openmpi/lib/libmpi.so.0 [0x2ac4c041c491]</div><div>[node-57-02:23529] [ 4] /usr/lib/openmpi/lib/libmpi.so.0(MPI_Comm_create+0xb1) [0x2ac4c0446e51]</div><div>[node-57-02:23529] [ 5] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(Cblacs_gridmap+0x13b) [0x18510bb]</div>
<div>[node-57-02:23529] [ 6] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(Cpdgemr2d+0x1e0) [0x1728260]</div><div>[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]</div>
<div>[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]</div><div>[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]</div>
<div>[node-57-02:23529] [10] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__qs_scf_MOD_init_scf_loop+0x445a) [0x93c90a]</div><div>[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]</div>
<div>[node-57-02:23529] [12] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__qs_scf_MOD_scf+0x653) [0x9437c3]</div><div>[node-57-02:23529] [13] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__qs_energy_MOD_qs_energies_scf+0x606) [0x7ba016]</div>
<div>[node-57-02:23529] [14] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__qs_energy_MOD_qs_energies+0x521) [0x7bbcb1]</div><div>[node-57-02:23529] [15] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__qs_force_MOD_qs_forces+0xb5b) [0x7d267b]</div>
<div>[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]</div><div>[node-57-02:23529] [17] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__f77_interface_MOD_calc_energy_force+0x9c) [0x4d033c]</div>
<div>[node-57-02:23529] [18] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__f77_interface_MOD_calc_force+0xa8) [0x4d1e38]</div><div>[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]</div>
<div>[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]</div><div>[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]</div>
<div>[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]</div><div>[node-57-02:23529] [23] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__neb_methods_MOD_neb_diis+0xb5f) [0x6fda2f]</div>
<div>[node-57-02:23529] [24] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__neb_methods_MOD_neb+0x14b5) [0x701cd5]</div><div>[node-57-02:23529] [25] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__cp2k_runs_MOD_cp2k_run+0x2693) [0x4a5bc3]</div>
<div>[node-57-02:23529] [26] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(__cp2k_runs_MOD_run_input+0xad) [0x4a939d]</div><div>[node-57-02:23529] [27] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt [0x49eb5f]</div>
<div>[node-57-02:23529] [28] /home/vakula/disser/cp2k/exe/Linux-x86-64-gfortran/cp2k.popt(main+0x1f) [0x49fcbf]</div><div>[node-57-02:23529] [29] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2ac4c1b37cf4]</div></div><div><br>
</div><div>The problem appears to be in your libraries. Maybe somebody else here can help you.</div><div>Best,</div><div>Teo</div><div><br></div><div><br></div><div><br></div><div><div><div></div><div class="h5">on Sep 16, 2011, at 5:36 PM, Nikita Vakula wrote:</div>
</div><div><br><blockquote type="cite"><div><div></div><div class="h5">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:<br><br>
*******************************************************************************<br>
*******************************************************************************<br> ** **<br> ** ######## ### ## ## ######## Nudged Elastic Band Method **<br>
** ## ## ## ## ### ## ## ## String Method **<br> ** ## ## ## ## #### ## ## ## **<br> ** ######## ## ## ## ## ## ## ## Number of Images : 5 **<br>
** ## ## ######### ## #### ## ## Number of Replicas: 5 **<br> ** ## ## ## ## ## ### ## ## Number of Procs/Rep: 10 **<br> ** ######## ## ## ## ## ######## **<br>
** T. Laino 2009-2010 **<br> *******************************************************************************<br> *******************************************************************************<br>
<br> NEB| Building initial set of coordinates. START<br> NEB| Building initial set of coordinates. END<br><br> NEB| Computing Energies and Forces<br>[node-35-05:00410] *** Process received signal ***<br>[node-35-05:00410] Signal: Segmentation fault (11)<br>
[node-35-05:00410] Signal code: (128)<br><br>The output is attached in the letter. Could you please tell me what's wrong?<br><br>Best regards,<br>Nikita<br><div class="gmail_quote"><br><br>2011/9/16 Teodoro Laino <span dir="ltr"><<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Ok : then this explains why you have 30 replicas.<br>
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.<br>
<br>
Teo<br>
<div><div></div><div><br>
On Sep 16, 2011, at 11:57 AM, Nikita wrote:<br>
<br>
> Thanks for your reply!<br>
> I used 120 procs.<br>
> Best regards,<br>
> Nikita<br>
><br>
> On Sep 16, 10:06 am, Teodoro Laino <<a href="mailto:teodor...@gmail.com" target="_blank">teodor...@gmail.com</a>> wrote:<br>
>> 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.<br>
>><br>
>> Let's go back and see your output:<br>
>><br>
>>> I sent the output on your email (there's no option to attach files in google groups)<br>
>>> *******************************************************************************<br>
>>> *******************************************************************************<br>
>>> ** **<br>
>>> ** ######## ### ## ## ######## Nudged Elastic Band Method **<br>
>>> ** ## ## ## ## ### ## ## ## String Method **<br>
>>> ** ## ## ## ## #### ## ## ## **<br>
>>> ** ######## ## ## ## ## ## ## ## Number of Images : 5 **<br>
>><br>
>> That's correct.. you specified 5 images in your input and this is what you get in your output.<br>
>><br>
>>> ** ## ## ######### ## #### ## ## Number of Replicas: 30 **<br>
>><br>
>> This depends on the number of your processors: the number of replicas is (tot numb procs) / (number of procs/rep) .<br>
>><br>
>>> ** ## ## ## ## ## ### ## ## Number of Procs/Rep: 4 **<br>
>><br>
>> This should be self-explicative...<br>
>><br>
>>> ** ######## ## ## ## ## ######## **<br>
>>> ** T. Laino 2009-2010 **<br>
>>> *******************************************************************************<br>
>>> *******************************************************************************<br>
>><br>
>>>> (the number of processors used in calculation was 120).<br>
>>>> And the second question is how to set coordinates of images correctly?<br>
>>>> I mean if I have 5 images with xyz files 1.xyz, 2.xyz, 3.xyz, 4.xyz,<br>
>>>> 5.xyz: where the first and the last xyz correspond to optimized<br>
>>>> initial and final configurations, consequently, and 2,3,4 correspond<br>
>>>> to some intermidiate configurations, what should I write in &coord<br>
>>>> section and in &replica?<br>
>>> please refer to the regtest: you can find this information in them..<br>
>>> 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?<br>
>><br>
>> yes.<br>
>><br>
>> p.s.: output files can be attached to the google list, exactly as attachments, sending an email to cp2k .AT. <a href="http://googlegroups.com/" target="_blank">googlegroups.com</a> and putting an attachment.<br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>>> Best regards,<br>
>>> Nikita<br>
>>> <cp2k.popt.out-47248><br>
><br>
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