Re: [scipion-users] test for relion 2D classification failed: MPI error

[Laura d. C. <su...@bc...>]

Hi Valerie, 
 what do you mean with 'desktop computer that does not have MPI facility'? You  mean it does not have openmpi package installed? 
 It is not a problem to install it if you have administrator privileges but if you dont want to you can use relion and other programs inside Scipion without MPIs, just using threads. Some tests are predefine to use MPIs (such as Relion classification 2D) but if you want to run them you could change it manually on the python script, I can tell you where. 
   
 let me know 
 Laura  
  
   
 
 
 
                 
         Activo Mie, 24 Mayo at 12:06 PM
          ,  Valerie.biou <val...@ib...>  Escrito:
           Hi Laura,  it's nice that you asked about this. the answer is that I haven't solved the problem but I have an idea: I talked yesterday with a person from our institute who found out that the programs that don't run all have issues with MPI. I am using a desktop computer that does not have MPI facility so it seems that MPI is failing because of this.  we saw that relion executables come in two versions: with and without mpi  relion_autopick                    relion_project relion_autopick_mpi                relion_qsub.csh relion_display                     relion_reconstruct relion_find_tiltpairs              relion_refine relion_helix_toolbox               relion_refine_mpi relion_image_handler               relion_run_ctffind relion_maingui                     relion_run_ctffind_mpi relion_manualpick                  relion_run_motioncorr relion_mask_create                 relion_run_motioncorr_mpi relion_particle_polish             relion_stack_create relion_particle_polish_mpi         relion_star_combine relion_particle_reposition         relion_star_compare relion_particle_sort               relion_star_datablock_ctfdat relion_particle_sort_mpi           relion_star_datablock_singlefiles relion_particle_symmetry_expand    relion_star_datablock_stack relion_pipeliner                   relion_star_loopheader relion_postprocess                 relion_star_plottable relion_postprocess_mpi             relion_star_printtable relion_preprocess                  relion_tiltpair_plot  so my question is : is there a way to configure scipion so it calls the non-mpi executables?  Cheers,  Valérie Biou  Laboratoire de Biologie Physico-Chimique des Protéines Membranaires  UMR 7099 CNRS/Univ. Paris Diderot P7  Institut de Biologie Physico-Chimique  13 rue Pierre et Marie Curie  75005 Paris - France  Tel : +33 (0)1 5841 5099  Fax : +33 (0)1 5841 5024  ----- Mail original ----- De: "Laura del Caño" <su...@bc...> À: "Valerie Biou" <val...@ib...> Cc: sci...@li... Envoyé: Mercredi 24 Mai 2017 11:38:41 Objet: Re: [scipion-users] test for relion 2D classification failed: MPI error  Hi Valerie.biou,       Did you solve this problem with relion classification test?       cheers   Laura     Ticket: https://bcucnb.freshdesk.com/helpdesk/tickets/119                                           Activo Vie, 28 Abril at 11:02 AM           ,  Valerie.biou <val...@ib...>  Escrito:            Hello   the test for 2D classification using CL2D worked and I tried to run the test for 2D classification using Relion  which failed with an MPI error (see attached log file).   Do you have any suggestion?  thanks, best regards   Valérie Biou  Laboratoire de Biologie Physico-Chimique des Protéines Membranaires  UMR 7099 CNRS/Univ. Paris Diderot P7  Institut de Biologie Physico-Chimique  13 rue Pierre et Marie Curie  75005 Paris - France