Re: [scipion-users] Issue about xmipp3-localMonoRes

[Pablo C. <su...@bc...>]

Hi Dmitry, 
   
 We have also done some changes recently in monoRes, and the developer thinks latest changes could also fix the issue. 
   
 So to do that just need to do the standard procedure: 
   
 From the scipion home folder:  
   
 git pull 
 ./scipion install -j 5 
   
 Since you are in a cluster, better ask the admins to to this. 
   
 Thanks once more for the feedback. 
   
 
 All the best, Pablo. 
 Scipion team 
   
 
 
 
                 
         Activo Lun, 29 Mayo at  4:30 PM
          ,  Biocomputing unit - National Center for Biotechnology <sc...@cn...>  Escrito:
           
     On 29/05/17 16:17, Dmitry Semchonok
      wrote: 
     
     
       
         
           Dear Pablo, 
           Yes indeed it is a
            cluster. 
           I already
            envisaged this option
            and contacted the admin at the same time :). But currently
            no reply... 
           Thank you. 
           Sincerely, 
            Dmitry 
         
         
           On
            May 29, 2017 16:05:46 Pablo Conesa
            <pc...@cn...> wrote: 
           
             Hi Dmitry, is that your machine or a cluster. 
             If it's a Cluster, then you should talk to the cluster
              admins, they should know what is this about, 
             If it's your machine, you should have cmake installed in
              your machine. 
             
             
             On 29/05/17 10:15, Dmitry
              Semchonok wrote: 
             
             
               
                 
                   
                     
                       
                         
                           Dear Pablo, 
                             
                           
                          Thank you very much for the answer. 
                           
                         
                        When I tried the command: scipion install -j
                          5  
                       
                      I ended up with the error 
                       
                      Error: Cannot run
                        'cmake'. Please install it in your system first. 
                         
                      
 
                    Am I doing something
                        wrong? 
                       
                    
 
                  Sincerely, 
                  
 
                Dmitry 
                
                 
                   
 
                       
                    
                     
 
                       
                     
                   
                 
               
               
 
                 2017-05-28 20:13 GMT+02:00
                  Pablo Conesa - CNB <p.c...@gm...>: 
                   Hi
                    Dmitry, every time you update the code (git
                    pull....or git checkout) you are bringing new code
                    to your computer. 
                     
                    This, depending on what has changed might require
                    compiling Xmipp again, which looks like it's what is
                    happening. 
                     
                    Try to run from the command line: 
                     
                    scipion install -j 5 
                     
                    If I remember right you run scipion without "./" 
                     
                    Try this and run localMonoRes again. 
                     
                      > On 27 May 2017, at 13:20, Dmitry Semchonok
                      <sem...@gm...>
                      wrote: 
                      > 
                      > Dear colleague, 
                      > 
                      > Using xmipp3-localMonoRes I get the error. 
                      > 
                      > The parameters used -  (input from
                      relion-postprocessing; the same for the binary
                      mask) 
                      > 
                    > <изображение.png> 
                    > 
                      > 
                      > The error 
                      > 
                      > XMIPP_ERROR 1: Errors on command line
                      parameters 
                      > 00019:   Unrecognized parameter: --mask_out 
                      > 00020:   Unrecognized parameter:
                      --md_outputdata 
                      > 00021: 
                      > 00022:   File:
                      software/em/xmipp/libraries/data/argsparser.cpp
                      line: 1036 
                      > 
                    > <изображение.png> 
                    > 
                    > <изображение.png> 
                    > 
                      > 
                      > 
                      > 
                      > Any ideas what can be done? 
                      > 
                      > 
                      > Thank you! 
                      > 
                      > Sincerely, 
                      > Dmitry 
                      > 
                      > 
                      > 
                      > 
                    >
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