Re: [scipion-users] relion-2.1 crash issue

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

Hi Abhisek,     did you install Relion through Scipion or you had it  before?    You should also make sure MPI variables at SCIPION_HOME/config/scipion.conf are correctly set (I guess they are, otherwise you would have seen some complaint when running scipion config). These are my variables on an Ubuntu16 using openmpi.     MPI_CC = mpicc MPI_CXX = mpiCC MPI_LINKERFORPROGRAMS = mpiCC MPI_LIB = mpi MPI_LIBDIR = /usr/lib/openmpi/lib MPI_INCLUDE = /usr/lib/openmpi/include MPI_BINDIR = /usr/bin    best regards  Laura    Ticket: https://bcucnb.freshdesk.com/helpdesk/tickets/316    
   
  
 
                 
         Activo Sab, 7 Abril at  8:27 AM
          ,  Mailing list for Scipion users <sci...@li...>  Escrito:
           
 Hi, 
   
 My Relion-2.1 in scipion keep raising this error: 
   
 [localhost.localdomain:05066] PMIX ERROR: BAD-PARAM in file ../../../../../../../opal/mca/pmix/pmix2x/pmix/src/dstore/pmix_esh.c at line 1005 
 00036:   *** An error occurred in MPI_Init 
 00037:   *** on a NULL communicator 
 00038:   *** MPI_ERRORS_ARE_FATAL (processes in this communicator will now abort, 
 00039:   ***    and potentially your MPI job) 
 00040:   [localhost.localdomain:5066] Local abort before MPI_INIT completed completed successfully, but am not able to aggregate error messages, and not able to guarantee that all other processes were killed! 
   
 What is surprising to me is Xmipp3-cl2d is running alright in MPI but Relion-2D classification is getting crashed. 
   
 Please help me out here. 
   
 thank you 
   --          
 
 
 Abhisek Mondal 
 
 Senior Research Fellow  
 Structural Biology and Bioinformatics Division  
CSIR-Indian Institute of Chemical Biology 
 
Kolkata 700032 
 
INDIA