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Dear Prem, You probably made an error in combining STAR files from the different classes, as the rlnRandomSubset is not always 1 or 2. Be aware that column numbering may be different in different STAR files: the header defines the order of the columns! HTH, Sjors > Dear all, > > I am refining a data set after successful 2D and 3D Classification in > relion 1.4. my input script is > > mpirun -pernode -n 30 `which relion_refine_mpi` --o Ref-class-1-2-3/run1 > --auto_refine --split_random_halves --i Class-1-2-3-merg.star > --particle_diameter 430 --angpix 1.25 --ref run3_6.0A_class001.mrc > --ini_high 50 --ctf --ctf_corrected_ref --flatten_solvent --zero_mask > --oversampling 1 --healpix_order 2 --auto_local_healpix_order 4 > --offset_range 5 --offset_step 2 --sym C1 --low_resol_join_halves 40 > --norm --scale --j 8 --memory_per_thread 4 > -------------- > it is giving following error > ------------------- > Warning: no access to tty (Bad file descriptor). > Thus no job control in this shell. > /usr15/data/psk01/DATA1 > === RELION MPI setup === > + Number of MPI processes = 30 > + Number of threads per MPI process = 8 > + Total number of threads therefore = 240 > + Master (0) runs on host = node54 > + Slave 1 runs on host = node53 > + Slave 2 runs on host = node52 > + Slave 3 runs on host = node51 > + Slave 4 runs on host = node50 > + Slave 5 runs on host = node49 > + Slave 6 runs on host = node48 > + Slave 7 runs on host = node47 > + Slave 8 runs on host = node46 > + Slave 9 runs on host = node45 > + Slave 10 runs on host = node44 > + Slave 11 runs on host = node43 > + Slave 12 runs on host = node42 > + Slave 13 runs on host = node41 > + Slave 14 runs on host = node40 > + Slave 15 runs on host = node39 > + Slave 16 runs on host = node38 > + Slave 17 runs on host = node37 > + Slave 18 runs on host = node36 > + Slave 19 runs on host = node35 > + Slave 20 runs on host = node34 > + Slave 21 runs on host = node33 > + Slave 22 runs on host = node32 > + Slave 23 runs on host = node31 > + Slave 24 runs on host = node30 > + Slave 25 runs on host = node29 > + Slave 26 runs on host = node28 > + Slave 27 runs on host = node27 > + Slave 28 runs on host = node26 > + Slave 29 runs on host = node25 > ================= > Running in double precision. > ERROR Experiment::divideParticlesInRandomHalves: invalid number for random > subset (i.e. not 1 or 2): 7 > File: src/exp_model.cpp line: 211 > -------------------------------------------------------------------------- > MPI_ABORT was invoked on rank 5 in communicator MPI_COMM_WORLD > with errorcode 1. > > NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. > You may or may not see output from other processes, depending on > exactly when Open MPI kills them. > -------------------------------------------------------------------------- > ERROR Experiment::divideParticlesInRandomHalves: invalid number for random > subset (i.e. not 1 or 2): 7 > File: src/exp_model.cpp line: 211 > ERROR Experiment::divideParticlesInRandomHalves: invalid number for random > subset (i.e. not 1 or 2): 7 > File: src/exp_model.cpp line: 211 > [node54:19017] 1 more process has sent help message help-mpi-api.txt / > mpi-abort > [node54:19017] Set MCA parameter "orte_base_help_aggregate" to 0 to see > all help / error messages > --------------------- > Your advice and suggestion would be greatly appreciated > > with regards > -Prem > > -- Sjors Scheres MRC Laboratory of Molecular Biology Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. tel: +44 (0)1223 267061 http://www2.mrc-lmb.cam.ac.uk/groups/scheres