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Hi, I am having trouble doing Ctfrefine. On the same machine, I have run Ctfrefine successfully before but when I tried particles from a different class, Ctfrefine keeps crashing. I could continue the run and see new files being written in the Ctfrefine folder. But the program will crash randomly and throw out the same error message. Any comments would be appreciated. Thank you. Best, Chia The run.err shows the following in: /programs/x86_64-linux/relion/3.0_beta_cu9.0/src/rwMRC.h, line 191 terminate called after throwing an instance of 'RelionError' [Dirac:07859] *** Process received signal *** [Dirac:07859] Signal: Aborted (6) [Dirac:07859] Signal code: (-6) [Dirac:07859] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x11390)[0x1489f8b8b390] [Dirac:07859] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0x38)[0x1489f87e5428] [Dirac:07859] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x16a)[0x1489f87e702a] [Dirac:07859] [ 3] /programs/x86_64-linux/relion/3.0_beta_cu9.0/extlib/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d)[0x33144bea8d] [Dirac:07859] [ 4] /programs/x86_64-linux/relion/3.0_beta_cu9.0/extlib/libstdc++.so.6[0x33144bcbe6] [Dirac:07859] [ 5] /programs/x86_64-linux/relion/3.0_beta_cu9.0/extlib/libstdc++.so.6[0x33144bbb69] [Dirac:07859] [ 6] /programs/x86_64-linux/relion/3.0_beta_cu9.0/extlib/libstdc++.so.6(__gxx_personality_v0+0x261)[0x33144bc5c1] [Dirac:07859] [ 7] /programs/x86_64-linux/relion/3.0_beta_cu9.0/extlib/libgcc_s.so.1[0x3314010383] [Dirac:07859] [ 8] /programs/x86_64-linux/relion/3.0_beta_cu9.0/extlib/libgcc_s.so.1(_Unwind_Resume+0x77)[0x3314010457] [Dirac:07859] [ 9] /programs/x86_64-linux/relion/3.0_beta_cu9.0/bin/relion_ctf_refine_mpi[0x4a1617] [Dirac:07859] [10] /programs/x86_64-linux/relion/3.0_beta_cu9.0/bin/relion_ctf_refine_mpi[0x4a9b3c] [Dirac:07859] [11] /programs/x86_64-linux/relion/3.0_beta_cu9.0/extlib/libgomp.so.1(+0x331440e0d5)[0x1489f8da50d5] [Dirac:07859] [12] /lib/x86_64-linux-gnu/libpthread.so.0(+0x76ba)[0x1489f8b816ba] [Dirac:07859] [13] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x1489f88b741d] [Dirac:07859] *** End of error message *** The run.out shows the following Local host: Dirac -------------------------------------------------------------------------- === RELION MPI setup === + Number of MPI processes = 3 + Master (0) runs on host = Dirac ================= + Slave 1 runs on host = Dirac + Slave 2 runs on host = Dirac + Reading Refine3D/job100/run_data.star... - Using spherical aberration from the input STAR file: 2.7 - Using voltage from the input STAR file: 300 kV - Using pixel size calculated from magnification and detector pixel size in the input STAR file: 1.03 - Using beam tilt from star file. + Reading references ... + Masking references ... + Transforming references ... + Performing loop over all micrographs ... 000/??? sec ~~(,_,"> [oo]-------------------------------------------------------------------------- mpirun noticed that process rank 2 with PID 0 on node Dirac exited on signal 6 (Aborted). -------------------------------------------------------------------------- ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1