Hello all,
I am trying to run relion_ctf_refine but incurred in following error. What could be wrong? Though this was posted before but i cannot find any reply for that post (Sat, 20 Oct 2018:Ctfrefine error). All suugestions are appreciated.
Here is the command printed from the gui:
srun --mpi=pmix_v1 relion_ctf_refine_mpi --i Refine3D/twodata_3dcls2_cls2/run_data.star --f PostProcess/job096/postprocess.star --m1 Refine3D/twodata_3dcls2_cls2/run_half1_class001_unfil.mrc --m2 Refine3D/twodata_3dcls2_cls2/run_half2_class001_unfil.mrc --mask MaskCreate/job095/mask.mrc --o CtfRefine/ref_3dcls2_cls2/ --kmin_defocus 30 --fit_defocus --range 2000 --j 4
Here is the error:
in: /home/chasman/git/relion/3.0-beta/src/rwMRC.h, line 191
terminate called after throwing an instance of 'RelionError'
relion_ctf_refine_mpi:15382 terminated with signal 6 at PC=2b6812e02207 SP=2b682a312bf8. Backtrace:
/usr/lib64/libc.so.6(gsignal+0x37)[0x2b6812e02207]
/usr/lib64/libc.so.6(abort+0x148)[0x2b6812e038f8]
/apps/compilers/gcc/5.2.0/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x15d)[0x2b6812399b6d]
/apps/compilers/gcc/5.2.0/lib64/libstdc++.so.6(+0x8cbb6)[0x2b6812397bb6]
/apps/compilers/gcc/5.2.0/lib64/libstdc++.so.6(+0x8cc01)[0x2b6812397c01]
/apps/compilers/gcc/5.2.0/lib64/libstdc++.so.6(+0x8ce18)[0x2b6812397e18]
/apps/cuda/9.2.88/intel/2017.4.056/openmpi/3.1.0/relion/3.0b/bin/relion_ctf_refine_mpi(_ZN5ImageIdE7readMRCElbRK8FileName+0x921)[0x477991]
/apps/cuda/9.2.88/intel/2017.4.056/openmpi/3.1.0/relion/3.0b/bin/relion_ctf_refine_mpi(_ZN5ImageIdE5_readERK8FileNameR13fImageHandlerblbb+0x44d)[0x476a4d]
/apps/cuda/9.2.88/intel/2017.4.056/openmpi/3.1.0/relion/3.0b/bin/relion_ctf_refine_mpi(_ZN5ImageIdE4readERK8FileNameblbb+0xdb)[0x4752bb]
/apps/cuda/9.2.88/intel/2017.4.056/openmpi/3.1.0/relion/3.0b/bin/relion_ctf_refine_mpi(_ZN11StackHelper11loadStackFSEPK13MetaDataTableNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiPSt6vectorI21ParFourierTransformerSaISA_EEb+0xd60)[0x55db10]
/apps/compilers/intel/2017/4.056/compilers_and_libraries/linux/lib/intel64/libiomp5.so(__kmp_invoke_microtask+0x93)[0x2b6807c9fc53]
/apps/compilers/intel/2017/4.056/compilers_and_libraries/linux/lib/intel64/libiomp5.so(+0x84357)[0x2b6807c6f357]
/apps/compilers/intel/2017/4.056/compilers_and_libraries/linux/lib/intel64/libiomp5.so(+0x839d5)[0x2b6807c6e9d5]
/apps/compilers/intel/2017/4.056/compilers_and_libraries/linux/lib/intel64/libiomp5.so(+0xb5133)[0x2b6807ca0133]
/usr/lib64/libpthread.so.0(+0x7dd5)[0x2b6812bb7dd5]
/usr/lib64/libc.so.6(clone+0x6d)[0x2b6812ecab3d]
slurmstepd: error: c31b-s21 [1] pmixp_client_v1.c:198 [_errhandler] mpi/pmix: ERROR: Error handler invoked: status = -25, nranges = 0: Success (0)
slurmstepd: error: *** STEP 28367348.0 ON c31a-s2 CANCELLED AT 2018-11-26T08:17:09 ***
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
Thanks
Gaya
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