Hi,
Are your particles properly normalised?
Is the diameter you specified in Class2D more or less
the same as the background diameter used in Extract?
(Note that the units are different)
Best regards,
Takanori Nakane
> Hi all,
>
> I'm getting the following error on RELION-3.0.6. while I'm performing a 2D
> class of my particles. 2D class stops at 2nd iteration. I'm not sure on
> what to do to get around the problem
>
> Thank you in advance for your help
>
> 2D class command:
>
> `which relion_refine_mpi` --o Class2D/job069/run --i
> Select/job063/particles.star --dont_combine_weights_via_disc
> --preread_images --pool 30 --pad 2 --ctf --iter 25 --tau2_fudge 2
> --particle_diameter 180 --K 100 --flatten_solvent --zero_mask
> --oversampling 1 --skip_align --norm --scale --j 4
>
> Error I am getting:
>
>
> exp_thisparticle_sumweight= 0
> exp_thisparticle_sumweight= 0
> exp_thisparticle_sumweight= 0
> exp_thisparticle_sumweight= 0
> part_id= part_id= 1740021621
> ipart= 0
> part_id= part_id= 32224
> ipart= 0
>
> ipart= 0375
> ipart= 0
> group_id=
> group_id= 128 mymodel.scale_correction[group_id]= group_id= 100
> mymodel.scale_correction[group_id]= 2.62994
> 0.105198
> exp_ipass= 0
> sampling.NrDirections(0, true)= exp_ipass= 0
> sampling.NrDirections(0, true)= 60 sampling.NrDirections(0, false)= 60
> 60 sampling.NrDirections(0, false)= 60
> group_id= 188 mymodel.scale_correction[group_id]= 2
> mymodel.scale_correction[group_id]= 1.83436
> 0.35762
> exp_ipass= exp_ipass= 0
> sampling.NrDirections(0, true)= 0
> sampling.NrDirections(0, true)= 6060 sampling.NrDirections(0, false)=
> sampling.NrDirections(0, false)= 60
> sampling.NrPsiSamplings(0, true)= 60
> sampling.NrPsiSamplings(0, true)= 60 sampling.NrPsiSamplings(0, false)=
> 60
> mymodel.sigma2_noise[group_id]= sampling.NrPsiSamplings(0, true)= 60
> sampling.NrPsiSamplings(0, false)= 60
>
> mymodel.sigma2_noise[group_id]=
> 0.00129 0.00122
>
> sampling.NrPsiSamplings(0, true)= 6060 sampling.NrPsiSamplings(0, false)=
> 60
> mymodel.sigma2_noise[group_id]= sampling.NrPsiSamplings(0, false)= 60
> mymodel.sigma2_noise[group_id]=
>
> 0.00052 0.00113
>
> 0.000516
> 0.000468
> 0.000468
> 0.000401
> 0.000319
> 0.000407
> 0.000264
> 0.00022 0.000172
> 0.000444
> 0.00015
> 0.00014
> 0.000401
> 0.00015
> 0.000337 0.00014
>
> 0.0001
> 0.000239 7.4e-05
>
>
> 0.000101
> 0.000151 7.07e-05
>
> 5.49e-05
> 9.83e-05 4.08e-05
>
> 2.94e-05
> 6.84e-05 2.24e-05
>
> 1.94e-05
> 5.54e-05 1.77e-05
>
> 5.9e-05
> 0.00016 5.1e-05
>
> 4.7e-05
> 9.55e-05 4e-05
>
> 3.7e-05
> 6.79e-05 3.4e-05
>
> 3.3e-05
> 5.49e-05 3.1e-05
>
> 2.8e-05
> 1.8e-05
> 4.45e-05 1.9e-05
>
> 1.84e-05
> 3.52e-05 2.02e-05
>
> 2.05e-05
> 2.83e-05 1.99e-05
>
> 1.89e-05
> 2.38e-05 1.74e-05
>
> 1.62e-05
> 4.44e-05 2.3e-05
>
> 2.2e-05
> 3.29e-05 2.1e-05
>
> 1.9e-05 2.69e-05
>
> 2.27e-05
> 1.9e-05 1.95e-05
>
> 1.8e-05
> 1.73e-05
> 2e-05 1.58e-05
>
> 1.62e-05
> 1.8e-05 1.67e-05
>
> 1.74e-05
> 1.81e-05 1.73e-05
>
> 1.68e-05
> 1.71e-05 1.66e-05
>
> 1.61e-05
> 1.94e-05 1.54e-05
>
> 1.53e-05
> 1.9e-05 1.66e-05
>
> 1.93e-05
> 1.9e-05 2.04e-05
>
> 2.1e-05
> 2e-05 2.07e-05
>
> 2.03e-05
> 2.1e-05 1.92e-05
>
> 1.81e-05
> 2.06e-05 1.54e-05
>
> 1.55e-05
> 2.12e-05 1.53e-05
>
> 1.54e-05
> 2.06e-05 1.51e-05
>
> 1.5e-05
> 2e-05 1.43e-05
>
> 1.41e-05
>
> mymodel.avg_norm_correction= 1.89e-05
> 2.1e-05 1.73e-05
>
> 1.65e-05 2.1e-05
>
> 2.1e-05
> 1.63e-05 2e-05
>
> 1.9e-05
> 1.65e-05 1.8e-05
>
> 1.8e-05
> 1.66e-05 1.8e-05
>
> 1.8e-05
> 1.67e-05 1.9e-05
>
> 1.8e-05
> 0.4977 1.79e-05
>
> wsum_model.avg_norm_correction= 0
> written out Mweight.spi
> exp_thisparticle_sumweight= 0
> exp_min_diff2[ipart]= 1.72e-05
> 1.68e-05
> 368.88
> 1.67e-05
> 1.71e-05
> 1.76e-05
> 1.78e-05
> 1.7e-05 1.8e-05
>
> 1.8e-05
> 1.72e-05 1.7e-05
>
> 1.7e-05
> 1.69e-05
> 1.65e-05
> 1.6e-05 1.62e-05
>
>
> mymodel.avg_norm_correction= 0.4977
> wsum_model.avg_norm_correction= 0
> 1.79e-05
> 1.72e-05
> 1.66e-05
> 1.65e-05
> 1.62e-05
> 1.59e-05
> 1.59e-05
> 1.58e-05
> 1.58e-05
> 1.57e-05
> 1.52e-05
>
> mymodel.avg_norm_correction= 0.4977
> wsum_model.avg_norm_correction= 0
> written out Mweight.spi
> exp_thisparticle_sumweight= 0
> exp_min_diff2[ipart]= 350.41
> written out Mweight.spi
> exp_thisparticle_sumweight= 1.57e-05
> 0
> exp_min_diff2[ipart]= 1.53e-05301.098
>
> 1.53e-05
> 1.55e-05
> 1.54e-05
> 1.5e-05
>
> mymodel.avg_norm_correction= 0.4977
> wsum_model.avg_norm_correction= 0
> written out Mweight.spi
> exp_thisparticle_sumweight= 0
> exp_min_diff2[ipart]= 326.314
> in: /net/prog/relion3/relion/src/ml_optimiser.cpp, line in:
> /net/prog/relion3/relion/src/ml_optimiser.cpp, line 6871
> in: /net/prog/relion3/relion/src/ml_optimiser.cpp, line in:
> /net/prog/relion3/relion/src/ml_optimiser.cpp, line 6871
> 6871
> 6871
> in: /net/prog/relion3/relion/src/ml_optimiser.cppin:
> /net/prog/relion3/relion/src/ml_optimiser.cpp, line 6871
> in: /net/prog/relion3/relion/src/ml_optimiser.cppin:
> /net/prog/relion3/relion/src/ml_optimiser.cpp, line 6871, line 6871
>
> , line 6871
> slave 1 encountered error: === Backtrace ===
> slave 2 encountered error: === Backtrace ===
> /net/prog/relion3/relion3_latest/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x45)
> [0x470e15]
> /net/prog/relion3/relion3_latest/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x45)
> [0x470e15]
> /net/prog/relion3/relion3_latest/bin/relion_refine_mpi(_Z36globalThreadExpectationSomeParticlesR14ThreadArgument+0xf3)
> [0x5c8793]
> /net/prog/relion3/relion3_latest/bin/relion_refine_mpi(_Z11_threadMainPv+0x36)
> [0x4f9456]
> /lib64/libpthread.so.0(+0x7e25) [0x2adac215ae25]
> /lib64/libc.so.6(clone+0x6d) [0x2adac7bff34d]
> ==================
> ERROR:
> ERROR!!! zero sum of weights....
> /net/prog/relion3/relion3_latest/bin/relion_refine_mpi(_Z36globalThreadExpectationSomeParticlesR14ThreadArgument+0xf3)
> [0x5c8793]
> /net/prog/relion3/relion3_latest/bin/relion_refine_mpi(_Z11_threadMainPv+0x36)
> [0x4f9456]
> /lib64/libpthread.so.0(+0x7e25) [0x2ad892219e25]
> /lib64/libc.so.6(clone+0x6d) [0x2ad897cbe34d]
> ==================
> ERROR:
> ERROR!!! zero sum of weights....
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1
> In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process
> 1)
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
> In: PMI_Abort(1, application called MPI_Abort(MPI_COMM_WORLD, 1) - process
> 2)
> srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
> slurmstepd: error: *** STEP 42473.0 ON compute6 CANCELLED AT
> 2019-09-03T12:05:50 ***
> srun: error: compute6: task 0: Killed
> srun: error: compute6: tasks 1-2: Exited with exit code 1
>
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