Hi,
I am not sure about the error about PDF, but there is an alternative
solution. Please re-run (not continue) the job with 'Skip padding: Yes'.
Best regards,
Takanori Nakane
> Dear Sjors and Team,
>
> I am trying to run 3d multi-body refine process on my dataset with two
> bodies. However, the program crashed out after the data converged with the
> following error:
>
> ERROR: out of memory in
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/src/acc/acc_backprojector_impl.h
> at line 36 (error-code 2)
> in:
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/src/acc/cuda/cuda_settings.h,
> line 67
> === Backtrace ===
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41)
> [0x449131]
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_refine_mpi()
> [0x6309ae]
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_refine_mpi(_ZN16AccBackprojector9setMdlDimEiiiiiii+0xd1)
> [0x630b31]
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_refine_mpi(_ZN14MlDeviceBundle22setupFixedSizedObjectsEv+0x3ac)
> [0x634d0c]
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_refine_mpi(_ZN14MlOptimiserMpi11expectationEv+0x1555)
> [0x467005]
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_refine_mpi(_ZN14MlOptimiserMpi7iterateEv+0xaa)
> [0x4755ea]
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_refine_mpi(main+0x69)
> [0x4342c9]
> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x2b9ec2790830]
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_refine_mpi()
> [0x436701]
> ==================
>
> As the error stated that it ran out of memory (not surprising as my box is
> 450px, and I am running the proc on 4 titan xp each with 12 GB of memory.)
> Therefore, I switched to processing the data on CPU only but this process
> died with the following error:
>
> XSIZE(pdf_direction)= 196608 rot_angles.size()= 786432
> in: /programs/x86_64-linux/relion/3.0_beta_cu8.0/src/healpix_sampling.cpp,
> line 1861
> === Backtrace ===
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41)
> [0x449131]
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_refine_mpi(_ZN15HealpixSampling38writeBildFileOrientationalDistributionER13MultidimArrayIdER8FileNameddPK8Matrix2DIdEPK8Matrix1DIdEdd+0xd41)
> [0x61d7b1]
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_refine_mpi(_ZN7MlModel5writeE8FileNameR15HealpixSamplingbb+0x642)
> [0x58d002]
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_refine_mpi(_ZN11MlOptimiser5writeEbbbbi+0x5bd)
> [0x5c58bd]
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_refine_mpi(_ZN14MlOptimiserMpi10initialiseEv+0xd02)
> [0x46c0c2]
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_refine_mpi(main+0x5f)
> [0x4342bf]
> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0) [0x2b9753a24830]
> /programs/x86_64-linux/relion/3.0_beta_cu8.0/bin/relion_refine_mpi()
> [0x436701]
> ==================
> ERROR:
> HealpixSampling::writeBildFileOrientationalDistribution
> XSIZE(pdf_direction) != rot_angles.size()!
>
> In this case I am not sure, why the job died, as I merely continued the
> job
> from the last iteration. Could you please advise me on how to deal with
> this error? I am happy to provide more details, off-list.
>
> Warm regards,
> Pranav
>
> --
> Pranav Shah
> Postdoctoral Research Fellow.
>
> Hogle Lab
> Harvard Medical School
> 240 Longwood Avenue
> Boston, MA 02115
> (617) 432-4360 (fax)
> (617) 432-3839 (lab)
>
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