Hi
We have 512 GB memory and the box size of the reference is 320 pxl (1.1 A/pix).
Xinchao
> On Jan 4, 2019, at 1:29 AM, Takanori Nakane <[log in to unmask]> wrote:
>
> Hi,
>
> What is the box size of your reference and how much (CPU) memory
> do you have?
>
> Please try down-sampling your 3D reference to 8 or 10 A / pix.
> Don't forget to specify the reference pixel size.
>
> Best regards,
>
> Takanori Nakane
>
>> On 2019/01/04 5:10, Yu Xinchao wrote:
>> 1. I tried 4 mpi with GPU 0:1:2:3 and got same error.
>> 2. The references are generated from the data and I used 6
>> Xinchao
>> On Jan 3, 2019, at 6:52 PM, Joshua Lobo <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>> Hi Xinchao
>> 1.Have you tried 4 MPI by specifically designting the gpus like -gpu '0:1:2:3'.
>> 2.how many autopick references are you picking with and are they generated from the data?
>> Sincerely
>> Joshua
>> On Fri, 4 Jan 2019, 03:46 Yu Xinchao <[log in to unmask]<mailto:[log in to unmask]> wrote:
>> I tried that option, got the same message
>> Sent from my iPhone
>> On Jan 3, 2019, at 1:54 PM, Dong-Hua Chen <[log in to unmask]<mailto:[log in to unmask]>> wrote:
>> Xinchao,
>> I usually use the following option for autopick:
>> --shrink 0
>> Thanks,
>> Dong-Hua
>> On Thu, Jan 3, 2019, 11:53 Xinchao Yu <[log in to unmask]<mailto:[log in to unmask]> wrote:
>> Hi Joshua:
>> I used the following command and asked for 8 mpi processes (we have 4x K80):
>> `which relion_autopick_mpi` --i CtfFind/job002/micrographs_ctf.star --odir AutoPick/job006/ --pickname autopick --ref ../../Talos_UMass/auto_temp.mrcs --invert --ctf --ang 5 --shrink 1 --lowpass 20 --threshold 0.8 --min_distance 150 --max_stddev_noise 1.1 --gpu ""
>> echo CtfFind/job002/micrographs_ctf.star > AutoPick/job006/coords_suffix_autopick.star
>> Thanks,
>> Xinchao
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