Hi,

When this set2DSlice error occurred, did you have enough CPU memory?

RELION reads metadata (orientations, CTF parameters, etc) of ALL
particles into memory, regardless of "pre-read all particles into RAM".
 (this option toggles whether to pre-read all particle images or not;
  metadata are always read)

So, if you have millions of particles and running many MPI processes,
you can run out of CPU memory.

Best regards,

Takanori Nakane

> Hi all,
>
> Splitting data works for me.
>
> Thanks,
>
> Xiaofeng
>
> Yu Xinchao <[log in to unmask]> 于2018年10月26日周五 上午8:33写道：
>
>> Hi Thomas and Joe,
>>     2D classification works after splitting the data into two halves.
>> Hopefully this issue will be resolved in future releases.
>>   Best
>>
>> > On Oct 26, 2018, at 5:14 AM, Joseph Atherton <
>> [log in to unmask]> wrote:
>> >
>> > Yes, splitting the data in half worked nicely for me too when I had
>> this
>> error.
>> >
>> > Cheers,
>> > Joe
>> >
>> >> On 25/10/2018, 20:27, Yu Xinchao wrote:
>> >> Thanks Thomas, I do have a very large data set (9000+ movies) and
>> that
>> might be the reason. I will try split the data in half and rerun it.
>> >> Best
>> >> Xinchao
>> >>
>> >> Sent from my iPhone
>> >>
>> >>> On Oct 25, 2018, at 12:22 PM, Thomas Bausewein <
>> [log in to unmask]> wrote:
>> >>>
>> >>> Hi Xinchao,
>> >>>
>> >>> im my case I had a really large dataset and the set2Dslice error
>> vanished when I split the dataset in half (using the Relion GUI) and
>> classified the smaller datasets individually.
>> >>> I did not remove any particles, neither from the folders nor from
>> the
>> particle.star files.
>> >>>
>> >>> You should also do relion_image_handler --stats --i
>> Extract/Job006/particles.star in your project folder and not in the
>> Extract/job006 folder, since it reads the path that is written in the
>> particles.star file.
>> >>>
>> >>> Thomas
>> >>>
>> >>>
>> >>>> On 25 Oct 2018, at 20:59, Xinchao Yu <[log in to unmask]> wrote:
>> >>>>
>> >>>> Hi All, I got the the same error message when I tried to do 2D
>> classfication: Backprojector::set2DSlice%%: Dimension of the data array
>> should be 2 or 3
>> >>>> I was able do MotionCor2, Gctf, Autopicking and particle extraction
>> without any error messages.
>> >>>> I checked the files with relion_image_handler --stats --i
>> particles.star and it's always the first file that give the following
>> message:
>> >>>> ERROR:
>> >>>>  Cannot read file Extract/Job006/Micrographs/NP146-g1_06973.mrcs It
>> does not exist.
>> >>>> I checked the folder and the file does exist and when I deleted the
>> file from the .star files I would get same error message for the next
>> file.
>> >>>> Does anyone have a solution to this?
>> >>>> Thanks,
>> >>>> Xinchao Yu
>> >>>>
>> >>>>
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