Dear Chen,
First, update your installation to the stable version: 2.1.0. Then, try
adding "--pad 1" as an additional argument. I think that will solve your
problems.
HTH,
Sjors
On 01/24/2018 12:26 AM, Chen Sun wrote:
>
> Hi Adrian,
>
>
> We have 128GB memory on our motherboard. However, the particle mrcs
> files has 150GB. So is it ok if I exclude some particles in the final
> refinement?
>
>
> Chen
>
> ------------------------------------------------------------------------
> *From:* Adrian Koh <[log in to unmask]>
> *Sent:* Tuesday, January 23, 2018 6:21:41 PM
> *To:* Chen Sun
> *Cc:* [log in to unmask]
> *Subject:* RE: [ccpem] Relion 3D autorefine
>
>
> Dear Chen,
>
>
>
> How much system memory (RAM) do you have? I suspect that might be the
> bottleneck.
>
>
>
> Best Regards
>
> Adrian
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
> *From: *Chen Sun <mailto:[log in to unmask]>
> *Sent: *Tuesday, 23 January 2018 5:22 PM
> *To: *[log in to unmask] <mailto:[log in to unmask]>
> *Subject: *Re: [ccpem] Relion 3D autorefine
>
>
>
> Hi Shitaro,
>
>
>
> I have been using the 3 MPI for my autorefine jobs. And most of the
> time I am the only one using the GPUs. That is why I am really confused.
>
>
>
> Chen
>
> *From:*Shintaro Aibara <[log in to unmask]>
> *Sent:* Tuesday, January 23, 2018 3:27:56 PM
> *To:* Chen Sun
> *Cc:* [log in to unmask]
> *Subject:* Re: [ccpem] Relion 3D autorefine
>
>
>
> I am imagining that you are running 5 MPI processes. Try dropping that
> to 3. Having said that you may still crash because of other processes
> like X taking up some memory.
>
>
>
> Best wishes,
>
> Shintaro
>
>
>
> On Tue, Jan 23, 2018 at 9:17 PM, Chen Sun <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Dear Relion developers and users,
>
>
>
> I have been processing some large datasets with more than 100k
> particles (512 pixel boxsize) with Relion/2.1b1. However, the last
> iteration of my 3D refinement always crashed with the following
> error message:
>
>
>
> "ERROR: out of memory in
> /apps/relion/relion/src/gpu_utils/cuda_projector.cu
> <http://cuda_projector.cu> at line 116 (error-code 2)"
>
>
>
> And everytime I restarted it, it will give me such warning at the
> beginning:
>
>
>
> "With the current settings and hardware, you will be able to
>
> use an estimated image-size of 365 pixels during the last iteration...
>
>
>
> ...but your input box-size (image_size) is however 512. This means
> that
>
> you will likely run out of memory on the GPU(s), and will have to
> then re-start
>
> from the last completed iteration (i.e. continue from it)
> *without* the use of GPUs."
>
>
>
> We are equipped with two 1080Ti 11GB GPUs which should be
> sufficient for the memory that it requires. Does anyone have the
> same problem? Is there any way to fix it? Any suggestions would be
> appreciated.
>
>
>
> Thanks,
>
> Chen
>
>
>
>
>
>
>
> --
>
> Yours Sincerely,
> Shintaro Aibara
>
>
>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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