 |
 |
Hi Chen, No, it's simply a "non-modifiable" parameter, meaning that you would need to use --pad 1 from the beginning. Some parameters are protected because it does not make sense to (in general) change them partway through a refinement, using the continuation function. Future version will permit changing of padding with a continue, but we were unable to test it sufficiently in time for 2.1.0. /Björn On 01/24/2018 04:02 PM, Chen Sun wrote: > > Hi Sjors, > > > I module loaded Relion/2.1 and added "--pad 1" to continue my > refinement. However, it gave me a warning that: > > > " > > The following warnings were encountered upon command-line parsing: > WARNING: Option --padis not a valid RELION argument > > " > > Does it indicate that there might be something wrong in our compiling > process? > > > > Chen > > ------------------------------------------------------------------------ > *From:* Sjors Scheres <[log in to unmask]> > *Sent:* Wednesday, January 24, 2018 4:06:22 AM > *To:* Chen Sun; [log in to unmask] > *Subject:* Re: [ccpem] Relion 3D autorefine > 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 >