 |
 |
is what we are currently doing. Our sys admin wants to set it up so that Relion can send the job info to SLURM directly so that the jobs can be put in queue internally. Best, Qiu-Xing From: Hamidreza Rahmani <[log in to unmask]> Sent: Monday, August 6, 2018 5:40 PM To: Jiang,Qiu-Xing <[log in to unmask]>; [log in to unmask] Subject: RE: [ccpem] [3dem] Relion3.0 Hi, We also use slurm with srun at FSU. As far as I know, we just compile it with generic settings and use run scripts like this: #!/bin/tcsh #SBATCH --job-name="name" #SBATCH -N 1 #SBATCH -p ktaylor_q #SBATCH -o log.out #SBATCH --gres=gpu:2 #SBATCH --mem=50G module unload relion2-1-nogpu module load relion2-1 module load cuda srun -n 3 relion_refine_mpi --o [options] --j 2 -gpu I hope this helps. Best, Hamidreza Rahmani PhD Candidate Institute of Molecular Biophysics Florida State University From: Jiang,Qiu-Xing <mailto:[log in to unmask]> Sent: Monday, August 6, 2018 12:40 PM To: [log in to unmask] <mailto:[log in to unmask]> Subject: Re: [ccpem] [3dem] Relion3.0 Dear all, The supercomputer on our campus uses SLURM to schedule GUI, CPU and GPU nodes shared among users. Our sys admin is seeking detailed information on how to make the scheduler in Relion submit job requests the system slurm directly and integrate it into our local environment. Is there a detailed doc on this part? If some on this list has sorted out the slurm part and is willing to share, I would really appreciate it. Thanks. Qiu-Xing On 8/4/18, 1:20 AM, "3dem on behalf of Takanori Nakane" <[log in to unmask] on behalf of [log in to unmask] <mailto:[log in to unmask]@mrc-lmb.cam .ac.uk> > wrote: >Hi, > >Unfortunately no. > >Technically speaking, one can write a script >to parse MotionCor2 log files and produce STAR files. >But this is very error prone and not officially supported. > >Best regards, > >Takanori Nakane > >On 2018/08/04 0:09, Elad Binshtein wrote: >>> >>> Hi all >> >> The Bayesian polishing in the new version of Relion3.0 required metadata >> about the motion correction to be written out (within Relion). >> Is there a way to get this done outside Relion? >> >> Thanks, >> >>> >> >> >> >> _______________________________________________ >> 3dem mailing list >> [log in to unmask] <mailto:[log in to unmask]> >> >>https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_ >>mailman_listinfo_3dem&d=DwICAg&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpW >>lZM&r=P2JY4Ggp34jCrKsRhFNcaQ&m=pvCRsTHcuI8b2ccChHhRoyH38B4YczHnPO8llIC4PA >>s&s=KxPOLRCqappku3mjy5fPs_Sk8BMCd2zhTIcOuk7tyTw&e= >> > >_______________________________________________ >3dem mailing list >[log in to unmask] <mailto:[log in to unmask]> >https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_m >ailman_listinfo_3dem&d=DwICAg&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZ >M&r=P2JY4Ggp34jCrKsRhFNcaQ&m=pvCRsTHcuI8b2ccChHhRoyH38B4YczHnPO8llIC4PAs&s >=KxPOLRCqappku3mjy5fPs_Sk8BMCd2zhTIcOuk7tyTw&e= ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi -2Dbin_webadmin-3FSUBED1-3DCCPEM-26A-3D1&d=DwMF-g&c=pZJPUDQ3SB9JplYbifm4nt2l EVG5pWx2KikqINpWlZM&r=P2JY4Ggp34jCrKsRhFNcaQ&m=78XbgBqKRy0fIQd6St4Lf2UGX-zZ3 bGpf0cPA12Q4ws&s=kr-D3PFKGj53hcbB5y-0YxgV_K9PuI3TW4D3x3DswKc&e=> &A=1 --- This email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1