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Thanks Takanori! On 12/17/18 5:37 AM, Takanori Nakane wrote: > Hi, > >> 1) I did a quick benchmark on a system with 16 3.2 GHz core-I7's and 4 >> gtx1080's using 1000 super-res K2 movies. >> 4 mpi's with 1 gpu each is faster (2.6 hours) than 1 mpi with 4 gpus >> (3.5 hours) on this system. > Thank you very much for testing. > > Although it might be slower, I updated the wrapper (commit 5dc615767) to > allow > use of more than one GPU per MPI process by explicitly specifying GPUs. > For example, specify "0,1:2,3" for 2 MPI processes, 2 GPUs each. > >> I'd mistakenly assumed that if you simply >> specified 4 mpi's and let Relion automatically choose gpu's, > This should work, as long as you are running on a single machine. > > If more than two machines are present, it is safer to assign > explicitly. Suppose you want to run 2 MPI processes times > 2 nodes and each node has 2 GPUs. If MPI ranks are assigned > as (0, 1), (2, 3), they will use GPU (0, 1), (0, 1), which is good. > However, if MPI ranks are assigned as (0, 2), (1, 3), they will use > GPU (0, 0), (1, 1). In this case, specify "--gpu 0:0:1:1". > > Best regards, > > Takanori Nakane > >> 1) I did a quick benchmark on a system with 16 3.2 GHz core-I7's and 4 >> gtx1080's using 1000 super-res K2 movies. >> 4 mpi's with 1 gpu each is faster (2.6 hours) than 1 mpi with 4 gpus >> (3.5 hours) on this system. >> >> 2) Ialso? found the reason I originally concluded this didn't work. As >> Alpay pointed out, if running from the gui you must manually assign >> gpu's using ":" notation. I'd mistakenly assumed that if you simply >> specified 4 mpi's and let Relion automatically choose gpu's, it would >> default to sequential assignment as it does with 2D and 3D >> classification. That doesn't seem to work in this case. >> >> Regards, >> -jh- >> >> On 12/15/18 8:57 PM, Daniel Asarnow wrote: >>> Is assigning all 4 GPUs to one MotionCor2 faster than >>> running 4 instances of MotionCor2? >>> >>> >>> It's supposed to be, and that's how we use it at UCSF for on-the-fly >>> correction. I'll double check our benchmarks. >>> >>> Best, >>> -da >>> >>> ------------------------------------------------------------------------ >>> >>> To unsubscribe from the CCPEM list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 >>> >> -- >> John M. Heumann >> Department of Molecular, Cellular, and Developmental Biology >> 347 UCB, University of Colorado >> Boulder, CO 80309-0347 >> >> ######################################################################## >> >> To unsubscribe from the CCPEM list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 >> > -- John M. Heumann Department of Molecular, Cellular, and Developmental Biology 347 UCB, University of Colorado Boulder, CO 80309-0347 ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1