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Hi Alberto, Odd number of cards will be used equally efficiency as even numbers for 2D and 3D classification. It's only the 3D auto-refine that makes better use of even number of cards (as each half-set is processed by a different MPI process). If you need 1 card for something else, I would probably choose to run relion with 3 cards rather than complicating your setup with 5 cards.... HTH, Sjors On 07/18/2016 10:42 AM, Alberto Riera wrote: > Thank you for all the advice! > > I was thinking a little bit more about this computer and I wonder if > it would be advantageous for us to install an additional GPU. I know > that Relion uses the GPUs better in pairs, so the idea would be to let > 4 cards just for it and use the spare one for some other tasks if > needed. Alternatively, we could use the fifth card with Relion as > well, although it would be less efficient than having six of them. > > > On 14/07/16 16:01, Craig Yoshioka wrote: >> Hi Alberto, >> >> I’d like to add, it might be worthwhile to keep a few of those CPUs >> and RAM on the side for ZFS. I’d highly recommend turning on ZFS LZ4 >> compression, especially on raw frame stacks it’ll save a lot of space >> and be faster I/O. >> >> >> >>> On Jul 14, 2016, at 5:09 AM, Erik Lindahl <[log in to unmask] >>> <mailto:[log in to unmask]>> wrote: >>> >>> Hi Alberto, >>> >>> On vacation, so sorry if I'm a bit brief. >>> >>> I think your machine will work great if it's intended as a staging >>> server where you do all/most processing. We have a highly similar >>> one, where we also got an external 44-disk enclosure for storage. >>> >>> However, if you want to get more than one machine, we prefer to >>> separate CPU-heavy and GPU-heavy nodes. The reason is that even the >>> GPU code will use CPUs, so you will hurt your GPU performance a lot >>> if you start to run a CPU job on the same machine - and if you >>> don't, you waste those expensive CPUs. For this reason we bought >>> one set of CPU-only nodes with fast processors and then cheap CPUs >>> for the GPU nodes - on the whole I think that provides better value >>> for cluster nodes. >>> >>> We no longer use RAID cards, but have moved to ZFS instead. If you >>> use ubuntu 16.04 it even comes built-in. >>> >>> The released version of oculus rift unfortunately no longer supports >>> plain display mode, so unless a program has been adapted to their >>> devkit, you won't be able to use it. >>> >>> Cheers, >>> >>> Erik >>> >>> >>> >>> Erik Lindahl <[log in to unmask] >>> <mailto:[log in to unmask]>> >>> Professor of Biophysics >>> Science for Life Laboratory >>> Stockholm University & KTH >>> Office (SciLifeLab): +46 8 524 81567 >>> Cell (Sweden): +46 73 4618050 >>> Cell (US): +1 267 3078746 >>> >>> >>> On 14 juli 2016, at 07:24, Alberto Riera >>> <[log in to unmask] <mailto:[log in to unmask]>> >>> wrote: >>> >>>> Hi guys! >>>> >>>> After a lot of days working on this we finally have defined a >>>> system to work with the GPU implementation of Relion and it would >>>> be great it you could tell us your opinion. Currently it is a bit >>>> on the overkill side from the CPU point of view, but we managed to >>>> obtain a very good price and, on the other hand, it is future proof >>>> in this regard and in case we need to install more RAM (it goes up >>>> to 2TB). >>>> >>>> So, it is going to be a Supermicro 4U GPU chassis (workstation >>>> format) with the following: >>>> >>>> 2x Intel E5-2697v4 2.3Ghz Processors (36 cores) >>>> 8x Supermicro 16GB DDR4 ECC REG Memory >>>> 1x 960GB SATA Read Intensive Enterprise Level SSD >>>> 4x 2TB SATA Mixed Workload Enterprise Level SSD (RAID 5) >>>> 1x LSI 9361-8i RAID Controller inc CacheVault >>>> 4x NVidia GTX 1080 >>>> 1x Mellanox Single Port 10Gb SFP+ NIC >>>> >>>> Any opinions on it? >>>> >>>> On the other hand, we are looking to do some 3D visualization with >>>> the system and I wonder if any of you has experience with Linux and >>>> the new VR headsets. They seem very promising but I still did not >>>> have the chance to test them. If you have any other preferred >>>> option, suggestions are very welcome :). >>>> >>>> Thanks! >>>> >>>> Alberto >>>> >>>> -- >>>> Alberto Riera PhD >>>> Imperial College London >>>> Faculty of Medicine >>>> Institute of Clinical Sciences (CRB room 3006) >>>> Hammersmith Hospital Campus >>>> Du Cane Road >>>> London W12 0NN >>>> >>>> [log in to unmask] >> > -- 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