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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.
[log in to unmask]" type="cite">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]> 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]>Professor of BiophysicsScience for Life LaboratoryStockholm University & KTHOffice (SciLifeLab): +46 8 524 81567Cell (Sweden): +46 73 4618050Cell (US): +1 267 3078746
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+ NICAny 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]
-- 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]