Hi Peter,
thanks for your comment ! As I mentioned before am thinking about "Asus
P6T7 WS SuperComputer - Intel X58"
http://www.scan.co.uk/products/asus-p6t7-ws-supercomputer-intel-x58-s-1366-ddr3-sata-ii-3gb-s-sas-sata-raid-pcie-20-%28x16%29-ceb
seems to be OK for 4 x GPU.
Best wishes,
Marek
Dne Tue, 13 Sep 2011 19:57:29 +0200
<peter.stauffert.boehringer-ingelheim.com> napsal/-a:
> Hi Ross,
>
> to run GPUs it is essential to put them in PCI-E X16 slots.
> On a normal motherboard there are only 1 or 2 PCI-E X16 slots available,
> but
> there are some special motherboards on the market with additional chip
> sets,
> which supply more PCI-E X16 slots.
> We did some benchmarks on our HP SL390 system.
> This node is equipped with an additional chipset and supplies 4 PCI-E X16
> slots, one for the onboard QDR Infiniband and the other to be used by 3
> GPUs.
> The performance degration was less than 2% when we ran 3 separated GPU
> jobs
> and one non-GPU pmemd.MPI with 8 cores in parallel on this dual-CPU
> 6-core
> system. In principal, it is a good idea, not to use all cores, normally
> core-1 handles all interrupts.
> On our system, the GPU utilization was only 90% but the CPU runs with
> 100%,
> so using faster CPUs (with higher clock rate than our 2.67 GHz CPUs) may
> be
> useful.
>
> All the best
>
> Peter
>
> Dr. Peter Stauffert
> Boehringer Ingelheim Pharma GmbH & Co. KG
> -----Ursprüngliche Nachricht-----
> Von: Ross Walker [mailto:ross.rosswalker.co.uk]
> Gesendet: Dienstag, 13. September 2011 18:54
> An: 'AMBER Mailing List'
> Betreff: Re: [AMBER] Sufficient CPU cores/GPU ratio ?
>
> Hi Marek,
>
> I would say that the answer is, with caveats, not really. The reason for
> this is not a core to GPU ratio argument per se but actually one of
> memory
> bandwidth. For a single socket motherboard there is no way that it can
> drive
> 4 PCI-E sockets flat out at x16 speed. Hence you are always going to get
> contention. Typically I would say never go beyond 2 GPUs per node for a
> single socket system. 4 GPUs per node is pushing it for a dual socket
> system
> even with the highest CPU FSB speed you can get so on a single socket
> system
> with a low end CPU it is definitely not going to cut it.
>
> Now if you only plan to run single GPU jobs. I.e. 4 independent jobs at
> once
> with reasonably large values for ntpr, ntwx etc then it is probably not
> an
> issue since the memory bandwidth only really comes into play at each
> output
> file or trajectory write for most types of calculations. However, trying
> to
> run in parallel where a single job spans GPUs it really all comes down
> to a
> combination of the aggregate memory bandwidth of the main CPU memory per
> GPU
> and the PCI-E bandwidth to each GPU when all are communicating flat out
> at
> the same time. You might be able to get speedup across 2 of the GPUs if
> you
> leave the other two idle. However, running two sets of dual GPU runs or
> running a single 4 GPU run is likely to cause so much contention that see
> little or no speedup.
>
> So it really comes down to a case of the type of jobs you want to run.
>
> I hope that helps.
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: Marek Maly [mailto:marek.maly.ujep.cz]
>> Sent: Tuesday, September 13, 2011 7:19 AM
>> To: amber.ambermd.org
>> Subject: [AMBER] Sufficient CPU cores/GPU ratio ?
>>
>> Hi all,
>>
>> just a very quick technical question. I would like to know if 4 core
>> CPU
>> "Intel Core i7-960" might be sufficient for
>> 4 GPU machine (motherboard: Asus P6T7 WS SuperComputer - Intel X58 ).
>> I
>> mean if ratio 1 CPU core/ 1 GPU might
>> be here sufficient also considering some requirements (on CPU) for
>> managing operating system etc.
>>
>> Thanks in advance for any relevant comment !
>>
>> Best wishes,
>>
>> Marek
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Sep 13 2011 - 11:30:05 PDT
