Re: [AMBER] Sufficient CPU cores/GPU ratio ?

From: filip fratev <filipfratev.yahoo.com>
Date: Wed, 30 Nov 2011 14:09:27 -0800 (PST)

Hi Marek,

>Meanwhile I decided for the AMD solution ( ASUS CROSSHAIR IV Extreme ) 
>with the "AMD Phenom II X6 1100T Black Edition" six core processor/ 16 GB RAM + 3 
>GTX 580 ( MSI N580GTX Lightning Xtreme Edition ), as I would like partially use 
>this machines also for the analyses (mainly energetic) and the HW with the comparable 


Don't make this mistake. One of my machines is AMD based (ASUS CROSSHAIR IV + Phenom II X6 1090T.4.0Ghz, Suse 11.4) and the results with two GTX580 3GB and maximum overclock are (NPT):

JAC: 51.18 ns/day ( just 46.7 not overclocked), i.e. the scale is not good the CPU is..
Factor IX: 14.48 ns/day ( just 13.35 not overclocked)

The same tests on my second machine (Intel 2600K.4.6 and Asrok  Z68 Extreme7 Gen3) :
JAC: 56.36 ns/day

Factor IX: 16.78 ns/day

All the best,
Filip




________________________________
 From: Marek Maly <marek.maly.ujep.cz>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, November 30, 2011 1:39 AM
Subject: Re: [AMBER] Sufficient CPU cores/GPU ratio ?
 
Hi Jodi,

nice to hear that God answered your prayers :))

Meanwhile I decided for the AMD solution ( ASUS CROSSHAIR IV Extreme ) 
with the
"AMD Phenom II X6 1100T Black Edition" six core processor/ 16 GB RAM + 3 
GTX 580
( MSI N580GTX Lightning Xtreme Edition ), as I would like partially use 
this machines also
for the analyses (mainly energetic) and the HW with the comparable 
performance from Intel would be above my budget.

I was just a bit disappointed that to have the possibility of triple GPU 
configuration with X16/X16/X16 speed
I had to buy one year or more old motherboard which supports just up to 16 
GB RAM which is really not much considering
for example normal mode analysis of some bigger system. The actual AMD MBs 
(not so drastically more expensive)
supports up to 32 GB and also the newest bulldozers processors (even 
cheaper than mentioned Phenom but providing up to
8 physical cores). I really do not understand this crazy philosophy ... 
but OK this is world of money which
is sometime hard to understand ...

  Best wishes,

      Marek



Dne Tue, 29 Nov 2011 18:43:19 +0100 Jodi Ann Hadden <jodih.uga.edu> 
napsal/-a:

> Just a quick update for anyone who was interested... We've had this 
> machine back for about 2 months now and have encountered no problems 
> with running AMBER on all 4 C2070s at once for days at a time. This 
> hardware configuration seems to be working out for us, though I'm still 
> keeping my fingers crossed just in case... ;-)
>
> Jodi
>
> On Sep 21, 2011, at 2:10 PM, Marek Maly wrote:
>
>> OK,
>> I wish to your new machine long life !
>>
>> Would be anyway interesting to hear from you after
>> this machine is sufficiently tested (I mean Amber longer calculations 
>> with
>> all 4 GPUs fully "loaded") if everything
>> is OK and you are fully satisfied with this HW combination.
>>
>>    Best wishes,
>>
>>        Marek
>>
>>
>>
>> Dne Wed, 21 Sep 2011 19:54:08 +0200 Jodi Ann Hadden <jodih.uga.edu>
>> napsal/-a:
>>
>>> Just un update on our GPU machine with the motherboard socket burn:
>>>
>>> I received an email from Microway today saying the machine is being
>>> shipped back to us. They have installed a new motherboard of the same
>>> model and a 1350W PSU and claim to have stress tested it with the 4
>>> C2070s according to their protocol for testing a newly assembled
>>> machine. They only thing they had to say with regard to what went wrong
>>> after examining the old motherboard and PSU was that "results were
>>> inconclusive". I have lots of work lined up for the machine upon its
>>> return, so we should find out pretty quickly if there is some
>>> fundamental insufficiency in this particular grouping of hardware
>>> components... I'm still hoping for the lemon explanation and that all
>>> will be well now, but I'll be saying a prayer to Glycon, patron deity 
>>> of
>>> the GLYCAM lab, before booting it up just in case...
>>>
>>> Jodi
>>>
>>> On Sep 18, 2011, at 10:34 AM, Marek Maly wrote:
>>>
>>>> Hello Ross,
>>>> thanks for deep analysis ! So let's see what answer/solution will be
>>>> offered to Jodi.
>>>>
>>>> Regarding to me I definitely decided not to go over 3 x GTX 580 (3GB)
>>>> using
>>>> common (one socket) motherboard (like mentioned "Asus P6T7 WS
>>>> SuperComputer").
>>>>
>>>> I will also buy some 1400W or 1500W PSU (even for "just" 3 x GTX 580) 
>>>> to
>>>> ensure
>>>> safe/long-term functioning of these machines.
>>>>
>>>> Best wishes,
>>>>
>>>>    Marek
>>>>
>>>>
>>>>
>>>>
>>>> Dne Sun, 18 Sep 2011 02:01:49 +0200 Ross Walker 
>>>> <ross.rosswalker.co.uk>
>>>> napsal/-a:
>>>>
>>>>> Hi Marek,
>>>>>
>>>>>> However I would assume that insufficient PSU will cause just 
>>>>>> GPUs/CPU
>>>>>> errors but not
>>>>>> the melting of PSU connector ... but I am definitely not an expert
>>>>>> here.
>>>>>
>>>>> Yes BUT there should be no way an overloaded power supply would short
>>>>> out
>>>>> and melt the motherboard power connector. In principal it should just
>>>>> trip
>>>>> the power supply. However I suppose it is possible that either the
>>>>> current
>>>>> draw through the PCI-E slots from the 4 C2070s was too high causing a
>>>>> motherboard voltage regulator to fail and subsequently short out. 
>>>>> This
>>>>> would
>>>>> be a fundamental design flaw in the motherboard but seems unlikely.
>>>>>
>>>>> The other possibility is the power supply was up against the limit 
>>>>> and
>>>>> shorted in some way and put too much voltage on the motherboard power
>>>>> connector and that caused it to burn out.
>>>>>
>>>>> Either way it is simply not a failure that should be possible even if
>>>>> the
>>>>> power supply got overloaded. But then one only has to look at San
>>>>> Diego's
>>>>> power company trying to blame some lowly technician for blacking out
>>>>> the
>>>>> whole of southern California, Arizona and New Mexico to realize that
>>>>> everybody takes short cuts not bothering to make things fail safe.
>>>>>
>>>>> Oh well.
>>>>>
>>>>> Let's wait to see what happens when the machine comes back.
>>>>>
>>>>> BTW, people should note that all the 4 GPU boxes I have built, that
>>>>> are 2
>>>>> socket with 4 C2070 or 4 x M2090 and supermicro boards ALL have dual
>>>>> 1.4KW
>>>>> redundant power supplies. Trying to run 4 GPUs (4 GTX580s would be
>>>>> crazy)
>>>>> off a single power supply is really pushing the envelope. Especially 
>>>>> in
>>>>> the
>>>>> US where the voltage is an appallingly low 110V so you can only get
>>>>> 2.2KW
>>>>> total off a single circuit. 2 x 1.4KW independent power supplies
>>>>> plugged
>>>>> in
>>>>> independent circuits (but sharing the same earth) is probably the
>>>>> correct
>>>>> way to go for building such systems. In Europe you can plug both 
>>>>> power
>>>>> supplies in the same circuit. :-)
>>>>>
>>>>> All the best
>>>>> Ross
>>>>>
>>>>> /\
>>>>> \/
>>>>> |\oss Walker
>>>>>
>>>>> ---------------------------------------------------------
>>>>> |            Assistant Research Professor              |
>>>>> |            San Diego Supercomputer Center            |
>>>>> |            Adjunct Assistant Professor              |
>>>>> |        Dept. of Chemistry and Biochemistry          |
>>>>> |          University of California San Diego          |
>>>>> |                    NVIDIA Fellow                    |
>>>>> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>>>>> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk  |
>>>>> ---------------------------------------------------------
>>>>>
>>>>> Note: Electronic Mail is not secure, has no guarantee of delivery, 
>>>>> may
>>>>> not
>>>>> be read every day, and should not be used for urgent or sensitive
>>>>> issues.
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
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Received on Wed Nov 30 2011 - 14:30:03 PST
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