Re: [AMBER] Amber18 on NVIDIA Quadro Cards

From: mish <smncbr.gmail.com>
Date: Fri, 10 Aug 2018 12:01:41 +0100

Ross, I accept your point! This kind of rules are inadequate in certain
situations.

For the purchase where the university is not having centralized contracts,
one is asked to provide multiple quotations and then one has to go through
a longer route with unexpected delays. I was not having that much time for
this purchase.

Anyways, many thanks for the suggestions.

Regards,
Mish



On Thu, Aug 9, 2018 at 2:56 PM, Ross Walker <ross.rosswalker.co.uk> wrote:

> LOL. It always amazes me how efficient IT departments can be at hindering
> scientific research as opposed to enabling it.
>
> Remember your role is to make the IT department's job as simple as
> possible, not the other way around.
>
> My advice would be to simply tell IT that you will not be supporting their
> monopoly and to take a hike and circumvent them. First step would be to
> make sure your purchase gets labelled properly. It is a scientific
> instrument and not a Windows laptop and thus it does not fall under the
> purview of IT or any related exclusive computer supplier agreements.
>
> Or you can just suffer in silence.
>
> All the best
> Ross
>
> > On Aug 9, 2018, at 02:10, mish <smncbr.gmail.com> wrote:
> >
> > Thanks, Malkeet! I dad a quote from Exxact but the university turned down
> > the request to buy anything other than some agreed machines from Dell!
> >
> > Best,
> > Mish
> >
> >
> > On Thu, Aug 9, 2018 at 10:09 AM, malkeet singh Bahia <
> msbahia17.gmail.com>
> > wrote:
> >
> >> Hello Mish!
> >>
> >> Have a look at this, if it would be helpful.
> >>
> >> http://ambermd.org/gpus/recommended_hardware.htm#exxact
> >>
> >>
> >>
> >> [image: Mailtrack]
> >> <https://mailtrack.io?utm_source=gmail&utm_medium=
> signature&utm_campaign=
> >> signaturevirality5&>
> >> Sender
> >> notified by
> >> Mailtrack
> >> <https://mailtrack.io?utm_source=gmail&utm_medium=
> signature&utm_campaign=
> >> signaturevirality5&>
> >> 09/08/18,
> >> 12:09:23 PM
> >>
> >> On Thu, 9 Aug 2018 at 11:54 mish <smncbr.gmail.com> wrote:
> >>
> >>> Hi all,
> >>>
> >>> Many thanks to everyone for the kind advice.
> >>>
> >>> I already had off the table discussion with the concerned people about
> >>> putting-in GPUs on my own, but that is a risky way to go. Dell is
> >> offering
> >>> them additional discounts, and 2 years of additional warranty in all
> the
> >>> machines. I (and also University) may have issues if Dell figures will
> it
> >>> out when repairing.
> >>>
> >>> I am also afraid that it may be possible to figure it out easily
> (through
> >>> logs) that which components were being used at the time of ( or caused)
> >>> crash!
> >>>
> >>> But many thanks Ross, I would settle this with P4000 as of now.
> >>>
> >>>
> >>> Regards,
> >>> Mish
> >>>
> >>>
> >>> On Wed, Aug 8, 2018 at 8:13 PM, James Kress <
> jimkress_58.kressworks.org>
> >>> wrote:
> >>>
> >>>> In the 30 years I have been dealing with Dell, and many other vendors,
> >>> the
> >>>> mantra is always the same. I.e. you may put the foreign components
> >> into
> >>>> the
> >>>> computer your purchase/ lease from us. However, we will not provide
> >>>> support
> >>>> (i.e. including warranty) for your SYSTEM for problems involving/
> >> caused
> >>> by
> >>>> the foreign components you have installed. They will provide support
> >> for
> >>>> the unmodified system.
> >>>>
> >>>> My comment was just a warning so you do not get burned if something
> >> goes
> >>>> wrong with the modified SYSTEM.
> >>>>
> >>>> You can believe or ignore other's opinions. The choice is yours.
> >>>>
> >>>> Jim
> >>>>
> >>>> -----Original Message-----
> >>>> From: Ross Walker <ross.rosswalker.co.uk>
> >>>> Sent: Wednesday, August 08, 2018 2:54 PM
> >>>> To: AMBER Mailing List <amber.ambermd.org>
> >>>> Subject: Re: [AMBER] Amber18 on NVIDIA Quadro Cards
> >>>>
> >>>> You do not invalidate your warranty with Dell by placing 1080TI cards
> >> in
> >>>> their workstations. You just don't inherit the Dell warranty onto the
> >>>> 1080TI
> >>>> cards.
> >>>>
> >>>>> On Aug 8, 2018, at 1:48 PM, David Cerutti <dscerutti.gmail.com>
> >> wrote:
> >>>>>
> >>>>> Agreed. While GTX-1080Ti has long been the price point for
> >>>>> simulations, Dell's going to bite you back if you start doing things
> >> to
> >>>> their machines.
> >>>>> The contract that locks you into Dell is probably built on incentives
> >>>>> like discounts and a deluxe warranty, which you will be forfeiting if
> >>>>> you change the hardware (or OS). I'd talk to your acquisitions
> >> people
> >>>>> (start with your department administrator, ask him or her who to
> >> speak
> >>>>> to, and go from there). See If you can get a special dispensation
> >> and
> >>>>> start constructing your own machine. Gaming systems companies will
> >>>>> build you a desktop with dual GTX-1080Ti cards no problem, but they
> >>>>> may be politically impossible for your acquisitions department to do
> >>>> business with.
> >>>>>
> >>>>> Dave
> >>>>>
> >>>>>
> >>>>> On Wed, Aug 8, 2018 at 1:23 PM James Kress
> >>>>> <jimkress_58.kressworks.org>
> >>>>> wrote:
> >>>>>
> >>>>>> "buy a couple of 1080TIs on Amazon and put those in in its place"
> >>>>>>
> >>>>>> Be careful. Dell will probably not support these cards and their
> >>>>>> implementation. You should contact Dell and get clarification of
> >> how
> >>>>>> adding these cards will affect your warranty and service contracts.
> >>>>>>
> >>>>>> Jim Kress
> >>>>>>
> >>>>>>
> >>>>>> -----Original Message-----
> >>>>>> From: Ross Walker <ross.rosswalker.co.uk>
> >>>>>> Sent: Wednesday, August 08, 2018 12:55 PM
> >>>>>> To: AMBER Mailing List <amber.ambermd.org>
> >>>>>> Subject: Re: [AMBER] Amber18 on NVIDIA Quadro Cards
> >>>>>>
> >>>>>> Hi Mish,
> >>>>>>
> >>>>>> Amber will run fine on those Quadro card. A P4000 will be about
> >>>>>> halfway between a GTX1070 and a GTX1060 in terms of speed. So not
> >>>>>> great considering what they cost. I'd guesstimate about 300 ns/day
> >>>>>> for DHFR NVE 4fs on a
> >>>>>> P4000
> >>>>>> - so about half the speed, maybe a little less of a P6000 / 1080TI.
> >>>>>>
> >>>>>> If your IT department are forcing you to buy Dell then the best
> >>>>>> option is to buy it with the cheapest graphics card you can, throw
> >>>>>> that out when it arrives, buy a couple of 1080TIs on Amazon and put
> >>>>>> those in in it's place.
> >>>>>> Just make sure the power supply is beefy enough and there are enough
> >>>>>> open PCIe X16 slots in the machine.
> >>>>>>
> >>>>>> All the best
> >>>>>> Ross
> >>>>>>
> >>>>>>> On Aug 8, 2018, at 11:51 AM, mish <smncbr.gmail.com> wrote:
> >>>>>>>
> >>>>>>> Dear all
> >>>>>>>
> >>>>>>> Just in case some is using NVIDIA Quadro P2000/P4000 cards, I want
> >>>>>>> to ask if pmemd.cuda can run on NVIDIA Quadro P2000/P4000(8GB, 4DP
> >>>>>>> (7X20T)
> >>>>>> cards?
> >>>>>>> If yes, how slow these can be compared to Quadro P6000 (~ 600
> >> ns/day
> >>>>>>> on ~23K atoms)?
> >>>>>>>
> >>>>>>> We are bound to buy a machine from DELL only, and they can not
> >> offer
> >>>>>>> a workstation with GeForce cards as of now.
> >>>>>>>
> >>>>>>> In general, which Quadro can be a reasonable choice for Amber18 in
> >>>>>>> this
> >>>>>>> GTX-1080 budget?
> >>>>>>>
> >>>>>>> Best,
> >>>>>>> Mish
> >>>>>>> _______________________________________________
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> >>>>>>
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> >> --
> >> Thanks & Warm Regards
> >>
> >> ​
> >> Malkeet S. Bahia, PhD
> >> Post Doctoral Fellow at the lab of Prof. Hanoch Senderowitz
> >> PBC Indo-Israel Post-doc fellowship
> >> Dept. of Chemistry, Building 211, Room no. 211
> >> Bar Ilan University, Ramat Gan, 5290002, ISRAEL
> >>
> >> Mobile: +91-9815988501 (India, watts app only)
> >> +972-584553434 (Israel number)
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Received on Fri Aug 10 2018 - 04:30:02 PDT
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