Id go for the i7 6 core,
To the other message, funny. I bought ATI's as they clock faster and cost 1/3 the price of Nvidia's but then the software all went to Nvidia. The new ATI with twice the shaders runs at the same speed (around 1-1.3 terflops ) due to the same problems the Nvidias ran into with IO (or maybe onboard RAM does solve the problem if they went up to 16 or 32 MB) Gromacs, etc...doesn't run on ATI's, and I've been hoping they, AMD, catch up, but all I ever see is the constant in 6 months then nothing.
I ran around 40 4 ns simulations on University blades with 8 AMD quad cores, using 3 blades I only was able to get 1 ns/day, but never pressed it as far as why so slow, as I needed to finish. With the Nvidia at even 5 ns/day I or alot of people could do some really nice work as far as publishing, with raw data in 2 weeks time, so now I feel a bit saddened...
I also just found openCL profilling with CUDA 5 that will take any C or C++ software, and mark all sections you need to convert to openCL, but the trial software is 30 day, then 250 US$...
Stephan
Gesendet: Samstag, 25. Mai 2013 um 15:19 Uhr
Von: "James Starlight" <jmsstarli...@gmail.com>
An: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Betreff: Re: Aw: Re: [gmx-users] GPU-based workstation
Von: "James Starlight" <jmsstarli...@gmail.com>
An: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Betreff: Re: Aw: Re: [gmx-users] GPU-based workstation
Richard,
thanks for suggestion!
Assuming that I'm using 2 high end GeForce's what performance be better
1) in case of one i7 (4 or 6 nodes ) ?
2) in case of 8 core Xeon like CPU Intel Xeon E5-2650 2.0 GHz / 8core
What properties of MB should take into account primarily for such
Xenon-based system. Does such MBs support multi-GPU ( I noticed that many
such MBs lack for PCI)?
James
2013/5/25 Broadbent, Richard <richard.broadben...@imperial.ac.uk>
> I've been running on my Universities GPU nodes these are one E5-xeon
> (6-cores 12 threads) and have 4 Nvidia 690gtx's. My system is 93 000 atoms
> of DMF under NVE. The performance has been a little disappointing
> ~10ns/day. On my home system using a core i5-2500 and a nvidia 560ti I get
> 5.4ns/day for the same system. On our HPC system using 32 nodes each with 2
> quad-core xeon processors I get 30-40ns/day.
>
> I think that to achieve reasonable performance the system has to be
> balanced between CPU's and GPU's probably getting 2 high end GPU's and a
> top end xeon E5 or core i7 would be a good choice.
>
>
> Richard
>
> From: lloyd riggs <lloyd.ri...@gmx.ch<mailto:lloyd.ri...@gmx.ch>>
> Reply-To: Discussion users <gmx-users@gromacs.org<mailto:
> gmx-users@gromacs.org>>
> Date: Saturday, 25 May 2013 12:02
> To: Discussion users <gmx-users@gromacs.org<mailto:gmx-users@gromacs.org>>
> Subject: Aw: Re: [gmx-users] GPU-based workstation
>
> More RAM the better, and the best I have seen is 4 GPU work station. I
> can use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is
> really 3-4 GPU, except the tyan mentioned (there designed as blades so an 8
> or 10 slot board really holds 8 or 10 GPU's). There's cooling problems
> though with GPU's, as on a board there packed, so extra cooling things may
> help not blow a GPU, but I would look for good ones (ask around), as its a
> video game market and they go for looks even though its in casing? The
> external RAM (not onboard GPU RAM) helps if you do a larger sim, but I dont
> know performance wise, the onboard GPU, the more RAM the marrier...so yes,
> normal work stations you can get 4 GPU's for a 300 US$ board, but then the
> price goes way up (3-4000 US$ for an 8-10 gpu board). RAM ordered abroad
> is also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests
> software, not Gromacs, so would be nice to see performance...for a small
> 100 atom molecule and 500 solvent, using just the CPU I get it to run 5-10
> minutes real for 1 ns sim, but tried simple large 800 amino, 25,000
> solvent eq (NVT or NPT) runs and they clock at around 1 hour real for say
> 50 ps eq's....
>
> Stephan
>
> Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr
> Von: "James Starlight" <jmsstarli...@gmail.com<mailto:
> jmsstarli...@gmail.com>>
> An: "Discussion list for GROMACS users" <gmx-users@gromacs.org<mailto:
> gmx-users@gromacs.org>>
> Betreff: Re: [gmx-users] GPU-based workstation
> Dear Dr. Watkins!
>
> Thank you for the suggestions!
>
> In the local shops I've found only Core i7 with 6 cores (like Core
> i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores
> than with 4 cores in case of i7 cpu (assuming that I run simulation in
> cpu+gpu mode )?
>
> Also you've mentioned about 4 PCeI MD. Does it means that modern
> work-station could have 4 GPU's in one home-like desktop ? According to my
> current task I suppose that 2 GPU's would be suitable for my simulations
> (assuming that I use typical ASUS MB and 650 Watt power unit). Have
> someone tried to use several GPU's on one workstation ? What attributes of
> MB should be taken into account for best performance on such multi-gpu
> station ?
>
> James
>
> 2013/5/25 lloyd riggs <lloyd.ri...@gmx.ch<mailto:lloyd.ri...@gmx.ch>>
>
> > There's also these, but 1 chip runs 6K US, they can get performance up to
> > 2.3 teraflops per chip though double percission...but have no clue about
> > integration with GPU's...Intell also sells their chips on PCIe
> cards...but
> > get only about 350 Gflops, and run 1K US$.
> >
> > http://en.wikipedia.org/wiki/Field-programmable_gate_array and vendor
> > http://www.xilinx.com/
> >
> > They can design them though to fit a PCIe slot and run about the same,
> but
> > still need the board, ram etc...
> >
> > Mostly just to dream about, they say you can order them with radiation
> > shielding as well...so...
> >
> > Stephan Watkins
> >
> > *Gesendet:* Freitag, 24. Mai 2013 um 13:17 Uhr
> > *Von:* "James Starlight" <jmsstarli...@gmail.com<mailto:
> jmsstarli...@gmail.com>>
> > *An:* "Discussion list for GROMACS users" <gmx-users@gromacs.org<mailto:
> gmx-users@gromacs.org>>
> > *Betreff:* [gmx-users] GPU-based workstation
> > Dear Gromacs Users!
> >
> >
> > I'd like to build new workstation for performing simulation on GPU with
> > Gromacs 4.6 native cuda support.
> > Recently I've used such setup with Core i5 cpu and nvidia 670 GTX video
> > and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system
> > with SD integrator)
> >
> >
> > Now I'd like to build multi-gpu wokstation.
> >
> > My question - How much GPU would give me best performance on the typical
> > home-like workstation. What algorithm of Ncidia GPU integration should I
> > use (e.g SLI etc) ?
> >
> >
> > Thanks for help,
> >
> >
> > James
> > --
> > gmx-users mailing list gmx-users@gromacs.org<mailto:
> gmx-users@gromacs.org>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org<mailto:
> gmx-users-requ...@gromacs.org>.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > --
> > gmx-users mailing list gmx-users@gromacs.org<mailto:
> gmx-users@gromacs.org>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
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> gmx-users-requ...@gromacs.org>.
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> >
> --
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thanks for suggestion!
Assuming that I'm using 2 high end GeForce's what performance be better
1) in case of one i7 (4 or 6 nodes ) ?
2) in case of 8 core Xeon like CPU Intel Xeon E5-2650 2.0 GHz / 8core
What properties of MB should take into account primarily for such
Xenon-based system. Does such MBs support multi-GPU ( I noticed that many
such MBs lack for PCI)?
James
2013/5/25 Broadbent, Richard <richard.broadben...@imperial.ac.uk>
> I've been running on my Universities GPU nodes these are one E5-xeon
> (6-cores 12 threads) and have 4 Nvidia 690gtx's. My system is 93 000 atoms
> of DMF under NVE. The performance has been a little disappointing
> ~10ns/day. On my home system using a core i5-2500 and a nvidia 560ti I get
> 5.4ns/day for the same system. On our HPC system using 32 nodes each with 2
> quad-core xeon processors I get 30-40ns/day.
>
> I think that to achieve reasonable performance the system has to be
> balanced between CPU's and GPU's probably getting 2 high end GPU's and a
> top end xeon E5 or core i7 would be a good choice.
>
>
> Richard
>
> From: lloyd riggs <lloyd.ri...@gmx.ch<mailto:lloyd.ri...@gmx.ch>>
> Reply-To: Discussion users <gmx-users@gromacs.org<mailto:
> gmx-users@gromacs.org>>
> Date: Saturday, 25 May 2013 12:02
> To: Discussion users <gmx-users@gromacs.org<mailto:gmx-users@gromacs.org>>
> Subject: Aw: Re: [gmx-users] GPU-based workstation
>
> More RAM the better, and the best I have seen is 4 GPU work station. I
> can use/have used 4. The GPU takes 2 slots though, so a 7-8 PCIe board is
> really 3-4 GPU, except the tyan mentioned (there designed as blades so an 8
> or 10 slot board really holds 8 or 10 GPU's). There's cooling problems
> though with GPU's, as on a board there packed, so extra cooling things may
> help not blow a GPU, but I would look for good ones (ask around), as its a
> video game market and they go for looks even though its in casing? The
> external RAM (not onboard GPU RAM) helps if you do a larger sim, but I dont
> know performance wise, the onboard GPU, the more RAM the marrier...so yes,
> normal work stations you can get 4 GPU's for a 300 US$ board, but then the
> price goes way up (3-4000 US$ for an 8-10 gpu board). RAM ordered abroad
> is also cheep, 8 or 16 MB Vs. Shop...I have used 4 GPU's but only on tests
> software, not Gromacs, so would be nice to see performance...for a small
> 100 atom molecule and 500 solvent, using just the CPU I get it to run 5-10
> minutes real for 1 ns sim, but tried simple large 800 amino, 25,000
> solvent eq (NVT or NPT) runs and they clock at around 1 hour real for say
> 50 ps eq's....
>
> Stephan
>
> Gesendet: Samstag, 25. Mai 2013 um 07:54 Uhr
> Von: "James Starlight" <jmsstarli...@gmail.com<mailto:
> jmsstarli...@gmail.com>>
> An: "Discussion list for GROMACS users" <gmx-users@gromacs.org<mailto:
> gmx-users@gromacs.org>>
> Betreff: Re: [gmx-users] GPU-based workstation
> Dear Dr. Watkins!
>
> Thank you for the suggestions!
>
> In the local shops I've found only Core i7 with 6 cores (like Core
> i7-39xx) and 4 cores. Should I obtain much better performance with 6 cores
> than with 4 cores in case of i7 cpu (assuming that I run simulation in
> cpu+gpu mode )?
>
> Also you've mentioned about 4 PCeI MD. Does it means that modern
> work-station could have 4 GPU's in one home-like desktop ? According to my
> current task I suppose that 2 GPU's would be suitable for my simulations
> (assuming that I use typical ASUS MB and 650 Watt power unit). Have
> someone tried to use several GPU's on one workstation ? What attributes of
> MB should be taken into account for best performance on such multi-gpu
> station ?
>
> James
>
> 2013/5/25 lloyd riggs <lloyd.ri...@gmx.ch<mailto:lloyd.ri...@gmx.ch>>
>
> > There's also these, but 1 chip runs 6K US, they can get performance up to
> > 2.3 teraflops per chip though double percission...but have no clue about
> > integration with GPU's...Intell also sells their chips on PCIe
> cards...but
> > get only about 350 Gflops, and run 1K US$.
> >
> > http://en.wikipedia.org/wiki/Field-programmable_gate_array and vendor
> > http://www.xilinx.com/
> >
> > They can design them though to fit a PCIe slot and run about the same,
> but
> > still need the board, ram etc...
> >
> > Mostly just to dream about, they say you can order them with radiation
> > shielding as well...so...
> >
> > Stephan Watkins
> >
> > *Gesendet:* Freitag, 24. Mai 2013 um 13:17 Uhr
> > *Von:* "James Starlight" <jmsstarli...@gmail.com<mailto:
> jmsstarli...@gmail.com>>
> > *An:* "Discussion list for GROMACS users" <gmx-users@gromacs.org<mailto:
> gmx-users@gromacs.org>>
> > *Betreff:* [gmx-users] GPU-based workstation
> > Dear Gromacs Users!
> >
> >
> > I'd like to build new workstation for performing simulation on GPU with
> > Gromacs 4.6 native cuda support.
> > Recently I've used such setup with Core i5 cpu and nvidia 670 GTX video
> > and obtain good performance ( ~ 20 ns\day for typical 60.000 atom system
> > with SD integrator)
> >
> >
> > Now I'd like to build multi-gpu wokstation.
> >
> > My question - How much GPU would give me best performance on the typical
> > home-like workstation. What algorithm of Ncidia GPU integration should I
> > use (e.g SLI etc) ?
> >
> >
> > Thanks for help,
> >
> >
> > James
> > --
> > gmx-users mailing list gmx-users@gromacs.org<mailto:
> gmx-users@gromacs.org>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org<mailto:
> gmx-users-requ...@gromacs.org>.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > --
> > gmx-users mailing list gmx-users@gromacs.org<mailto:
> gmx-users@gromacs.org>
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-requ...@gromacs.org<mailto:
> gmx-users-requ...@gromacs.org>.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> --
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> * Please search the archive at
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