Re: [gmx-users] Xeon Gold + RTX 5000

[Moir, Michael (MMoir)]

Alex,
The motherboard I am using with the 9900K is the ASUS WS Z390 PRO.  The PRO 
version has the extra PCIe controller.  I am using two RTX 1070ti GPUs, and I 
can hear everyone snorting with derision, but with this configuration I get 
performance with 100,000 atoms of about 72 ns/day with 2019.1 which is adequate 
for my needs.  I’ll upgrade to the 2080ti when the price drops to <$1000. 
Another tip is to get the highest speed memory that the motherboard will 
handle.  It doesn’t make a huge difference, maybe 2-3% over the cheapest memory 
but it is something that is easy and low cost to do.

Mike

Sent from my iPhone

> On Jul 17, 2019, at 11:16 AM, Alex  wrote:
>
> Gentlemen, thank you both!
>
> Michael, would you be able to suggest a specific motherboard that removes the 
> bottleneck? We aren't really limited by price in this case and would prefer 
> to get every bit of benefit out of the processing components, if possible.
>
> Thanks,
>
> Alex
>
>> On 7/17/2019 10:44 AM, Moir, Michael (MMoir) wrote:
>> This is not quite true.  I certainly observed this degradation in 
>> performance using the 9900K with two GPUs as Szilárd states using a 
>> motherboard with one PCIe controller, but the limitation is from the 
>> motherboard not from the CPU.  It is possible to obtain a motherboard that 
>> contains two PCIe controllers which overcomes this obstacle for not a whole 
>> lot more money.
>>
>> Mike
>>
>> -Original Message-
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>>  On Behalf Of Szilárd Páll
>> Sent: Wednesday, July 17, 2019 8:14 AM
>> To: Discussion list for GROMACS users 
>> Subject: [**EXTERNAL**] Re: [gmx-users] Xeon Gold + RTX 5000
>>
>> Hi Alex,
>>
>> I've not had a chance to test the new 3rd gen Ryzen CPUs, but all
>> public benchmarks out there point to the fact that they are a major
>> improvement over the previous generation Ryzen -- which were already
>> quite competitive for GPU-accelerated GROMACS runs compared to Intel,
>> especially in perf/price.
>>
>> One caveat for dual-GPU setups on the i9 9900 or the Ryzen 3900X is
>> that they don't have enough PCI lanes for peak CPU-GPU transfer (x8
>> for both of the GPUs) which will lead to a slightly less performance
>> (I'd estimate <5-10%) in particular compared to i) having a single GPU
>> plugged in into the machine ii) compare to CPUs like Threadripper or
>> the i9 79xx series processors which have more PCIe lanes.
>>
>> However, if throughput is the goal, the ideal use-case especially for
>> small simulation systems like <=50k atoms is to run e.g. 2 runs / GPU,
>> hence 4 runs on a 2-GPU system case in which the impact of the
>> aforementioned limitation will be further decreased.
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>>> On Tue, Jul 16, 2019 at 7:18 PM Alex  wrote:
>>> That is excellent information, thank you. None of us have dealt with AMD
>>> CPUs in a while, so would the combination of a Ryzen 3900X and two
>>> Quadro 2080 Ti be a good choice?
>>>
>>> Again, thanks!
>>>
>>> Alex
>>>
>>>
>>>> On 7/16/2019 8:41 AM, Szilárd Páll wrote:
>>>> Hi Alex,
>>>>
>>>>> On Mon, Jul 15, 2019 at 8:53 PM Alex  wrote:
>>>>> Hi all and especially Szilard!
>>>>>
>>>>> My glorious management asked me to post this here. One of our group
>>>>> members, an ex-NAMD guy, wants to use Gromacs for biophysics and the
>>>>> following basics have been spec'ed for him:
>>>>>
>>>>> CPU: Xeon Gold 6244
>>>>> GPU: RTX 5000 or 6000
>>>>>
>>>>> I'll be surprised if he runs systems with more than 50K particles. Could
>>>>> you please comment on whether this is a cost-efficient and reasonably
>>>>> powerful setup? Your past suggestions have been invaluable for us.
>>>> That will be reasonably fast, but cost efficiency will be awful, to be 
>>>> honest:
>>>> - that CPU is a ~$3000 part and won't perform much better than a
>>>> $4-500 desktop CPU like an i9 9900, let alone a Ryzen 3900X which
>>>> would be significantly faster.
>>>> - Quadro cards also pretty low in bang for buck: a 2080 Ti will be
>>>> close to the RTX 6000 for ~5x less and the 2080 or 2070 Super a bit
>>>> slower for at least another 1.5x less.
>>>>
>>>> Single run at a time or possibly multiple? The proposed (or any 8+
>>>&

Re: [gmx-users] Xeon Gold + RTX 5000

[Moir, Michael (MMoir)]

Certainly.  When I get home this evening I will post the information.

Mike

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Alex
Sent: Wednesday, July 17, 2019 11:16 AM
To: gmx-us...@gromacs.org
Subject: [**EXTERNAL**] Re: [gmx-users] Xeon Gold + RTX 5000

Gentlemen, thank you both!

Michael, would you be able to suggest a specific motherboard that
removes the bottleneck? We aren't really limited by price in this case
and would prefer to get every bit of benefit out of the processing
components, if possible.

Thanks,

Alex

On 7/17/2019 10:44 AM, Moir, Michael (MMoir) wrote:
> This is not quite true.  I certainly observed this degradation in performance 
> using the 9900K with two GPUs as Szilárd states using a motherboard with one 
> PCIe controller, but the limitation is from the motherboard not from the CPU. 
>  It is possible to obtain a motherboard that contains two PCIe controllers 
> which overcomes this obstacle for not a whole lot more money.
>
> Mike
>
> -Original Message-
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
>  On Behalf Of Szilárd Páll
> Sent: Wednesday, July 17, 2019 8:14 AM
> To: Discussion list for GROMACS users 
> Subject: [**EXTERNAL**] Re: [gmx-users] Xeon Gold + RTX 5000
>
> Hi Alex,
>
> I've not had a chance to test the new 3rd gen Ryzen CPUs, but all
> public benchmarks out there point to the fact that they are a major
> improvement over the previous generation Ryzen -- which were already
> quite competitive for GPU-accelerated GROMACS runs compared to Intel,
> especially in perf/price.
>
> One caveat for dual-GPU setups on the i9 9900 or the Ryzen 3900X is
> that they don't have enough PCI lanes for peak CPU-GPU transfer (x8
> for both of the GPUs) which will lead to a slightly less performance
> (I'd estimate <5-10%) in particular compared to i) having a single GPU
> plugged in into the machine ii) compare to CPUs like Threadripper or
> the i9 79xx series processors which have more PCIe lanes.
>
> However, if throughput is the goal, the ideal use-case especially for
> small simulation systems like <=50k atoms is to run e.g. 2 runs / GPU,
> hence 4 runs on a 2-GPU system case in which the impact of the
> aforementioned limitation will be further decreased.
>
> Cheers,
> --
> Szilárd
>
>
> On Tue, Jul 16, 2019 at 7:18 PM Alex  wrote:
>> That is excellent information, thank you. None of us have dealt with AMD
>> CPUs in a while, so would the combination of a Ryzen 3900X and two
>> Quadro 2080 Ti be a good choice?
>>
>> Again, thanks!
>>
>> Alex
>>
>>
>> On 7/16/2019 8:41 AM, Szilárd Páll wrote:
>>> Hi Alex,
>>>
>>> On Mon, Jul 15, 2019 at 8:53 PM Alex  wrote:
>>>> Hi all and especially Szilard!
>>>>
>>>> My glorious management asked me to post this here. One of our group
>>>> members, an ex-NAMD guy, wants to use Gromacs for biophysics and the
>>>> following basics have been spec'ed for him:
>>>>
>>>> CPU: Xeon Gold 6244
>>>> GPU: RTX 5000 or 6000
>>>>
>>>> I'll be surprised if he runs systems with more than 50K particles. Could
>>>> you please comment on whether this is a cost-efficient and reasonably
>>>> powerful setup? Your past suggestions have been invaluable for us.
>>> That will be reasonably fast, but cost efficiency will be awful, to be 
>>> honest:
>>> - that CPU is a ~$3000 part and won't perform much better than a
>>> $4-500 desktop CPU like an i9 9900, let alone a Ryzen 3900X which
>>> would be significantly faster.
>>> - Quadro cards also pretty low in bang for buck: a 2080 Ti will be
>>> close to the RTX 6000 for ~5x less and the 2080 or 2070 Super a bit
>>> slower for at least another 1.5x less.
>>>
>>> Single run at a time or possibly multiple? The proposed (or any 8+
>>> core) workstation CPU is fast enough in the majority of the
>>> simulations to pair well with two of those GPUs if used for two
>>> concurrent simulations. If that's a relevant use-case, I'd recommend
>>> two 2070 Super or 2080 cards.
>>>
>>> Cheers,
>>> --
>>> Szilárd
>>>
>>>
>>>> Thank you,
>>>>
>>>> Alex
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at 
>>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>>>
>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>
>>>&

Re: [gmx-users] Xeon Gold + RTX 5000

[Moir, Michael (MMoir)]

This is not quite true.  I certainly observed this degradation in performance 
using the 9900K with two GPUs as Szilárd states using a motherboard with one 
PCIe controller, but the limitation is from the motherboard not from the CPU.  
It is possible to obtain a motherboard that contains two PCIe controllers which 
overcomes this obstacle for not a whole lot more money.

Mike

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Szilárd Páll
Sent: Wednesday, July 17, 2019 8:14 AM
To: Discussion list for GROMACS users 
Subject: [**EXTERNAL**] Re: [gmx-users] Xeon Gold + RTX 5000

Hi Alex,

I've not had a chance to test the new 3rd gen Ryzen CPUs, but all
public benchmarks out there point to the fact that they are a major
improvement over the previous generation Ryzen -- which were already
quite competitive for GPU-accelerated GROMACS runs compared to Intel,
especially in perf/price.

One caveat for dual-GPU setups on the i9 9900 or the Ryzen 3900X is
that they don't have enough PCI lanes for peak CPU-GPU transfer (x8
for both of the GPUs) which will lead to a slightly less performance
(I'd estimate <5-10%) in particular compared to i) having a single GPU
plugged in into the machine ii) compare to CPUs like Threadripper or
the i9 79xx series processors which have more PCIe lanes.

However, if throughput is the goal, the ideal use-case especially for
small simulation systems like <=50k atoms is to run e.g. 2 runs / GPU,
hence 4 runs on a 2-GPU system case in which the impact of the
aforementioned limitation will be further decreased.

Cheers,
--
Szilárd


On Tue, Jul 16, 2019 at 7:18 PM Alex  wrote:
>
> That is excellent information, thank you. None of us have dealt with AMD
> CPUs in a while, so would the combination of a Ryzen 3900X and two
> Quadro 2080 Ti be a good choice?
>
> Again, thanks!
>
> Alex
>
>
> On 7/16/2019 8:41 AM, Szilárd Páll wrote:
> > Hi Alex,
> >
> > On Mon, Jul 15, 2019 at 8:53 PM Alex  wrote:
> >> Hi all and especially Szilard!
> >>
> >> My glorious management asked me to post this here. One of our group
> >> members, an ex-NAMD guy, wants to use Gromacs for biophysics and the
> >> following basics have been spec'ed for him:
> >>
> >> CPU: Xeon Gold 6244
> >> GPU: RTX 5000 or 6000
> >>
> >> I'll be surprised if he runs systems with more than 50K particles. Could
> >> you please comment on whether this is a cost-efficient and reasonably
> >> powerful setup? Your past suggestions have been invaluable for us.
> > That will be reasonably fast, but cost efficiency will be awful, to be 
> > honest:
> > - that CPU is a ~$3000 part and won't perform much better than a
> > $4-500 desktop CPU like an i9 9900, let alone a Ryzen 3900X which
> > would be significantly faster.
> > - Quadro cards also pretty low in bang for buck: a 2080 Ti will be
> > close to the RTX 6000 for ~5x less and the 2080 or 2070 Super a bit
> > slower for at least another 1.5x less.
> >
> > Single run at a time or possibly multiple? The proposed (or any 8+
> > core) workstation CPU is fast enough in the majority of the
> > simulations to pair well with two of those GPUs if used for two
> > concurrent simulations. If that's a relevant use-case, I'd recommend
> > two 2070 Super or 2080 cards.
> >
> > Cheers,
> > --
> > Szilárd
> >
> >
> >> Thank you,
> >>
> >> Alex
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at 
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> >>
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> >> a mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Simulation is very slow

[Moir, Michael (MMoir)]

Did you remember to use the -DGMX_GPU =ON CMake option when you built the new 
version?

Mike Moir

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of ???
Sent: Thursday, March 14, 2019 8:56 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [**EXTERNAL**] [gmx-users] Simulation is very slow

Dear gromacs users,

I installed gromacs 2019 today. When I run gromacs, it is really slow. I
don't know the reason. I am using GTX 1080 TI and TITAN XP for GPU and I
have 8 cores. Please help me.

Sincerely

-- 

Yeongkyu Lee

M.S student

Department of Physics

501, Jinjudaero, Jinju, Gyeongnam
,
52828, Korea

Email: monsterpl...@gmail.com

Phone: +82-10-8771-2190
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Re: [gmx-users] info about gpus

[Moir, Michael (MMoir)]

Sorry, that's 32 GB of RAM.  I'm old, a MB used to be a lot of memory!

Mike

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Moir, Michael 
(MMoir)
Sent: Thursday, January 31, 2019 6:29 PM
To: 'gmx-us...@gromacs.org' 
Subject: [**EXTERNAL**] Re: [gmx-users] info about gpus

Stephano,

With a motherboard that doesn't split the PCI-E bandwidth, I get a 20% 
improvement in computation speed with 2 GPUs.  Whether or not you think this is 
worth the extra $, I leave that up to you!  My system is:  i9-9900K, ASUS WS 
Z390 Pro motherboard, 2x 1070ti GPUs, 32 MB 3200 MHz RAM.  With my modest 
system of about 100,000 atoms, I go from 30 ns/day with 1 GPU, to 36 ns/day 
with 2 GPUs.  -ntmpi 4 -npme 1 -pme gpu -nb gpu, all other combinations of 
-ntmpi give inferior results with 2 GPUs compared to 1 GPU.  I am using 
Gromacs-2019.  It is also important to use the fastest memory you want to 
afford.  The amount of memory is not important but the speed is.

Mike

-Original Message-
From: Moir, Michael (MMoir) 
Sent: Thursday, January 31, 2019 9:44 AM
To: gmx-us...@gromacs.org
Subject: RE: [**EXTERNAL**] [gmx-users] info about gpus

Stefano,
I'm investigating that myself.  If your motherboard splits the bandwidth 
between your PCI-E slots then there is no advantage to having 2 GPUs for a GPU 
like the 1080.  I have just upgraded to a better motherboard that does not 
split the  bandwidth but I am not finished my testing.  Going to the 2080 
offers a 40% increase in speed over the 1080 in terms of raw computing power 
but it is unclear that it is worth the extra $.
Mike

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Stefano 
Guglielmo
Sent: Thursday, January 31, 2019 9:14 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [**EXTERNAL**] [gmx-users] info about gpus

 Dear all,
I am tryin to set a new workstation and I would like to know if there is a
significant improvement in performance with two gpus (gtx 1080 ti or rtx
2080) rather than just one, and eventually with which cpu/ram requisite.

Thanks in advance for any advice and suggestions
Stefano

-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178


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Re: [gmx-users] info about gpus

[Moir, Michael (MMoir)]

Stephano,

With a motherboard that doesn't split the PCI-E bandwidth, I get a 20% 
improvement in computation speed with 2 GPUs.  Whether or not you think this is 
worth the extra $, I leave that up to you!  My system is:  i9-9900K, ASUS WS 
Z390 Pro motherboard, 2x 1070ti GPUs, 32 MB 3200 MHz RAM.  With my modest 
system of about 100,000 atoms, I go from 30 ns/day with 1 GPU, to 36 ns/day 
with 2 GPUs.  -ntmpi 4 -npme 1 -pme gpu -nb gpu, all other combinations of 
-ntmpi give inferior results with 2 GPUs compared to 1 GPU.  I am using 
Gromacs-2019.  It is also important to use the fastest memory you want to 
afford.  The amount of memory is not important but the speed is.

Mike

-Original Message-
From: Moir, Michael (MMoir) 
Sent: Thursday, January 31, 2019 9:44 AM
To: gmx-us...@gromacs.org
Subject: RE: [**EXTERNAL**] [gmx-users] info about gpus

Stefano,
I'm investigating that myself.  If your motherboard splits the bandwidth 
between your PCI-E slots then there is no advantage to having 2 GPUs for a GPU 
like the 1080.  I have just upgraded to a better motherboard that does not 
split the  bandwidth but I am not finished my testing.  Going to the 2080 
offers a 40% increase in speed over the 1080 in terms of raw computing power 
but it is unclear that it is worth the extra $.
Mike

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Stefano 
Guglielmo
Sent: Thursday, January 31, 2019 9:14 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [**EXTERNAL**] [gmx-users] info about gpus

 Dear all,
I am tryin to set a new workstation and I would like to know if there is a
significant improvement in performance with two gpus (gtx 1080 ti or rtx
2080) rather than just one, and eventually with which cpu/ram requisite.

Thanks in advance for any advice and suggestions
Stefano

-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178


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Re: [gmx-users] info about gpus

[Moir, Michael (MMoir)]

Stefano,
I'm investigating that myself.  If your motherboard splits the bandwidth 
between your PCI-E slots then there is no advantage to having 2 GPUs for a GPU 
like the 1080.  I have just upgraded to a better motherboard that does not 
split the  bandwidth but I am not finished my testing.  Going to the 2080 
offers a 40% increase in speed over the 1080 in terms of raw computing power 
but it is unclear that it is worth the extra $.
Mike

-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
 On Behalf Of Stefano 
Guglielmo
Sent: Thursday, January 31, 2019 9:14 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [**EXTERNAL**] [gmx-users] info about gpus

 Dear all,
I am tryin to set a new workstation and I would like to know if there is a
significant improvement in performance with two gpus (gtx 1080 ti or rtx
2080) rather than just one, and eventually with which cpu/ram requisite.

Thanks in advance for any advice and suggestions
Stefano

-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178



Mail
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[gmx-users] Clustsize and -mol option

[Moir, Michael (MMoir)]

Although I have successfully used clustsize for identifying clusters of atoms, 
I am stymied by the -mol option for evaluating clusters of  molecules.  A 
command such as:

gmx clustsize -s system1.tpr -f system1.xtc -nc -n index.ndx

Works fine for obtaining information about clusters of atoms, but:

gmx clustsize -s system1.tpr -f system1.xtc -nc -n index.ndx -mol

gives a fatal error in Source file: src/gromacs/fileio/matio.cpp (line 681)

My index file consists of the list of atoms under headings like [HP6].

Any thoughts?

Mike Moir
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