Re: [gmx-users] GPU load from nvidia-smi

2018-02-09 Thread Szilárd Páll 
On Thu, Feb 8, 2018 at 10:20 PM, Mark Abraham 
wrote:

> Hi,
>
> On Thu, Feb 8, 2018 at 8:50 PM Alex  wrote:
>
> > Got it, thanks. Even with the old style input I now have a 42% speed up
> > with PME on GPU. How, how can I express my enormous gratitude?!
> >
>
> Do the science, cite the papers, spread the word, help others, make quality
> bug reports :-) Glad you like it!
>

A few more things to add: participate in the community! E.g.

- help us with early testing (e.g. when we release a beta or release
candidate we generally get extremely limited interest in testing which
would help in ironing out issues early before the actual release)

- give us feedback what works and what does not work so well; it's easy for
developers to be biased by their own or their most vocally complaining
close fried's personal preferences (for features, user interface, command
line function, etc.)

- share your knowledge on the mailing list

Cheers,
--
Szilárd


>
> Mark
>
> On Thu, Feb 8, 2018 at 12:44 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Yes. Note the new use of -gputasks. And perhaps check out
> > > http://manual.gromacs.org/documentation/2018-latest/
> > > user-guide/mdrun-performance.html#types-of-gpu-tasks
> > > because
> > > things are now different.
> > >
> > > gmx mdrun -ntmpi 3 -npme 1 -nb gpu -pme gpu is more like what you want.
> > >
> > > Mark
> > >
> > > On Thu, Feb 8, 2018 at 8:36 PM Alex  wrote:
> > >
> > > > I think this should be a separate question, given all the recent mess
> > > with
> > > > the utils tests...
> > > >
> > > > I am testing mdrun (v 2018) on a system that's trivial and close to
> a 5
> > > x 5
> > > > x 5 box filled with water and some ions. We have three GPUs and the
> run
> > > is
> > > > with -nt 18 -gpu_id 012 -pme -gpu.
> > > >
> > > > nvidia-smi reports 65% load on 0 and nothing on 1 and 2. Is this
> > normal?
> > > >
> > > > Thanks,
> > > >
> > > > 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
> > > >
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> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
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Re: [gmx-users] GPU load from nvidia-smi

2018-02-08 Thread Alex 
>
> Do the science, cite the papers, spread the word, help others, make quality
> bug reports :-) Glad you like it!
>
>
>
Oh,  I do all of that (except maybe for bug reports), but when people read
my papers, they say "that is a VERY unusual use of Gromacs -- go learn
LAMMPS." So yes, I love GMX to the point of using it for stuff it was never
intended to do. I also hope you'll forgive the fact that my postdoc is
using LAMMPS. ;)

With the input keys you suggested, we are at almost 400 ns/day, compared
with 270 with the earlier version -- and that is close to a 50% boost from
-pme gpu. A colleague just walked in and I shared the bottom of that
md.log. Expletives of awe and admiration were loudly exchanged. We're doing
the upgrade for my 8-year old desktop-turned-linux-box with a single puny
GTX 960 -- just because it would be dumb not to.

Hats off to you guys, very well done.

Alex

On Thu, Feb 8, 2018 at 12:44 PM, Mark Abraham 
> > wrote:
> >
> > > Hi,
> > >
> > > Yes. Note the new use of -gputasks. And perhaps check out
> > > http://manual.gromacs.org/documentation/2018-latest/
> > > user-guide/mdrun-performance.html#types-of-gpu-tasks
> > > because
> > > things are now different.
> > >
> > > gmx mdrun -ntmpi 3 -npme 1 -nb gpu -pme gpu is more like what you want.
> > >
> > > Mark
> > >
> > > On Thu, Feb 8, 2018 at 8:36 PM Alex  wrote:
> > >
> > > > I think this should be a separate question, given all the recent mess
> > > with
> > > > the utils tests...
> > > >
> > > > I am testing mdrun (v 2018) on a system that's trivial and close to
> a 5
> > > x 5
> > > > x 5 box filled with water and some ions. We have three GPUs and the
> run
> > > is
> > > > with -nt 18 -gpu_id 012 -pme -gpu.
> > > >
> > > > nvidia-smi reports 65% load on 0 and nothing on 1 and 2. Is this
> > normal?
> > > >
> > > > Thanks,
> > > >
> > > > 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
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > > send a mail to gmx-users-requ...@gromacs.org.
> > > >
> > > --
> > > Gromacs Users mailing list
> > >
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> > > Support/Mailing_Lists/GMX-Users_List before posting!
> > >
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> > >
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Re: [gmx-users] GPU load from nvidia-smi

2018-02-08 Thread Mark Abraham 
Hi,

On Thu, Feb 8, 2018 at 9:11 PM Alex  wrote:

> Mark, a question about the input parameters you suggested:
>
> >  gmx mdrun -ntmpi 3 -npme 1 -nb gpu -pme gpu
>
> Where does this specify on which GPUs we're running? Or is this in addition
> -gpu_id key?
>

It's rather different now. -gputasks is a thing, see the link I posted.


> Also, I thought that -ntmpi was by default set to the number of GPUs in the
> system -- is this no longer a correct assumption?
>

Yes, per link. The old form doesn't work with more complex potential task
layouts. Formally -gpu_id mapped a pp task to a GPU, so stuff has to get
more complex if there's more than one type of task mappable to a GPU.

Mark


> Thanks,
>
> Alex
>
> On Thu, Feb 8, 2018 at 12:44 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Yes. Note the new use of -gputasks. And perhaps check out
> > http://manual.gromacs.org/documentation/2018-latest/
> > user-guide/mdrun-performance.html#types-of-gpu-tasks
> > because
> > things are now different.
> >
> > gmx mdrun -ntmpi 3 -npme 1 -nb gpu -pme gpu is more like what you want.
> >
> > Mark
> >
> > On Thu, Feb 8, 2018 at 8:36 PM Alex  wrote:
> >
> > > I think this should be a separate question, given all the recent mess
> > with
> > > the utils tests...
> > >
> > > I am testing mdrun (v 2018) on a system that's trivial and close to a 5
> > x 5
> > > x 5 box filled with water and some ions. We have three GPUs and the run
> > is
> > > with -nt 18 -gpu_id 012 -pme -gpu.
> > >
> > > nvidia-smi reports 65% load on 0 and nothing on 1 and 2. Is this
> normal?
> > >
> > > Thanks,
> > >
> > > 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
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > 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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> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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Re: [gmx-users] GPU load from nvidia-smi

2018-02-08 Thread Mark Abraham 
Hi,

On Thu, Feb 8, 2018 at 8:50 PM Alex  wrote:

> Got it, thanks. Even with the old style input I now have a 42% speed up
> with PME on GPU. How, how can I express my enormous gratitude?!
>

Do the science, cite the papers, spread the word, help others, make quality
bug reports :-) Glad you like it!

Mark

On Thu, Feb 8, 2018 at 12:44 PM, Mark Abraham 
> wrote:
>
> > Hi,
> >
> > Yes. Note the new use of -gputasks. And perhaps check out
> > http://manual.gromacs.org/documentation/2018-latest/
> > user-guide/mdrun-performance.html#types-of-gpu-tasks
> > because
> > things are now different.
> >
> > gmx mdrun -ntmpi 3 -npme 1 -nb gpu -pme gpu is more like what you want.
> >
> > Mark
> >
> > On Thu, Feb 8, 2018 at 8:36 PM Alex  wrote:
> >
> > > I think this should be a separate question, given all the recent mess
> > with
> > > the utils tests...
> > >
> > > I am testing mdrun (v 2018) on a system that's trivial and close to a 5
> > x 5
> > > x 5 box filled with water and some ions. We have three GPUs and the run
> > is
> > > with -nt 18 -gpu_id 012 -pme -gpu.
> > >
> > > nvidia-smi reports 65% load on 0 and nothing on 1 and 2. Is this
> normal?
> > >
> > > Thanks,
> > >
> > > 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
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-requ...@gromacs.org.
> > >
> > --
> > 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
> >
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> > send a mail to gmx-users-requ...@gromacs.org.
> >
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>
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Re: [gmx-users] GPU load from nvidia-smi

2018-02-08 Thread Alex 
Mark, a question about the input parameters you suggested:

>  gmx mdrun -ntmpi 3 -npme 1 -nb gpu -pme gpu

Where does this specify on which GPUs we're running? Or is this in addition
-gpu_id key?
Also, I thought that -ntmpi was by default set to the number of GPUs in the
system -- is this no longer a correct assumption?

Thanks,

Alex

On Thu, Feb 8, 2018 at 12:44 PM, Mark Abraham 
wrote:

> Hi,
>
> Yes. Note the new use of -gputasks. And perhaps check out
> http://manual.gromacs.org/documentation/2018-latest/
> user-guide/mdrun-performance.html#types-of-gpu-tasks
> because
> things are now different.
>
> gmx mdrun -ntmpi 3 -npme 1 -nb gpu -pme gpu is more like what you want.
>
> Mark
>
> On Thu, Feb 8, 2018 at 8:36 PM Alex  wrote:
>
> > I think this should be a separate question, given all the recent mess
> with
> > the utils tests...
> >
> > I am testing mdrun (v 2018) on a system that's trivial and close to a 5
> x 5
> > x 5 box filled with water and some ions. We have three GPUs and the run
> is
> > with -nt 18 -gpu_id 012 -pme -gpu.
> >
> > nvidia-smi reports 65% load on 0 and nothing on 1 and 2. Is this normal?
> >
> > Thanks,
> >
> > 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
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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>
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>
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>
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Re: [gmx-users] GPU load from nvidia-smi

2018-02-08 Thread Alex 
Got it, thanks. Even with the old style input I now have a 42% speed up
with PME on GPU. How, how can I express my enormous gratitude?!

On Thu, Feb 8, 2018 at 12:44 PM, Mark Abraham 
wrote:

> Hi,
>
> Yes. Note the new use of -gputasks. And perhaps check out
> http://manual.gromacs.org/documentation/2018-latest/
> user-guide/mdrun-performance.html#types-of-gpu-tasks
> because
> things are now different.
>
> gmx mdrun -ntmpi 3 -npme 1 -nb gpu -pme gpu is more like what you want.
>
> Mark
>
> On Thu, Feb 8, 2018 at 8:36 PM Alex  wrote:
>
> > I think this should be a separate question, given all the recent mess
> with
> > the utils tests...
> >
> > I am testing mdrun (v 2018) on a system that's trivial and close to a 5
> x 5
> > x 5 box filled with water and some ions. We have three GPUs and the run
> is
> > with -nt 18 -gpu_id 012 -pme -gpu.
> >
> > nvidia-smi reports 65% load on 0 and nothing on 1 and 2. Is this normal?
> >
> > Thanks,
> >
> > 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
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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>
> * Please search the archive at http://www.gromacs.org/
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