Re: 转发：[gmx-users] gromacs on GPU

[Mark Abraham]

On Sun, Jun 23, 2013 at 3:30 PM,   wrote:
> Dear gromcas users,
>
>  Can anyone tell me how to make a mdp file for gromacs mdrun on NVIDIA GPU 
> card, the following is a mdp file which runs well on cpu, but when I add the 
> option "-testverlet" to mdrun in order to run it on GPU, it returns error 
> "Fatal error:User non-bonded potentials are not (yet) supported with the 
> Verlet schemeFor more information and tips for troubleshooting".

Thanks, I can now use a copy-paste to see that this message should not
be generated by your .mdp file below. I have filed a bug report
http://redmine.gromacs.org/issues/1289. In the meantime, I suggest you
use normal PME. FYI, there is an ongoing debate elsewhere on Redmine
that PME-Switch might be a bad idea anyway...

Next time you post an .mdp file please make the line wrapping readable.

Mark

> Could you check the mdp file for me to see how to modefy it to make it 
> suitable to GPU? Thanks in advance!
> integrator = mdnsteps = 5000dt = 0.002constraints = all-bondsnstcomm = 
> 100ns_type = gridrlist = 1.2rcoulomb = 1.0 rcoulomb-switch = 0.9 rvdw 
> =1.0vdwtype = shiftrvdw-switch = 0.9coulombtype = PME-Switch;Tcoupl = 
> v-rescaletau_t = 0.1 0.1tc-grps = protein non-proteinref_t = 300 300Pcoupl = 
> parrinello-rahmanPcoupltype = isotropictau_p = 0.5compressibility = 
> 4.5e-5ref_p = 1.0gen_vel = nogen_temp = 310gen_seed = -1nstxout = 
> 500nstenergy = 100energygrps = chA chClincs-iter = 2DispCorr = 
> EnerPresoptimize_fft = yes
>  Yeping Sun
> --
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转发：[gmx-users] gromacs on GPU

[sunyeping]

Dear gromcas users,
 
 Can anyone tell me how to make a mdp file for gromacs mdrun on NVIDIA GPU 
card, the following is a mdp file which runs well on cpu, but when I add the 
option "-testverlet" to mdrun in order to run it on GPU, it returns error 
"Fatal error:User non-bonded potentials are not (yet) supported with the Verlet 
schemeFor more information and tips for troubleshooting". Could you check the 
mdp file for me to see how to modefy it to make it suitable to GPU? Thanks in 
advance! 
integrator = mdnsteps = 5000dt = 0.002constraints = all-bondsnstcomm = 
100ns_type = gridrlist = 1.2rcoulomb = 1.0 rcoulomb-switch = 0.9 rvdw 
=1.0vdwtype = shiftrvdw-switch = 0.9coulombtype = PME-Switch;Tcoupl = 
v-rescaletau_t = 0.1 0.1tc-grps = protein non-proteinref_t = 300 300Pcoupl = 
parrinello-rahmanPcoupltype = isotropictau_p = 0.5compressibility = 4.5e-5ref_p 
= 1.0gen_vel = nogen_temp = 310gen_seed = -1nstxout = 500nstenergy = 
100energygrps = chA chClincs-iter = 2DispCorr = EnerPresoptimize_fft = yes
 Yeping Sun 
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Re: [gmx-users] gromacs on GPU

[Mark Abraham]

On Fri, Jun 21, 2013 at 8:33 AM,   wrote:
>  Can anyone tell me how to make a mdp file for gromacs mdrun on NVIDIA GPU 
> card, the following is a mdp file which runs well on cpu, but when I add the 
> option "-testverlet" to mdrun in order to run it on GPU, it returns error 
> "nonbond potiential is not supported".

Please copy and paste actual error messages, not what you think was
important about it.

-testverlet is not an all-purpose magic bullet, and there are
algorithm combinations that are implemented differently in the group
and verlet schemes. See manual 7.3.10-11

Mark

> Could you check the mdp file for me to see how to modefy it to make it 
> suitable to GPU? Thanks in advance!
>
> integrator = mdnsteps = 5000dt = 0.002constraints = all-bondsnstcomm = 
> 100ns_type = gridrlist = 1.2rcoulomb = 1.0 rcoulomb-switch = 0.9 rvdw 
> =1.0vdwtype = shiftrvdw-switch = 0.9coulombtype = PME-SwitchTcoupl = 
> v-rescaletau_t = 0.1 0.1tc-grps = protein non-proteinref_t = 300 300Pcoupl = 
> parrinello-rahmanPcoupltype = isotropictau_p = 0.5compressibility = 
> 4.5e-5ref_p = 1.0gen_vel = nogen_temp = 310gen_seed = -1nstxout = 
> 1nstenergy = 5000energygrps = chA chClincs-iter = 2DispCorr = 
> EnerPresoptimize_fft = yes
>
>
>  Yeping Sun
>
> --
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> http://lists.gromacs.org/mailman/listinfo/gmx-users
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[gmx-users] gromacs on GPU

[sunyeping]

 Can anyone tell me how to make a mdp file for gromacs mdrun on NVIDIA GPU 
card, the following is a mdp file which runs well on cpu, but when I add the 
option "-testverlet" to mdrun in order to run it on GPU, it returns error 
"nonbond potiential is not supported". Could you check the mdp file for me 
to see how to modefy it to make it suitable to GPU? Thanks in advance!
 
integrator = mdnsteps = 5000dt = 0.002constraints = all-bondsnstcomm = 
100ns_type = gridrlist = 1.2rcoulomb = 1.0 rcoulomb-switch = 0.9 rvdw 
=1.0vdwtype = shiftrvdw-switch = 0.9coulombtype = PME-SwitchTcoupl = 
v-rescaletau_t = 0.1 0.1tc-grps = protein non-proteinref_t = 300 300Pcoupl = 
parrinello-rahmanPcoupltype = isotropictau_p = 0.5compressibility = 4.5e-5ref_p 
= 1.0gen_vel = nogen_temp = 310gen_seed = -1nstxout = 1nstenergy = 
5000energygrps = chA chClincs-iter = 2DispCorr = EnerPresoptimize_fft = yes
 
 
 Yeping Sun
 
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[gmx-users] GROMACS on GPU

[sunyeping]

Dear gromacs users,
 
Can anyone tell me how to make a mdp file for gromacs mdrun on NVIDIA GPU card, 
the following is a mdp file which runs well on cpu, but when I add the option 
"-testverlet" to mdrun in order to run it on GPU, it returns error "nonbond 
potiential is not supported". Could you check the mdp file for me to see 
how to modefy it to make it suitable to GPU? Thanks in advance!
 
Yeping Sun
 
--
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Re: [gmx-users] gromacs on GPU

[James Starlight]

Szilárd,

the regime with 4 cores + cut-offs 0.8 has been best still.

  PID USER  PR  NI  VIRT  RES  SHR S  %CPU %MEMTIME+  COMMAND
 1652 own   20   0 28.4g 135m  33m R 288.8  0.8   4:30.33 mdrun

 Force evaluation time GPU/CPU: 5.257 ms/5.187 ms = 1.013
For optimal performance this ratio should be close to 1!


   Core t (s)   Wall t (s)(%)
   Time:  494.240  171.719  287.8
 (ns/day)(hour/ns)
Performance:   10.0642.385
Finished mdrun on node 0 Fri Jan 11 09:38:38 2013

I've tried to use compination of the different core numbers but
results was the same ( below example with the 2 cores +gpu)
  PID USER  PR  NI  VIRT  RES  SHR S  %CPU %MEMTIME+  COMMAND
 1578 own   20   0 28.3g 163m  33m R 170.7  1.0   1:50.68 mdrun


Also cut-offs lower that 0.8 produced the same results. When I've used
cut-off 0.1 the simulation have been crushed :) Finally increassing of
nstlist up to 50 also gave slightly better results ( cpu usage up to
295) but I'm not sure about influence os such large cutoofs on other
aspects of simulation.

On that tests I'm using cpu CPU Intel Core i5-3570 3.4 ГГц / 4core /
SVGA HD Graphics 2500 / 1+6Мб / as well as GPU GeForce GTX 670.

Also I want to point out that all simulation have been run from debian
GE GNOME desktope. Should I run simulation from console mode only to
kill all hidden cpu-dependent processes?

By the way I wounder to know is it possible to use 2 gpu at the same
time (in the SLI mode) ? How It might increase overasl performance ?
In future I'd like to built new work-station on 8 cores i7 CPU + 2
GPU. What the performance of such work-station will be? ( in
comparison to the typical cluster from several nodes of 8-12 cpu ) ?


Thanks for suggestions,
James

2013/1/11 Szilárd Páll :
> Hi,
>
> On Thu, Jan 10, 2013 at 8:30 PM, James Starlight 
> wrote:
>
>> Szilárd,
>>
>> There are no any others cpu-usage tasks. Below you can see log from the
>> TOP.
>>
>> 26553 own   20   0 28.4g 106m  33m S 285.6  0.7   2263:57 mdrun
>>
>
> This still shows that the average CPU utilization is only 285.6 iso 400 and
> that matches with what mdrun's log shows. Try to run with a very short
> cut-off, one which leads to <=1 GPU/CPU balance (i.e no waiting) and if you
> still don't get 400, something weird is going on.
>
>
>>  1611 root  20   0  171m  65m  24m S   3.0  0.4   7:43.05 Xorg
>> 29647 own   20   0  381m  22m  17m S   3.0  0.1   0:01.77
>> mate-system-mon
>>  2344 own   20   0  358m  17m  11m S   1.3  0.1   0:33.76 mate-terminal
>> 29018 root  20   0 000 S   0.3  0.0   0:04.99 kworker/0:0
>> 29268 root  20   0 000 S   0.3  0.0   0:00.22 kworker/u:2
>> 29705 root  20   0 000 S   0.3  0.0   0:00.03 kworker/3:0
>> 29706 own   20   0 23284 1648 1188 R   0.3  0.0   0:00.05 top
>> 1 root  20   0  8584  872  736 S   0.0  0.0   0:02.34 init
>> 2 root  20   0 000 S   0.0  0.0   0:00.02 kthreadd
>> 3 root  20   0 000 S   0.0  0.0   0:00.57 ksoftirqd/0
>> 6 root  rt   0 000 S   0.0  0.0   0:00.00 migration/0
>> 7 root  rt   0 000 S   0.0  0.0   0:00.17 watchdog/0
>> 8 root  rt   0 000 S   0.0  0.0   0:00.00 migration/1
>>10 root  20   0 000 S   0.0  0.0   0:00.43 ksoftirqd/1
>>12 root  rt   0 000 S   0.0  0.0   0:00.17 watchdog/1
>>13 root  rt   0 000 S   0.0  0.0   0:00.00 migration/2
>>15 root  20   0 000 S   0.0  0.0   0:00.37 ksoftirqd/2
>>16 root  rt   0 000 S   0.0  0.0   0:00.16 watchdog/2
>>17 root  rt   0 000 S   0.0  0.0   0:00.00 migration/3
>>19 root  20   0 000 S   0.0  0.0   0:00.38 ksoftirqd/3
>>20 root  rt   0 000 S   0.0  0.0   0:00.16 watchdog/3
>>21 root   0 -20 000 S   0.0  0.0   0:00.00 cpuset
>>22 root   0 -20 000 S   0.0  0.0   0:00.00 khelper
>>23 root  20   0 000 S   0.0  0.0   0:00.00 kdevtmpfs
>>
>>
>> Usually I run my simulations by means of simple mdrun -v -deffnm md.
>> Should I specify number of cores manually by means of -nt (or -ntmpi)
>>
>
> If you just want to run on the full machine, simply running like that
> should in most cases still be the optimal run configuration or very close
> to the optimal, i.e. in your case:
> mdrun
> <=>
> mdrun -ntmpi 1 -ntomp 4 -gpu_id 0 -pinht
>
>
>> flagg? Also I notice that  -pinht flagg could give me Hyper-Threading
>> support. Does it reasonable in the simulation on cpu+gpu ? What
>>
>
> Correctly using HT is also fully automatic and optimal as long as you are
> using the full machine.
>
>
>> another possible options of md_run should I consider ? Finally is it
>> possible that problems due to openMP (4.7.2) or open-mpi (1.4.5)
>> drivers ?
>>
>
> No,

Re: [gmx-users] gromacs on GPU

[Szilárd Páll]

Hi,

On Thu, Jan 10, 2013 at 8:30 PM, James Starlight wrote:

> Szilárd,
>
> There are no any others cpu-usage tasks. Below you can see log from the
> TOP.
>
> 26553 own   20   0 28.4g 106m  33m S 285.6  0.7   2263:57 mdrun
>

This still shows that the average CPU utilization is only 285.6 iso 400 and
that matches with what mdrun's log shows. Try to run with a very short
cut-off, one which leads to <=1 GPU/CPU balance (i.e no waiting) and if you
still don't get 400, something weird is going on.


>  1611 root  20   0  171m  65m  24m S   3.0  0.4   7:43.05 Xorg
> 29647 own   20   0  381m  22m  17m S   3.0  0.1   0:01.77
> mate-system-mon
>  2344 own   20   0  358m  17m  11m S   1.3  0.1   0:33.76 mate-terminal
> 29018 root  20   0 000 S   0.3  0.0   0:04.99 kworker/0:0
> 29268 root  20   0 000 S   0.3  0.0   0:00.22 kworker/u:2
> 29705 root  20   0 000 S   0.3  0.0   0:00.03 kworker/3:0
> 29706 own   20   0 23284 1648 1188 R   0.3  0.0   0:00.05 top
> 1 root  20   0  8584  872  736 S   0.0  0.0   0:02.34 init
> 2 root  20   0 000 S   0.0  0.0   0:00.02 kthreadd
> 3 root  20   0 000 S   0.0  0.0   0:00.57 ksoftirqd/0
> 6 root  rt   0 000 S   0.0  0.0   0:00.00 migration/0
> 7 root  rt   0 000 S   0.0  0.0   0:00.17 watchdog/0
> 8 root  rt   0 000 S   0.0  0.0   0:00.00 migration/1
>10 root  20   0 000 S   0.0  0.0   0:00.43 ksoftirqd/1
>12 root  rt   0 000 S   0.0  0.0   0:00.17 watchdog/1
>13 root  rt   0 000 S   0.0  0.0   0:00.00 migration/2
>15 root  20   0 000 S   0.0  0.0   0:00.37 ksoftirqd/2
>16 root  rt   0 000 S   0.0  0.0   0:00.16 watchdog/2
>17 root  rt   0 000 S   0.0  0.0   0:00.00 migration/3
>19 root  20   0 000 S   0.0  0.0   0:00.38 ksoftirqd/3
>20 root  rt   0 000 S   0.0  0.0   0:00.16 watchdog/3
>21 root   0 -20 000 S   0.0  0.0   0:00.00 cpuset
>22 root   0 -20 000 S   0.0  0.0   0:00.00 khelper
>23 root  20   0 000 S   0.0  0.0   0:00.00 kdevtmpfs
>
>
> Usually I run my simulations by means of simple mdrun -v -deffnm md.
> Should I specify number of cores manually by means of -nt (or -ntmpi)
>

If you just want to run on the full machine, simply running like that
should in most cases still be the optimal run configuration or very close
to the optimal, i.e. in your case:
mdrun
<=>
mdrun -ntmpi 1 -ntomp 4 -gpu_id 0 -pinht


> flagg? Also I notice that  -pinht flagg could give me Hyper-Threading
> support. Does it reasonable in the simulation on cpu+gpu ? What
>

Correctly using HT is also fully automatic and optimal as long as you are
using the full machine.


> another possible options of md_run should I consider ? Finally is it
> possible that problems due to openMP (4.7.2) or open-mpi (1.4.5)
> drivers ?
>

No, you are using the latest version of compilers which is good. Other than
my earlier suggestions, there isn't much you can do to eliminate the idling
on the CPU (I assume that's what bugs you) - except getting a faster GPU.
Btw, have you tried the hybrid GPU-CPU mode (although I expect it to not be
faster)?

Cheers,
--
Szilárd



>
>
> Thanks for help
>
> James
>
>
> 2013/1/10 Szilárd Páll :
> > On Thu, Jan 10, 2013 at 7:25 AM, James Starlight  >wrote:
> >
> >> Szilárd ,
> >>
> >>  thanks again for explanation!
> >>
> >> Today I've performed some tests on my calmodulin in water system with
> >> different cutt-offs (I've used all cutt-ooffs 1.0 , 0.9 and 0.8
> >> respectually)
> >>
> >> Below you can see that the highest performance was in case of 0.8
> cut-offs
> >>
> >> all cut-offs 1.0
> >>  Force evaluation time GPU/CPU: 6.134 ms/4.700 ms = 1.305
> >>
> >> NOTE: The GPU has >20% more load than the CPU. This imbalance causes
> >>   performance loss, consider using a shorter cut-off and a finer PME
> >> grid.
> >>
> >>
> >>Core t (s)   Wall t (s)(%)
> >>Time: 1313.420  464.035  283.0
> >>  (ns/day)(hour/ns)
> >> Performance:9.3102.578
> >> Finished mdrun on node 0 Thu Jan 10 09:39:23 2013
> >>
> >>
> >> all cut-offs 0.9
> >> Force evaluation time GPU/CPU: 4.951 ms/4.675 ms = 1.059
> >>
> >>Core t (s)   Wall t (s)(%)
> >>Time: 2414.930  856.179  282.1
> >>  (ns/day)(hour/ns)
> >> Performance:   10.0922.378
> >> Finished mdrun on node 0 Thu Jan 10 10:09:52 2013
> >>
> >> all cut-offs 0.8
> >>  Force evaluation time GPU/CPU: 4.001 ms/4.659 ms = 0.859
> >>
> >>Core t (s)   Wall t (s)(%)
> >>Time: 1166.390  413.598  282.0
> >>  (ns/day)(hour/ns)
> >> Performance:   10.44

Re: [gmx-users] gromacs on GPU

[James Starlight]

Szilárd,

There are no any others cpu-usage tasks. Below you can see log from the TOP.

26553 own   20   0 28.4g 106m  33m S 285.6  0.7   2263:57 mdrun
 1611 root  20   0  171m  65m  24m S   3.0  0.4   7:43.05 Xorg
29647 own   20   0  381m  22m  17m S   3.0  0.1   0:01.77 mate-system-mon
 2344 own   20   0  358m  17m  11m S   1.3  0.1   0:33.76 mate-terminal
29018 root  20   0 000 S   0.3  0.0   0:04.99 kworker/0:0
29268 root  20   0 000 S   0.3  0.0   0:00.22 kworker/u:2
29705 root  20   0 000 S   0.3  0.0   0:00.03 kworker/3:0
29706 own   20   0 23284 1648 1188 R   0.3  0.0   0:00.05 top
1 root  20   0  8584  872  736 S   0.0  0.0   0:02.34 init
2 root  20   0 000 S   0.0  0.0   0:00.02 kthreadd
3 root  20   0 000 S   0.0  0.0   0:00.57 ksoftirqd/0
6 root  rt   0 000 S   0.0  0.0   0:00.00 migration/0
7 root  rt   0 000 S   0.0  0.0   0:00.17 watchdog/0
8 root  rt   0 000 S   0.0  0.0   0:00.00 migration/1
   10 root  20   0 000 S   0.0  0.0   0:00.43 ksoftirqd/1
   12 root  rt   0 000 S   0.0  0.0   0:00.17 watchdog/1
   13 root  rt   0 000 S   0.0  0.0   0:00.00 migration/2
   15 root  20   0 000 S   0.0  0.0   0:00.37 ksoftirqd/2
   16 root  rt   0 000 S   0.0  0.0   0:00.16 watchdog/2
   17 root  rt   0 000 S   0.0  0.0   0:00.00 migration/3
   19 root  20   0 000 S   0.0  0.0   0:00.38 ksoftirqd/3
   20 root  rt   0 000 S   0.0  0.0   0:00.16 watchdog/3
   21 root   0 -20 000 S   0.0  0.0   0:00.00 cpuset
   22 root   0 -20 000 S   0.0  0.0   0:00.00 khelper
   23 root  20   0 000 S   0.0  0.0   0:00.00 kdevtmpfs


Usually I run my simulations by means of simple mdrun -v -deffnm md.
Should I specify number of cores manually by means of -nt (or -ntmpi)
flagg? Also I notice that  -pinht flagg could give me Hyper-Threading
support. Does it reasonable in the simulation on cpu+gpu ? What
another possible options of md_run should I consider ? Finally is it
possible that problems due to openMP (4.7.2) or open-mpi (1.4.5)
drivers ?


Thanks for help

James


2013/1/10 Szilárd Páll :
> On Thu, Jan 10, 2013 at 7:25 AM, James Starlight 
> wrote:
>
>> Szilárd ,
>>
>>  thanks again for explanation!
>>
>> Today I've performed some tests on my calmodulin in water system with
>> different cutt-offs (I've used all cutt-ooffs 1.0 , 0.9 and 0.8
>> respectually)
>>
>> Below you can see that the highest performance was in case of 0.8 cut-offs
>>
>> all cut-offs 1.0
>>  Force evaluation time GPU/CPU: 6.134 ms/4.700 ms = 1.305
>>
>> NOTE: The GPU has >20% more load than the CPU. This imbalance causes
>>   performance loss, consider using a shorter cut-off and a finer PME
>> grid.
>>
>>
>>Core t (s)   Wall t (s)(%)
>>Time: 1313.420  464.035  283.0
>>  (ns/day)(hour/ns)
>> Performance:9.3102.578
>> Finished mdrun on node 0 Thu Jan 10 09:39:23 2013
>>
>>
>> all cut-offs 0.9
>> Force evaluation time GPU/CPU: 4.951 ms/4.675 ms = 1.059
>>
>>Core t (s)   Wall t (s)(%)
>>Time: 2414.930  856.179  282.1
>>  (ns/day)(hour/ns)
>> Performance:   10.0922.378
>> Finished mdrun on node 0 Thu Jan 10 10:09:52 2013
>>
>> all cut-offs 0.8
>>  Force evaluation time GPU/CPU: 4.001 ms/4.659 ms = 0.859
>>
>>Core t (s)   Wall t (s)(%)
>>Time: 1166.390  413.598  282.0
>>  (ns/day)(hour/ns)
>> Performance:   10.4452.298
>> Finished mdrun on node 0 Thu Jan 10 09:50:33 2013
>>
>> Also I've noticed that 2-4 CPU cores usage in 2 and 3rd case was only
>> 67%. Is there any other ways to increase performance by means of
>> neighboor search parameters ( e.g nstlist etc) ?
>>
>
> You can tweak nstlist and it often helps to increase it with GPUs,
> especially in parallel. However, as increasing nstlist requires larger
> rlist and more non-bonded calculations, this will not help you. You can try
> to decrease it to 10-15 which will increase the NS cost but decrease the
> GPU time, but it won't change the performance dramatically.
>
> What's strange is that your Core time/Wall time = (%) is quite low. If
> you're running on four threads on an otherwise empty machine, you should
> get close to 400 if the threads are not idling, e.g waiting for the GPU.
> For instance in the rc=0.8 case you can see that the GPU/CPU balance is
> <1.0 meaning that the GPU has less work than the CPU, case in which there
> should be no idling and you should be getting (%) = 400.
>
> Long story short: are you sure you're not running anything else on the
> computer while simulating? What do you get if you ru

Re: [gmx-users] gromacs on GPU

[Szilárd Páll]

On Thu, Jan 10, 2013 at 7:25 AM, James Starlight wrote:

> Szilárd ,
>
>  thanks again for explanation!
>
> Today I've performed some tests on my calmodulin in water system with
> different cutt-offs (I've used all cutt-ooffs 1.0 , 0.9 and 0.8
> respectually)
>
> Below you can see that the highest performance was in case of 0.8 cut-offs
>
> all cut-offs 1.0
>  Force evaluation time GPU/CPU: 6.134 ms/4.700 ms = 1.305
>
> NOTE: The GPU has >20% more load than the CPU. This imbalance causes
>   performance loss, consider using a shorter cut-off and a finer PME
> grid.
>
>
>Core t (s)   Wall t (s)(%)
>Time: 1313.420  464.035  283.0
>  (ns/day)(hour/ns)
> Performance:9.3102.578
> Finished mdrun on node 0 Thu Jan 10 09:39:23 2013
>
>
> all cut-offs 0.9
> Force evaluation time GPU/CPU: 4.951 ms/4.675 ms = 1.059
>
>Core t (s)   Wall t (s)(%)
>Time: 2414.930  856.179  282.1
>  (ns/day)(hour/ns)
> Performance:   10.0922.378
> Finished mdrun on node 0 Thu Jan 10 10:09:52 2013
>
> all cut-offs 0.8
>  Force evaluation time GPU/CPU: 4.001 ms/4.659 ms = 0.859
>
>Core t (s)   Wall t (s)(%)
>Time: 1166.390  413.598  282.0
>  (ns/day)(hour/ns)
> Performance:   10.4452.298
> Finished mdrun on node 0 Thu Jan 10 09:50:33 2013
>
> Also I've noticed that 2-4 CPU cores usage in 2 and 3rd case was only
> 67%. Is there any other ways to increase performance by means of
> neighboor search parameters ( e.g nstlist etc) ?
>

You can tweak nstlist and it often helps to increase it with GPUs,
especially in parallel. However, as increasing nstlist requires larger
rlist and more non-bonded calculations, this will not help you. You can try
to decrease it to 10-15 which will increase the NS cost but decrease the
GPU time, but it won't change the performance dramatically.

What's strange is that your Core time/Wall time = (%) is quite low. If
you're running on four threads on an otherwise empty machine, you should
get close to 400 if the threads are not idling, e.g waiting for the GPU.
For instance in the rc=0.8 case you can see that the GPU/CPU balance is
<1.0 meaning that the GPU has less work than the CPU, case in which there
should be no idling and you should be getting (%) = 400.

Long story short: are you sure you're not running anything else on the
computer while simulating? What do you get if you run on CPU only?

Might such reduced cut-off be used with the force fields ( e,g charmm)
> where initially usage of longest cut-offs have given better results
> (e,g in charmm27 and gromos56 I always use 1.2 and 1.4 nm for rvdw,
> respectually) ?
>

No, at least not without *carefully* checking whether a shorter LJ cut-off
makes sense and that it does not break the physics of your simulation.

Although we advise you to consider decreasing your cut-off - mostly because
these days a large number of simulations are carried out with overly long
cut-off chosen by the rule of thumb or folclore -, you should always either
make sure that this makes sense before doing it or not do it at all.

Cheers,
--
Szilárd


>
>
> James
>
> 2013/1/10 Szilárd Páll :
> > Hi James,
> >
> > The build looks mostly fine except that you are using fftw3 compiled with
> > AVX which is slower than with only SSE (even on AVX-capable CPUs) - you
> > should have been warned about this at configure-time.
> >
> > Now, performance-wise everything looks fine except that with a 1.2 nm
> > cut-off your GPU is not able to keep up with the CPU and finish the
> > non-bonded work before the CPU is done with Bonded + PME. That's why you
> > see the "Wait GPU" taking 20% of the total time and that's also why you
> see
> > some cores idling (because for 20% of the run-time thread 0 on core 0
> > is blocked waiting for the GPU while the rest idle).
> >
> > As the suggestion at the end of the log file point out, you can consider
> > using a shorter cut-off which will push more work back to the PME on the
> > CPU, but whether you can do this it depends on your very problem.
> >
> > There is one more alternative of running two MPI processes on the GPU
> > (mpirun -np 2 mdrun -gpu_id 00) and using the -nb gpu_cpu mode which will
> > execute part of the nonbonded on the CPU, but this might not help.
> >
> > Cheers,
> >
> > --
> > Szilárd
> >
> >
> > On Wed, Jan 9, 2013 at 8:27 PM, James Starlight  >wrote:
> >
> >> Dear Szilárd, thanks for help again!
> >>
> >> 2013/1/9 Szilárd Páll :
> >>
> >> >
> >> > There could be, but I/we can't well without more information on what
> and
> >> > how you compiled and ran. The minimum we need is a log file.
> >> >
> >> I've compilated gromacs 4.6-3 beta via simple
> >>
> >>
> >> cmake CMakeLists.txt -DGMX_GPU=ON
> >> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0
> >> make
> >> sudo make install
> >>
> >> I have not added any spe

Re: [gmx-users] gromacs on GPU

[James Starlight]

Szilárd ,

 thanks again for explanation!

Today I've performed some tests on my calmodulin in water system with
different cutt-offs (I've used all cutt-ooffs 1.0 , 0.9 and 0.8
respectually)

Below you can see that the highest performance was in case of 0.8 cut-offs

all cut-offs 1.0
 Force evaluation time GPU/CPU: 6.134 ms/4.700 ms = 1.305

NOTE: The GPU has >20% more load than the CPU. This imbalance causes
  performance loss, consider using a shorter cut-off and a finer PME grid.


   Core t (s)   Wall t (s)(%)
   Time: 1313.420  464.035  283.0
 (ns/day)(hour/ns)
Performance:9.3102.578
Finished mdrun on node 0 Thu Jan 10 09:39:23 2013


all cut-offs 0.9
Force evaluation time GPU/CPU: 4.951 ms/4.675 ms = 1.059

   Core t (s)   Wall t (s)(%)
   Time: 2414.930  856.179  282.1
 (ns/day)(hour/ns)
Performance:   10.0922.378
Finished mdrun on node 0 Thu Jan 10 10:09:52 2013

all cut-offs 0.8
 Force evaluation time GPU/CPU: 4.001 ms/4.659 ms = 0.859

   Core t (s)   Wall t (s)(%)
   Time: 1166.390  413.598  282.0
 (ns/day)(hour/ns)
Performance:   10.4452.298
Finished mdrun on node 0 Thu Jan 10 09:50:33 2013

Also I've noticed that 2-4 CPU cores usage in 2 and 3rd case was only
67%. Is there any other ways to increase performance by means of
neighboor search parameters ( e.g nstlist etc) ?
Might such reduced cut-off be used with the force fields ( e,g charmm)
where initially usage of longest cut-offs have given better results
(e,g in charmm27 and gromos56 I always use 1.2 and 1.4 nm for rvdw,
respectually) ?


James

2013/1/10 Szilárd Páll :
> Hi James,
>
> The build looks mostly fine except that you are using fftw3 compiled with
> AVX which is slower than with only SSE (even on AVX-capable CPUs) - you
> should have been warned about this at configure-time.
>
> Now, performance-wise everything looks fine except that with a 1.2 nm
> cut-off your GPU is not able to keep up with the CPU and finish the
> non-bonded work before the CPU is done with Bonded + PME. That's why you
> see the "Wait GPU" taking 20% of the total time and that's also why you see
> some cores idling (because for 20% of the run-time thread 0 on core 0
> is blocked waiting for the GPU while the rest idle).
>
> As the suggestion at the end of the log file point out, you can consider
> using a shorter cut-off which will push more work back to the PME on the
> CPU, but whether you can do this it depends on your very problem.
>
> There is one more alternative of running two MPI processes on the GPU
> (mpirun -np 2 mdrun -gpu_id 00) and using the -nb gpu_cpu mode which will
> execute part of the nonbonded on the CPU, but this might not help.
>
> Cheers,
>
> --
> Szilárd
>
>
> On Wed, Jan 9, 2013 at 8:27 PM, James Starlight wrote:
>
>> Dear Szilárd, thanks for help again!
>>
>> 2013/1/9 Szilárd Páll :
>>
>> >
>> > There could be, but I/we can't well without more information on what and
>> > how you compiled and ran. The minimum we need is a log file.
>> >
>> I've compilated gromacs 4.6-3 beta via simple
>>
>>
>> cmake CMakeLists.txt -DGMX_GPU=ON
>> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0
>> make
>> sudo make install
>>
>> I have not added any special params to the grompp or mdrun.
>>
>> After that I've run tested simulation of the calmodulin in explicit
>> water ( 60k atoms ) 100ps and obtain next output
>>
>> Host: starlight  pid: 21028  nodeid: 0  nnodes:  1
>> Gromacs version:VERSION 4.6-beta3
>> Precision:  single
>> MPI library:thread_mpi
>> OpenMP support: enabled
>> GPU support:enabled
>> invsqrt routine:gmx_software_invsqrt(x)
>> CPU acceleration:   AVX_256
>> FFT library:fftw-3.3.2-sse2-avx
>> Large file support: enabled
>> RDTSCP usage:   enabled
>> Built on:   Wed Jan  9 20:44:51 MSK 2013
>> Built by:   own@starlight [CMAKE]
>> Build OS/arch:  Linux 3.2.0-2-amd64 x86_64
>> Build CPU vendor:   GenuineIntel
>> Build CPU brand:Intel(R) Core(TM) i5-3570 CPU @ 3.40GHz
>> Build CPU family:   6   Model: 58   Stepping: 9
>> Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm
>> mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2
>> sse3 sse4.1 sse4.2 ssse3 tdt x2apic
>> C compiler: /usr/bin/gcc GNU gcc (Debian 4.6.3-11) 4.6.3
>> C compiler flags:   -mavx  -Wextra -Wno-missing-field-initializers
>> -Wno-sign-compare -Wall -Wno-unused -Wunused-value
>> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
>> -DNDEBUG
>> C++ compiler:   /usr/bin/c++ GNU c++ (Debian 4.6.3-11) 4.6.3
>> C++ compiler flags: -mavx  -Wextra -Wno-missing-field-initializers
>> -Wno-sign-compare -Wall -Wno-unused -Wunused-value
>> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
>> -DNDEBUG
>> CUDA compiler:  n

Re: [gmx-users] gromacs on GPU

[Szilárd Páll]

Hi James,

The build looks mostly fine except that you are using fftw3 compiled with
AVX which is slower than with only SSE (even on AVX-capable CPUs) - you
should have been warned about this at configure-time.

Now, performance-wise everything looks fine except that with a 1.2 nm
cut-off your GPU is not able to keep up with the CPU and finish the
non-bonded work before the CPU is done with Bonded + PME. That's why you
see the "Wait GPU" taking 20% of the total time and that's also why you see
some cores idling (because for 20% of the run-time thread 0 on core 0
is blocked waiting for the GPU while the rest idle).

As the suggestion at the end of the log file point out, you can consider
using a shorter cut-off which will push more work back to the PME on the
CPU, but whether you can do this it depends on your very problem.

There is one more alternative of running two MPI processes on the GPU
(mpirun -np 2 mdrun -gpu_id 00) and using the -nb gpu_cpu mode which will
execute part of the nonbonded on the CPU, but this might not help.

Cheers,

--
Szilárd


On Wed, Jan 9, 2013 at 8:27 PM, James Starlight wrote:

> Dear Szilárd, thanks for help again!
>
> 2013/1/9 Szilárd Páll :
>
> >
> > There could be, but I/we can't well without more information on what and
> > how you compiled and ran. The minimum we need is a log file.
> >
> I've compilated gromacs 4.6-3 beta via simple
>
>
> cmake CMakeLists.txt -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0
> make
> sudo make install
>
> I have not added any special params to the grompp or mdrun.
>
> After that I've run tested simulation of the calmodulin in explicit
> water ( 60k atoms ) 100ps and obtain next output
>
> Host: starlight  pid: 21028  nodeid: 0  nnodes:  1
> Gromacs version:VERSION 4.6-beta3
> Precision:  single
> MPI library:thread_mpi
> OpenMP support: enabled
> GPU support:enabled
> invsqrt routine:gmx_software_invsqrt(x)
> CPU acceleration:   AVX_256
> FFT library:fftw-3.3.2-sse2-avx
> Large file support: enabled
> RDTSCP usage:   enabled
> Built on:   Wed Jan  9 20:44:51 MSK 2013
> Built by:   own@starlight [CMAKE]
> Build OS/arch:  Linux 3.2.0-2-amd64 x86_64
> Build CPU vendor:   GenuineIntel
> Build CPU brand:Intel(R) Core(TM) i5-3570 CPU @ 3.40GHz
> Build CPU family:   6   Model: 58   Stepping: 9
> Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm
> mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2
> sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> C compiler: /usr/bin/gcc GNU gcc (Debian 4.6.3-11) 4.6.3
> C compiler flags:   -mavx  -Wextra -Wno-missing-field-initializers
> -Wno-sign-compare -Wall -Wno-unused -Wunused-value
> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
> -DNDEBUG
> C++ compiler:   /usr/bin/c++ GNU c++ (Debian 4.6.3-11) 4.6.3
> C++ compiler flags: -mavx  -Wextra -Wno-missing-field-initializers
> -Wno-sign-compare -Wall -Wno-unused -Wunused-value
> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
> -DNDEBUG
> CUDA compiler:  nvcc: NVIDIA (R) Cuda compiler driver;Copyright
> (c) 2005-2012 NVIDIA Corporation;Built on
> Fri_Sep_21_17:28:58_PDT_2012;Cuda compilation tools, release 5.0,
> V0.2.1221
> CUDA driver:5.0
> CUDA runtime:   5.0
>
> 
>
>Core t (s)   Wall t (s)(%)
>Time: 2770.700 1051.927  263.4
>  (ns/day)(hour/ns)
> Performance:8.2142.922
>
> full log can be found here http://www.sendspace.com/file/inum84
>
>
> Finally when I check CPU usage I notice that only 1 CPU was full
> loaded ( 100%) and 2-4 cores were loaded on only 60% but  gave me
> strange results that GPU is not used (I've only monitored temperature
> of video card and noticed increase of the temperature up to 65 degrees
> )
>
> +--+
> | NVIDIA-SMI 4.304.54   Driver Version: 304.54 |
>
> |---+--+--+
> | GPU  Name | Bus-IdDisp.  | Volatile Uncorr.
> ECC |
> | Fan  Temp  Perf  Pwr:Usage/Cap| Memory-Usage | GPU-Util  Compute
> M. |
>
> |===+==+==|
> |   0  GeForce GTX 670  | :02:00.0 N/A |
>  N/A |
> | 38%   63C  N/A N/A /  N/A |   9%  174MB / 2047MB | N/A
>  Default |
>
> +---+--+--+
>
>
> +-+
> | Compute processes:   GPU
> Memory |
> |  GPU   PID  Process name Usage
>|
>
> |=|
> |0Not Supported
> |
>
> +

Re: [gmx-users] gromacs on GPU

[Roland Schulz]

Hi,

is this an implicit water calculation? If so it shouldn't use PME.

Roland


On Wed, Jan 9, 2013 at 2:27 PM, James Starlight wrote:

> Dear Szilárd, thanks for help again!
>
> 2013/1/9 Szilárd Páll :
>
> >
> > There could be, but I/we can't well without more information on what and
> > how you compiled and ran. The minimum we need is a log file.
> >
> I've compilated gromacs 4.6-3 beta via simple
>
>
> cmake CMakeLists.txt -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0
> make
> sudo make install
>
> I have not added any special params to the grompp or mdrun.
>
> After that I've run tested simulation of the calmodulin in explicit
> water ( 60k atoms ) 100ps and obtain next output
>
> Host: starlight  pid: 21028  nodeid: 0  nnodes:  1
> Gromacs version:VERSION 4.6-beta3
> Precision:  single
> MPI library:thread_mpi
> OpenMP support: enabled
> GPU support:enabled
> invsqrt routine:gmx_software_invsqrt(x)
> CPU acceleration:   AVX_256
> FFT library:fftw-3.3.2-sse2-avx
> Large file support: enabled
> RDTSCP usage:   enabled
> Built on:   Wed Jan  9 20:44:51 MSK 2013
> Built by:   own@starlight [CMAKE]
> Build OS/arch:  Linux 3.2.0-2-amd64 x86_64
> Build CPU vendor:   GenuineIntel
> Build CPU brand:Intel(R) Core(TM) i5-3570 CPU @ 3.40GHz
> Build CPU family:   6   Model: 58   Stepping: 9
> Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm
> mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2
> sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> C compiler: /usr/bin/gcc GNU gcc (Debian 4.6.3-11) 4.6.3
> C compiler flags:   -mavx  -Wextra -Wno-missing-field-initializers
> -Wno-sign-compare -Wall -Wno-unused -Wunused-value
> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
> -DNDEBUG
> C++ compiler:   /usr/bin/c++ GNU c++ (Debian 4.6.3-11) 4.6.3
> C++ compiler flags: -mavx  -Wextra -Wno-missing-field-initializers
> -Wno-sign-compare -Wall -Wno-unused -Wunused-value
> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
> -DNDEBUG
> CUDA compiler:  nvcc: NVIDIA (R) Cuda compiler driver;Copyright
> (c) 2005-2012 NVIDIA Corporation;Built on
> Fri_Sep_21_17:28:58_PDT_2012;Cuda compilation tools, release 5.0,
> V0.2.1221
> CUDA driver:5.0
> CUDA runtime:   5.0
>
> 
>
>Core t (s)   Wall t (s)(%)
>Time: 2770.700 1051.927  263.4
>  (ns/day)(hour/ns)
> Performance:8.2142.922
>
> full log can be found here http://www.sendspace.com/file/inum84
>
>
> Finally when I check CPU usage I notice that only 1 CPU was full
> loaded ( 100%) and 2-4 cores were loaded on only 60% but  gave me
> strange results that GPU is not used (I've only monitored temperature
> of video card and noticed increase of the temperature up to 65 degrees
> )
>
> +--+
> | NVIDIA-SMI 4.304.54   Driver Version: 304.54 |
>
> |---+--+--+
> | GPU  Name | Bus-IdDisp.  | Volatile Uncorr.
> ECC |
> | Fan  Temp  Perf  Pwr:Usage/Cap| Memory-Usage | GPU-Util  Compute
> M. |
>
> |===+==+==|
> |   0  GeForce GTX 670  | :02:00.0 N/A |
>  N/A |
> | 38%   63C  N/A N/A /  N/A |   9%  174MB / 2047MB | N/A
>  Default |
>
> +---+--+--+
>
>
> +-+
> | Compute processes:   GPU
> Memory |
> |  GPU   PID  Process name Usage
>|
>
> |=|
> |0Not Supported
> |
>
> +-+
>
>
> Thanks for help again,
>
> James
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
>


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Re: [gmx-users] gromacs on GPU

[James Starlight]

Dear Szilárd, thanks for help again!

2013/1/9 Szilárd Páll :

>
> There could be, but I/we can't well without more information on what and
> how you compiled and ran. The minimum we need is a log file.
>
I've compilated gromacs 4.6-3 beta via simple


cmake CMakeLists.txt -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0
make
sudo make install

I have not added any special params to the grompp or mdrun.

After that I've run tested simulation of the calmodulin in explicit
water ( 60k atoms ) 100ps and obtain next output

Host: starlight  pid: 21028  nodeid: 0  nnodes:  1
Gromacs version:VERSION 4.6-beta3
Precision:  single
MPI library:thread_mpi
OpenMP support: enabled
GPU support:enabled
invsqrt routine:gmx_software_invsqrt(x)
CPU acceleration:   AVX_256
FFT library:fftw-3.3.2-sse2-avx
Large file support: enabled
RDTSCP usage:   enabled
Built on:   Wed Jan  9 20:44:51 MSK 2013
Built by:   own@starlight [CMAKE]
Build OS/arch:  Linux 3.2.0-2-amd64 x86_64
Build CPU vendor:   GenuineIntel
Build CPU brand:Intel(R) Core(TM) i5-3570 CPU @ 3.40GHz
Build CPU family:   6   Model: 58   Stepping: 9
Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm
mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2
sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /usr/bin/gcc GNU gcc (Debian 4.6.3-11) 4.6.3
C compiler flags:   -mavx  -Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
-DNDEBUG
C++ compiler:   /usr/bin/c++ GNU c++ (Debian 4.6.3-11) 4.6.3
C++ compiler flags: -mavx  -Wextra -Wno-missing-field-initializers
-Wno-sign-compare -Wall -Wno-unused -Wunused-value
-fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
-DNDEBUG
CUDA compiler:  nvcc: NVIDIA (R) Cuda compiler driver;Copyright
(c) 2005-2012 NVIDIA Corporation;Built on
Fri_Sep_21_17:28:58_PDT_2012;Cuda compilation tools, release 5.0,
V0.2.1221
CUDA driver:5.0
CUDA runtime:   5.0



   Core t (s)   Wall t (s)(%)
   Time: 2770.700 1051.927  263.4
 (ns/day)(hour/ns)
Performance:8.2142.922

full log can be found here http://www.sendspace.com/file/inum84


Finally when I check CPU usage I notice that only 1 CPU was full
loaded ( 100%) and 2-4 cores were loaded on only 60% but  gave me
strange results that GPU is not used (I've only monitored temperature
of video card and noticed increase of the temperature up to 65 degrees
)

+--+
| NVIDIA-SMI 4.304.54   Driver Version: 304.54 |
|---+--+--+
| GPU  Name | Bus-IdDisp.  | Volatile Uncorr. ECC |
| Fan  Temp  Perf  Pwr:Usage/Cap| Memory-Usage | GPU-Util  Compute M. |
|===+==+==|
|   0  GeForce GTX 670  | :02:00.0 N/A |  N/A |
| 38%   63C  N/A N/A /  N/A |   9%  174MB / 2047MB | N/A  Default |
+---+--+--+

+-+
| Compute processes:   GPU Memory |
|  GPU   PID  Process name Usage  |
|=|
|0Not Supported   |
+-+


Thanks for help again,

James
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Re: [gmx-users] gromacs on GPU

[Szilárd Páll]

Dear James,

On Wed, Jan 9, 2013 at 6:17 PM, James Starlight wrote:

> Roland,
>
> indeed the error was that I'have compilate mdrun-openmm which is not
> the native gpu.
>
> now I've made mdrun via
>
> cmake CMakeLists.txt -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0
>
> and obtain workable gromacs.
>
> My test system consist of calmodulin (charmm27) solvated in tip3p
> water. total size of the system: 67752 atoms.
> I have set below values on the mdp file as grompp told me
>
> nstlist = 20
> cutoff-scheme = Verlet   ; !not quite sure whai is this!
>

Again RTM:
http://www.gromacs.org/Documentation/Cut-off_schemes


> vdwtype = cut-off
>
>
>  Now on the mdrun output I have
>
> Using 1 MPI thread
> Using 4 OpenMP threads
>
> 1 GPU detected:
>   #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC:  no, stat: compatible
>
> 1 GPU auto-selected to be used for this run: #0
>
> does it mean that all 4 cores of my CPU + gpu are used at same time ?
>

Yes.


> is there any other ways to increase performance ? ( e.g I'm not quite
> sure if open_mpi is used with that build because during compilation
> cmake asked me only about fftw3 libs).
>

There could be, but I/we can't well without more information on what and
how you compiled and ran. The minimum we need is a log file.


>
> Is there any ways to monitor total performance ( e.g separate cpu and
> gpu usage ) ?
>

See the performance table and summary at the end of the log file. For
further CPU monitoring you can use top, for GPUs the nvidia-smi tool that
comes together with the driver has some monitoring capabilities.


Finally, I would strongly suggest that you check the links I posted in the
first mail. There is plenty of documentation and general description on
the heterogeneous (CPU+GPU) acceleration on the wiki and mailing list; the
google results of the searches I hinted will get you exactly that and more.

Let me reiterate: while questions and general interest are appreciated, the
*minimum* expectation is that you at least read the relevant part of the
documentation and related mailing list posts, especially if this has been
already suggested to you. Please do us and yourself a favor and browse
through the available resources.

Cheers,
--
Szilárd


>
>
> Thanks for suggestions,
>
> James
>
> 2013/1/9 Roland Schulz :
> > On Wed, Jan 9, 2013 at 3:17 AM, James Starlight  >wrote:
> >
> >> As I understood that gromacs version already has included openMM so
> >> the installation of the external openMM sources is not needed, isnt it
> >> ?
> >>
> >
> > No the new build in GPU implementation and openMM are two different
> things.
> > The Gromacs-OpenMM interface isn't actively maintained and thus not
> > recommended.
> >
> >
> >> also I wounder to know what exactly CUDA version is needed ? For
> >> example I've tried lattest cuda-5.0 but with that version i've obtain
> >> error from mdrun-openmm that platform cuda was not detected (gromacs
> >> was compilated without any errors).
> >>
> > with the natived gpu implementation (GMX_GPU) cuda 5.0 works fine.
> >
> >
> >> by the way is it possible to compilate gromacs-4.6 agains other
> >> platgorm ( e.g openCL) ? I have no problems with the compatibility of
> >> the openCL and openMM.
> >>
> > GMX_GPU doesn't support openCL.
> >
> > Roland
> >
> >
> >>
> >> James
> >>
> >> 2013/1/9 Szilárd Páll :
> >> > On Tue, Jan 8, 2013 at 3:22 PM, James Starlight <
> jmsstarli...@gmail.com
> >> >wrote:
> >> >
> >> >> So could someone provide me more about gpu-accelerated MD implemented
> >> >> in the 4.6 gromacs ? Does it require openMM (what version is
> supported
> >> >>
> >> >
> >> > FYI, if nobody can, trust G:
> >> > http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration
> >> > http://lmgtfy.com/?q=gromacs+4.6+installation+instructions
> >> >
> >> > The wiki and mailing list contains quite extensive information
> (indexed
> >> by
> >> > G).
> >> >
> >> > Otherwise, release notes (not final):
> >> > http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x
> >> >
> >> > Install guide is at the expected location:
> >> > http://www.gromacs.org/Documentation/Installation_Instructions
> >> >
> >> > Cheers,
> >> > --
> >> > Szilárd
> >> >
> >> >
> >> >> for that gromacs release ?) installed? By the way at present time I
> >> >> force with the problem of compilation 4.1.1 openMM (i need to compile
> >> >> openMM because of cuda-5.0 ). If someone have done it (openMM 4.11
> >> >> +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know.
> >> >>
> >> >>
> >> >> James
> >> >>
> >> >> 2013/1/7 James Starlight :
> >> >> > Hi Szilárd!
> >> >> >
> >> >> > As I understood you correctly gromacs-4.6 have specific algorithm
> >> >> > (independent on openMM?) for gpu-based calculations havent ? If it
> >> >> > true how I should compilate such new gpu-based gromacs? In the
> >> >> > gromacs-4.6-beta-3 folder I've found instructuon for t

Re: [gmx-users] gromacs on GPU

[Szilárd Páll]

On Wed, Jan 9, 2013 at 10:27 AM, James Starlight wrote:

> I've solved previous problem but havent been able to launch
> mdrun-openmm. Below you can find mdrun's output
>
> Back Off! I just backed up md_test.log to ./#md_test.log.3#
> Reading file md_test.tpr, VERSION 4.6-beta3 (single precision)
> Changing nstlist from 10 to 40, rlist from 1 to 1.146
>
> Compiled acceleration: None (Gromacs could use AVX_256 on this
> machine, which is better)
>

Have you set the CPU acceleration manually to "None"? If you did *don't* do
that, let the build system pick what's best for you. However, if you did
not do that, there is some issue with our auto-detection; a log file as a
start would possibly help in identifying the issue.


>
> 1 GPU detected:
>   #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC:  no, stat: compatible
>
> 1 GPU auto-selected to be used for this run: #0
>
> Program mdrun-openmm, VERSION 4.6-beta3
> Source code file:
> /home/own/gromacs-4.6-beta3/src/kernel/openmm_wrapper.cpp, line: 1367
>
> Fatal error:
> OpenMM exception caught while initializating: Error setting device
> flags cannot set while device is active in this process
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> I'm still using cuda-5-toolkit with the 304.54 driver. Also my
> question about openCL is still valid. I've browesed manual but didnt
> found how I can compile gromacs with openCL instead of Cuda. On openMM
> group developers told me that openCL would give much performance for
> gpu-accelerated simulation in comparison to the CUDA.
>
> James
>
> 2013/1/9 James Starlight :
> > As I understood that gromacs version already has included openMM so
> > the installation of the external openMM sources is not needed, isnt it
> > ?
> >
> > also I wounder to know what exactly CUDA version is needed ? For
> > example I've tried lattest cuda-5.0 but with that version i've obtain
> > error from mdrun-openmm that platform cuda was not detected (gromacs
> > was compilated without any errors). I've seen that erorr in other
> > posts in the mailing list but could not found any possible sollutions.
> >
> > by the way is it possible to compilate gromacs-4.6 agains other
> > platgorm ( e.g openCL) ? I have no problems with the compatibility of
> > the openCL and openMM.
> >
> > James
> >
> > 2013/1/9 Szilárd Páll :
> >> On Tue, Jan 8, 2013 at 3:22 PM, James Starlight  >wrote:
> >>
> >>> So could someone provide me more about gpu-accelerated MD implemented
> >>> in the 4.6 gromacs ? Does it require openMM (what version is supported
> >>>
> >>
> >> FYI, if nobody can, trust G:
> >> http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration
> >> http://lmgtfy.com/?q=gromacs+4.6+installation+instructions
> >>
> >> The wiki and mailing list contains quite extensive information (indexed
> by
> >> G).
> >>
> >> Otherwise, release notes (not final):
> >> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x
> >>
> >> Install guide is at the expected location:
> >> http://www.gromacs.org/Documentation/Installation_Instructions
> >>
> >> Cheers,
> >> --
> >> Szilárd
> >>
> >>
> >>> for that gromacs release ?) installed? By the way at present time I
> >>> force with the problem of compilation 4.1.1 openMM (i need to compile
> >>> openMM because of cuda-5.0 ). If someone have done it (openMM 4.11
> >>> +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know.
> >>>
> >>>
> >>> James
> >>>
> >>> 2013/1/7 James Starlight :
> >>> > Hi Szilárd!
> >>> >
> >>> > As I understood you correctly gromacs-4.6 have specific algorithm
> >>> > (independent on openMM?) for gpu-based calculations havent ? If it
> >>> > true how I should compilate such new gpu-based gromacs? In the
> >>> > gromacs-4.6-beta-3 folder I've found instructuon for the standart
> >>> > installation via cmake
> >>> >
> >>> > cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF
> >>> >
> >>> >
> >>> > James
> >>> >
> >>> > 2013/1/7 Szilárd Páll :
> >>> >> Szilárd
> >>> --
> >>> gmx-users mailing listgmx-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.
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>
> >> --
> >> gmx-users mailing listgmx-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.
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.

Re: [gmx-users] gromacs on GPU

[Szilárd Páll]

On Wed, Jan 9, 2013 at 9:17 AM, James Starlight wrote:

> As I understood that gromacs version already has included openMM so
> the installation of the external openMM sources is not needed, isnt it
> ?
>

The manual and wiki guides are meant to be read. Although they are a bit
dated, the main body of information is still valid. Please read the
documentation; aka RT(F)M:
http://www.gromacs.org/gpu#Compiling_and_installation_of_GROMACS-GPU_from_source


> also I wounder to know what exactly CUDA version is needed ? For
> example I've tried lattest cuda-5.0 but with that version i've obtain
> error from mdrun-openmm that platform cuda was not detected (gromacs
> was compilated without any errors). I've seen that erorr in other
> posts in the mailing list but could not found any possible sollutions.
>

It surely works with the (admittedly dated) versions the docs suggest,
you mileage may vary with other versions, but in principle everything
should work with the latest compilers, CUDA, and OpenMM (myself and others
have built and ran successfully).


>
> by the way is it possible to compilate gromacs-4.6 agains other
> platgorm ( e.g openCL) ? I have no problems with the compatibility of

the openCL and openMM.
>

No, RTM. OpenMM does have an OpenCL plugin, but that's not supported in
GROMACS, if you want to use it you'll have to write your own code around
the OpenMM library. We
have no resources to implement it ATM, but as GROMACS is OSS anyone is
welcome to contribute it.

And let me reiterate, if you're running explicit solvent you should be
using the native GPU acceleration as you've been told before.

Cheers,
Szilard


> James
>
> 2013/1/9 Szilárd Páll :
> > On Tue, Jan 8, 2013 at 3:22 PM, James Starlight  >wrote:
> >
> >> So could someone provide me more about gpu-accelerated MD implemented
> >> in the 4.6 gromacs ? Does it require openMM (what version is supported
> >>
> >
> > FYI, if nobody can, trust G:
> > http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration
> > http://lmgtfy.com/?q=gromacs+4.6+installation+instructions
> >
> > The wiki and mailing list contains quite extensive information (indexed
> by
> > G).
> >
> > Otherwise, release notes (not final):
> > http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x
> >
> > Install guide is at the expected location:
> > http://www.gromacs.org/Documentation/Installation_Instructions
> >
> > Cheers,
> > --
> > Szilárd
> >
> >
> >> for that gromacs release ?) installed? By the way at present time I
> >> force with the problem of compilation 4.1.1 openMM (i need to compile
> >> openMM because of cuda-5.0 ). If someone have done it (openMM 4.11
> >> +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know.
> >>
> >>
> >> James
> >>
> >> 2013/1/7 James Starlight :
> >> > Hi Szilárd!
> >> >
> >> > As I understood you correctly gromacs-4.6 have specific algorithm
> >> > (independent on openMM?) for gpu-based calculations havent ? If it
> >> > true how I should compilate such new gpu-based gromacs? In the
> >> > gromacs-4.6-beta-3 folder I've found instructuon for the standart
> >> > installation via cmake
> >> >
> >> > cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF
> >> >
> >> >
> >> > James
> >> >
> >> > 2013/1/7 Szilárd Páll :
> >> >> Szilárd
> >> --
> >> gmx-users mailing listgmx-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.
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> > --
> > gmx-users mailing listgmx-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.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
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Re: [gmx-users] gromacs on GPU

[James Starlight]

Roland,

indeed the error was that I'have compilate mdrun-openmm which is not
the native gpu.

now I've made mdrun via

cmake CMakeLists.txt -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0

and obtain workable gromacs.

My test system consist of calmodulin (charmm27) solvated in tip3p
water. total size of the system: 67752 atoms.
I have set below values on the mdp file as grompp told me

nstlist = 20
cutoff-scheme = Verlet   ; !not quite sure whai is this!
vdwtype = cut-off


 Now on the mdrun output I have

Using 1 MPI thread
Using 4 OpenMP threads

1 GPU detected:
  #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC:  no, stat: compatible

1 GPU auto-selected to be used for this run: #0

does it mean that all 4 cores of my CPU + gpu are used at same time ?
is there any other ways to increase performance ? ( e.g I'm not quite
sure if open_mpi is used with that build because during compilation
cmake asked me only about fftw3 libs).

Is there any ways to monitor total performance ( e.g separate cpu and
gpu usage ) ?


Thanks for suggestions,

James

2013/1/9 Roland Schulz :
> On Wed, Jan 9, 2013 at 3:17 AM, James Starlight wrote:
>
>> As I understood that gromacs version already has included openMM so
>> the installation of the external openMM sources is not needed, isnt it
>> ?
>>
>
> No the new build in GPU implementation and openMM are two different things.
> The Gromacs-OpenMM interface isn't actively maintained and thus not
> recommended.
>
>
>> also I wounder to know what exactly CUDA version is needed ? For
>> example I've tried lattest cuda-5.0 but with that version i've obtain
>> error from mdrun-openmm that platform cuda was not detected (gromacs
>> was compilated without any errors).
>>
> with the natived gpu implementation (GMX_GPU) cuda 5.0 works fine.
>
>
>> by the way is it possible to compilate gromacs-4.6 agains other
>> platgorm ( e.g openCL) ? I have no problems with the compatibility of
>> the openCL and openMM.
>>
> GMX_GPU doesn't support openCL.
>
> Roland
>
>
>>
>> James
>>
>> 2013/1/9 Szilárd Páll :
>> > On Tue, Jan 8, 2013 at 3:22 PM, James Starlight > >wrote:
>> >
>> >> So could someone provide me more about gpu-accelerated MD implemented
>> >> in the 4.6 gromacs ? Does it require openMM (what version is supported
>> >>
>> >
>> > FYI, if nobody can, trust G:
>> > http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration
>> > http://lmgtfy.com/?q=gromacs+4.6+installation+instructions
>> >
>> > The wiki and mailing list contains quite extensive information (indexed
>> by
>> > G).
>> >
>> > Otherwise, release notes (not final):
>> > http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x
>> >
>> > Install guide is at the expected location:
>> > http://www.gromacs.org/Documentation/Installation_Instructions
>> >
>> > Cheers,
>> > --
>> > Szilárd
>> >
>> >
>> >> for that gromacs release ?) installed? By the way at present time I
>> >> force with the problem of compilation 4.1.1 openMM (i need to compile
>> >> openMM because of cuda-5.0 ). If someone have done it (openMM 4.11
>> >> +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know.
>> >>
>> >>
>> >> James
>> >>
>> >> 2013/1/7 James Starlight :
>> >> > Hi Szilárd!
>> >> >
>> >> > As I understood you correctly gromacs-4.6 have specific algorithm
>> >> > (independent on openMM?) for gpu-based calculations havent ? If it
>> >> > true how I should compilate such new gpu-based gromacs? In the
>> >> > gromacs-4.6-beta-3 folder I've found instructuon for the standart
>> >> > installation via cmake
>> >> >
>> >> > cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF
>> >> >
>> >> >
>> >> > James
>> >> >
>> >> > 2013/1/7 Szilárd Páll :
>> >> >> Szilárd
>> >> --
>> >> gmx-users mailing listgmx-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.
>> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> >>
>> > --
>> > gmx-users mailing listgmx-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.
>> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>> --
>> gmx-users mailing listgmx-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.
>> * Can't post? Read http://www.gromacs.org/Support/Mail

Re: [gmx-users] gromacs on GPU

[Roland Schulz]

On Wed, Jan 9, 2013 at 3:17 AM, James Starlight wrote:

> As I understood that gromacs version already has included openMM so
> the installation of the external openMM sources is not needed, isnt it
> ?
>

No the new build in GPU implementation and openMM are two different things.
The Gromacs-OpenMM interface isn't actively maintained and thus not
recommended.


> also I wounder to know what exactly CUDA version is needed ? For
> example I've tried lattest cuda-5.0 but with that version i've obtain
> error from mdrun-openmm that platform cuda was not detected (gromacs
> was compilated without any errors).
>
with the natived gpu implementation (GMX_GPU) cuda 5.0 works fine.


> by the way is it possible to compilate gromacs-4.6 agains other
> platgorm ( e.g openCL) ? I have no problems with the compatibility of
> the openCL and openMM.
>
GMX_GPU doesn't support openCL.

Roland


>
> James
>
> 2013/1/9 Szilárd Páll :
> > On Tue, Jan 8, 2013 at 3:22 PM, James Starlight  >wrote:
> >
> >> So could someone provide me more about gpu-accelerated MD implemented
> >> in the 4.6 gromacs ? Does it require openMM (what version is supported
> >>
> >
> > FYI, if nobody can, trust G:
> > http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration
> > http://lmgtfy.com/?q=gromacs+4.6+installation+instructions
> >
> > The wiki and mailing list contains quite extensive information (indexed
> by
> > G).
> >
> > Otherwise, release notes (not final):
> > http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x
> >
> > Install guide is at the expected location:
> > http://www.gromacs.org/Documentation/Installation_Instructions
> >
> > Cheers,
> > --
> > Szilárd
> >
> >
> >> for that gromacs release ?) installed? By the way at present time I
> >> force with the problem of compilation 4.1.1 openMM (i need to compile
> >> openMM because of cuda-5.0 ). If someone have done it (openMM 4.11
> >> +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know.
> >>
> >>
> >> James
> >>
> >> 2013/1/7 James Starlight :
> >> > Hi Szilárd!
> >> >
> >> > As I understood you correctly gromacs-4.6 have specific algorithm
> >> > (independent on openMM?) for gpu-based calculations havent ? If it
> >> > true how I should compilate such new gpu-based gromacs? In the
> >> > gromacs-4.6-beta-3 folder I've found instructuon for the standart
> >> > installation via cmake
> >> >
> >> > cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF
> >> >
> >> >
> >> > James
> >> >
> >> > 2013/1/7 Szilárd Páll :
> >> >> Szilárd
> >> --
> >> gmx-users mailing listgmx-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.
> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> > --
> > gmx-users mailing listgmx-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!
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> > www interface or send it to gmx-users-requ...@gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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>


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Re: [gmx-users] gromacs on GPU

[James Starlight]

I've solved previous problem but havent been able to launch
mdrun-openmm. Below you can find mdrun's output

Back Off! I just backed up md_test.log to ./#md_test.log.3#
Reading file md_test.tpr, VERSION 4.6-beta3 (single precision)
Changing nstlist from 10 to 40, rlist from 1 to 1.146

Compiled acceleration: None (Gromacs could use AVX_256 on this
machine, which is better)

1 GPU detected:
  #0: NVIDIA GeForce GTX 670, compute cap.: 3.0, ECC:  no, stat: compatible

1 GPU auto-selected to be used for this run: #0

Program mdrun-openmm, VERSION 4.6-beta3
Source code file:
/home/own/gromacs-4.6-beta3/src/kernel/openmm_wrapper.cpp, line: 1367

Fatal error:
OpenMM exception caught while initializating: Error setting device
flags cannot set while device is active in this process
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


I'm still using cuda-5-toolkit with the 304.54 driver. Also my
question about openCL is still valid. I've browesed manual but didnt
found how I can compile gromacs with openCL instead of Cuda. On openMM
group developers told me that openCL would give much performance for
gpu-accelerated simulation in comparison to the CUDA.

James

2013/1/9 James Starlight :
> As I understood that gromacs version already has included openMM so
> the installation of the external openMM sources is not needed, isnt it
> ?
>
> also I wounder to know what exactly CUDA version is needed ? For
> example I've tried lattest cuda-5.0 but with that version i've obtain
> error from mdrun-openmm that platform cuda was not detected (gromacs
> was compilated without any errors). I've seen that erorr in other
> posts in the mailing list but could not found any possible sollutions.
>
> by the way is it possible to compilate gromacs-4.6 agains other
> platgorm ( e.g openCL) ? I have no problems with the compatibility of
> the openCL and openMM.
>
> James
>
> 2013/1/9 Szilárd Páll :
>> On Tue, Jan 8, 2013 at 3:22 PM, James Starlight 
>> wrote:
>>
>>> So could someone provide me more about gpu-accelerated MD implemented
>>> in the 4.6 gromacs ? Does it require openMM (what version is supported
>>>
>>
>> FYI, if nobody can, trust G:
>> http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration
>> http://lmgtfy.com/?q=gromacs+4.6+installation+instructions
>>
>> The wiki and mailing list contains quite extensive information (indexed by
>> G).
>>
>> Otherwise, release notes (not final):
>> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x
>>
>> Install guide is at the expected location:
>> http://www.gromacs.org/Documentation/Installation_Instructions
>>
>> Cheers,
>> --
>> Szilárd
>>
>>
>>> for that gromacs release ?) installed? By the way at present time I
>>> force with the problem of compilation 4.1.1 openMM (i need to compile
>>> openMM because of cuda-5.0 ). If someone have done it (openMM 4.11
>>> +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know.
>>>
>>>
>>> James
>>>
>>> 2013/1/7 James Starlight :
>>> > Hi Szilárd!
>>> >
>>> > As I understood you correctly gromacs-4.6 have specific algorithm
>>> > (independent on openMM?) for gpu-based calculations havent ? If it
>>> > true how I should compilate such new gpu-based gromacs? In the
>>> > gromacs-4.6-beta-3 folder I've found instructuon for the standart
>>> > installation via cmake
>>> >
>>> > cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF
>>> >
>>> >
>>> > James
>>> >
>>> > 2013/1/7 Szilárd Páll :
>>> >> Szilárd
>>> --
>>> gmx-users mailing listgmx-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.
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>> --
>> gmx-users mailing listgmx-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.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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Re: [gmx-users] gromacs on GPU

[James Starlight]

As I understood that gromacs version already has included openMM so
the installation of the external openMM sources is not needed, isnt it
?

also I wounder to know what exactly CUDA version is needed ? For
example I've tried lattest cuda-5.0 but with that version i've obtain
error from mdrun-openmm that platform cuda was not detected (gromacs
was compilated without any errors). I've seen that erorr in other
posts in the mailing list but could not found any possible sollutions.

by the way is it possible to compilate gromacs-4.6 agains other
platgorm ( e.g openCL) ? I have no problems with the compatibility of
the openCL and openMM.

James

2013/1/9 Szilárd Páll :
> On Tue, Jan 8, 2013 at 3:22 PM, James Starlight wrote:
>
>> So could someone provide me more about gpu-accelerated MD implemented
>> in the 4.6 gromacs ? Does it require openMM (what version is supported
>>
>
> FYI, if nobody can, trust G:
> http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration
> http://lmgtfy.com/?q=gromacs+4.6+installation+instructions
>
> The wiki and mailing list contains quite extensive information (indexed by
> G).
>
> Otherwise, release notes (not final):
> http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x
>
> Install guide is at the expected location:
> http://www.gromacs.org/Documentation/Installation_Instructions
>
> Cheers,
> --
> Szilárd
>
>
>> for that gromacs release ?) installed? By the way at present time I
>> force with the problem of compilation 4.1.1 openMM (i need to compile
>> openMM because of cuda-5.0 ). If someone have done it (openMM 4.11
>> +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know.
>>
>>
>> James
>>
>> 2013/1/7 James Starlight :
>> > Hi Szilárd!
>> >
>> > As I understood you correctly gromacs-4.6 have specific algorithm
>> > (independent on openMM?) for gpu-based calculations havent ? If it
>> > true how I should compilate such new gpu-based gromacs? In the
>> > gromacs-4.6-beta-3 folder I've found instructuon for the standart
>> > installation via cmake
>> >
>> > cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF
>> >
>> >
>> > James
>> >
>> > 2013/1/7 Szilárd Páll :
>> >> Szilárd
>> --
>> gmx-users mailing listgmx-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.
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
> --
> gmx-users mailing listgmx-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!
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Re: [gmx-users] gromacs on GPU

[Szilárd Páll]

On Tue, Jan 8, 2013 at 3:22 PM, James Starlight wrote:

> So could someone provide me more about gpu-accelerated MD implemented
> in the 4.6 gromacs ? Does it require openMM (what version is supported
>

FYI, if nobody can, trust G:
http://lmgtfy.com/?q=gromacs+4.6+gpu+acceleration
http://lmgtfy.com/?q=gromacs+4.6+installation+instructions

The wiki and mailing list contains quite extensive information (indexed by
G).

Otherwise, release notes (not final):
http://www.gromacs.org/About_Gromacs/Release_Notes/Versions_4.6.x

Install guide is at the expected location:
http://www.gromacs.org/Documentation/Installation_Instructions

Cheers,
--
Szilárd


> for that gromacs release ?) installed? By the way at present time I
> force with the problem of compilation 4.1.1 openMM (i need to compile
> openMM because of cuda-5.0 ). If someone have done it (openMM 4.11
> +cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know.
>
>
> James
>
> 2013/1/7 James Starlight :
> > Hi Szilárd!
> >
> > As I understood you correctly gromacs-4.6 have specific algorithm
> > (independent on openMM?) for gpu-based calculations havent ? If it
> > true how I should compilate such new gpu-based gromacs? In the
> > gromacs-4.6-beta-3 folder I've found instructuon for the standart
> > installation via cmake
> >
> > cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF
> >
> >
> > James
> >
> > 2013/1/7 Szilárd Páll :
> >> Szilárd
> --
> gmx-users mailing listgmx-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.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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Re: [gmx-users] gromacs on GPU

[James Starlight]

So could someone provide me more about gpu-accelerated MD implemented
in the 4.6 gromacs ? Does it require openMM (what version is supported
for that gromacs release ?) installed? By the way at present time I
force with the problem of compilation 4.1.1 openMM (i need to compile
openMM because of cuda-5.0 ). If someone have done it (openMM 4.11
+cuda 5.0 + gromacs-4.5 for lattest geforces) please let me know.


James

2013/1/7 James Starlight :
> Hi Szilárd!
>
> As I understood you correctly gromacs-4.6 have specific algorithm
> (independent on openMM?) for gpu-based calculations havent ? If it
> true how I should compilate such new gpu-based gromacs? In the
> gromacs-4.6-beta-3 folder I've found instructuon for the standart
> installation via cmake
>
> cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF
>
>
> James
>
> 2013/1/7 Szilárd Páll :
>> Szilárd
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Re: [gmx-users] gromacs on GPU

[James Starlight]

Hi Szilárd!

As I understood you correctly gromacs-4.6 have specific algorithm
(independent on openMM?) for gpu-based calculations havent ? If it
true how I should compilate such new gpu-based gromacs? In the
gromacs-4.6-beta-3 folder I've found instructuon for the standart
installation via cmake

cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF


James

2013/1/7 Szilárd Páll :
> Szilárd
--
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Re: [gmx-users] gromacs on GPU

[Szilárd Páll]

Hi James,

Don't use the OpenMM accelerated mdrun for explicit solvent simulations.
For such runs any modern CPU with 4-8 cores will probably be as fast or
faster than most GPUs.

However, do consider the 4.6 *native* heterogeneous GPU-accelerated code.
This new efficient code can provide 2-4x speedup and uses both CPU and GPU.

To get the latest 4.6 version use the 4.6-beta3 release (http://goo.gl/XFPoe)
or even better, get the code from git (git clone git://
git.gromacs.org/gromacs -b release-4-6).

Let us know how things worked out!

Cheers,

--
Szilárd


On Mon, Jan 7, 2013 at 8:05 AM, James Starlight wrote:

> Today I've tried to test gpu performance on the benchmark system (
> explicit solvent with pme )
>
> grompp-gpu -f md_sd.mdp -c conf -p topol.top -o md_test
> mdrun-gpu -device
> "OpenMM:platform=Cuda,DeviceID=1,Memtest=15,force-device=no" -v
> -deffnm md_test
>
> that produce the error
>
> Program mdrun-gpu, VERSION 4.5.5
> Source code file: /home/own/gromacs_gpu/src/kernel/openmm_wrapper.cpp,
> line: 1365
>
> Fatal error:
> OpenMM exception caught while initializating: cudaMemcpyToSymbol:
> SetSim copy to cSim failed invalid device symbol
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
>
>
> In the mailing list archive I've found the same error with the same
> card posted some time ago
>
> http://article.gmane.org/gmane.science.biology.gromacs.user/55577/match=openmm+exception+caught+while+initializating+cudaMemcpyToSymbol+setsim+copy+cSim+failed+invalid+device+symbol
>
> >From that topic I've understood that 670 graphic card is not supported
> yet in Gromacs (4.55). I've checked the manual for the 4.6 beta
> version and does not found anything about supporting of that card in
> the lattest gromacs realeses as well. IS there any ways to solve that
> problem ? Could that error be linked with some others ?  E.g I've
> installed nvidia drivers + cuda first and openMM 4.01 than. During
> gromacs compilation I've not forced with any errors.
>
> Thanks for help
> James
>
>  2013/1/6 Justin Lemkul :
> >
> >
> > On 1/6/13 1:53 PM, James Starlight wrote:
> >>
> >> OK!
> >>
> >> I've compilated gromacs-gpu from the source using that tutorial for
> >> the Debian OS
> >>
> >>
> http://verahill.blogspot.ru/2012/01/debian-testing-64-wheezy-compiling_20.html
> >>
> >> The only thing that it lack is the installation mdrun_d-gpu  but i'm
> >> not sure that double precission can be used with gpu.
> >>
> >> Could someone provide me with some tutorial which would show me basic
> >> mdrun options with the calculation on my gpu as well as some testing
> >> system?
> >>
> >
> > Everything you need to know (including benchmark systems) is posted at
> > http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GPUs.
> >
> > The invocation of mdrun-gpu is like any other mdrun, with GPU-specific
> > information available by reading mdrun-gpu -h.
> >
> >
> > -Justin
> >
> > --
> > 
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > 
> > --
> > gmx-users mailing listgmx-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.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> --
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Re: [gmx-users] gromacs on GPU

[James Starlight]

Today I've tried to test gpu performance on the benchmark system (
explicit solvent with pme )

grompp-gpu -f md_sd.mdp -c conf -p topol.top -o md_test
mdrun-gpu -device
"OpenMM:platform=Cuda,DeviceID=1,Memtest=15,force-device=no" -v
-deffnm md_test

that produce the error

Program mdrun-gpu, VERSION 4.5.5
Source code file: /home/own/gromacs_gpu/src/kernel/openmm_wrapper.cpp,
line: 1365

Fatal error:
OpenMM exception caught while initializating: cudaMemcpyToSymbol:
SetSim copy to cSim failed invalid device symbol
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors


In the mailing list archive I've found the same error with the same
card posted some time ago
http://article.gmane.org/gmane.science.biology.gromacs.user/55577/match=openmm+exception+caught+while+initializating+cudaMemcpyToSymbol+setsim+copy+cSim+failed+invalid+device+symbol

>From that topic I've understood that 670 graphic card is not supported
yet in Gromacs (4.55). I've checked the manual for the 4.6 beta
version and does not found anything about supporting of that card in
the lattest gromacs realeses as well. IS there any ways to solve that
problem ? Could that error be linked with some others ?  E.g I've
installed nvidia drivers + cuda first and openMM 4.01 than. During
gromacs compilation I've not forced with any errors.

Thanks for help
James

 2013/1/6 Justin Lemkul :
>
>
> On 1/6/13 1:53 PM, James Starlight wrote:
>>
>> OK!
>>
>> I've compilated gromacs-gpu from the source using that tutorial for
>> the Debian OS
>>
>> http://verahill.blogspot.ru/2012/01/debian-testing-64-wheezy-compiling_20.html
>>
>> The only thing that it lack is the installation mdrun_d-gpu  but i'm
>> not sure that double precission can be used with gpu.
>>
>> Could someone provide me with some tutorial which would show me basic
>> mdrun options with the calculation on my gpu as well as some testing
>> system?
>>
>
> Everything you need to know (including benchmark systems) is posted at
> http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GPUs.
>
> The invocation of mdrun-gpu is like any other mdrun, with GPU-specific
> information available by reading mdrun-gpu -h.
>
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] gromacs on GPU

[Justin Lemkul]

On 1/6/13 1:53 PM, James Starlight wrote:

OK!

I've compilated gromacs-gpu from the source using that tutorial for
the Debian OS
http://verahill.blogspot.ru/2012/01/debian-testing-64-wheezy-compiling_20.html

The only thing that it lack is the installation mdrun_d-gpu  but i'm
not sure that double precission can be used with gpu.

Could someone provide me with some tutorial which would show me basic
mdrun options with the calculation on my gpu as well as some testing
system?



Everything you need to know (including benchmark systems) is posted at 
http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GPUs.


The invocation of mdrun-gpu is like any other mdrun, with GPU-specific 
information available by reading mdrun-gpu -h.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] gromacs on GPU

[James Starlight]

OK!

I've compilated gromacs-gpu from the source using that tutorial for
the Debian OS
http://verahill.blogspot.ru/2012/01/debian-testing-64-wheezy-compiling_20.html

The only thing that it lack is the installation mdrun_d-gpu  but i'm
not sure that double precission can be used with gpu.

Could someone provide me with some tutorial which would show me basic
mdrun options with the calculation on my gpu as well as some testing
system?

James

2013/1/6 Justin Lemkul :
>
>
> On 1/6/13 7:41 AM, James Starlight wrote:
>>
>> Have someone tried to use gromacs-4.5-gpu binaries ? Would that
>> packages work on debian or its better to build from sources ? :)
>>
>
> The binaries online are very outdated.  Compiling from source is rather
> easy, and the website below has all the steps listed.
>
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] gromacs on GPU

[Justin Lemkul]

On 1/6/13 7:41 AM, James Starlight wrote:

Have someone tried to use gromacs-4.5-gpu binaries ? Would that
packages work on debian or its better to build from sources ? :)



The binaries online are very outdated.  Compiling from source is rather easy, 
and the website below has all the steps listed.


-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] gromacs on GPU

[James Starlight]

Have someone tried to use gromacs-4.5-gpu binaries ? Would that
packages work on debian or its better to build from sources ? :)

James

2013/1/6 Justin Lemkul :
>
>
> On 1/6/13 4:48 AM, James Starlight wrote:
>>
>> Dear Gromacs Users!
>>
>>
>> I want to install gromacs 4.55 on my Debian OS with the GPU support
>> (I'd like to make some calculations on the GeForce 670 gpu).
>>
>>
>> I have cuda-toolkit as well as openMM 4.01 installed from the binaries
>> as well as gromac's sources. Could you provide me with some tutorial
>> where I could found such step-by-step installation of the Gromacs with
>> gpu.
>>
>
> http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GPUs#Installing_and_running_GROMACS-GPU
>
> -Justin
>
> --
> 
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
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Re: [gmx-users] gromacs on GPU

[Justin Lemkul]

On 1/6/13 4:48 AM, James Starlight wrote:

Dear Gromacs Users!


I want to install gromacs 4.55 on my Debian OS with the GPU support
(I'd like to make some calculations on the GeForce 670 gpu).


I have cuda-toolkit as well as openMM 4.01 installed from the binaries
as well as gromac's sources. Could you provide me with some tutorial
where I could found such step-by-step installation of the Gromacs with
gpu.



http://www.gromacs.org/Documentation/Installation_Instructions_4.5/GPUs#Installing_and_running_GROMACS-GPU

-Justin

--


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] gromacs on GPU

[James Starlight]

Dear Gromacs Users!


I want to install gromacs 4.55 on my Debian OS with the GPU support
(I'd like to make some calculations on the GeForce 670 gpu).


I have cuda-toolkit as well as openMM 4.01 installed from the binaries
as well as gromac's sources. Could you provide me with some tutorial
where I could found such step-by-step installation of the Gromacs with
gpu.

Thanks for help


James
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Re: [gmx-users] Gromacs on GPU

[Matthew Lardy]

I should add that while we had runs that completed, all we got were
NaN for the coordinates and energies.

Personally, I have attributed our inability to execute the GPU code
cleanly to our C2050 Teslas [they are double precision].  (As I had
the GPUized code working with an earlier card, although the options
were pretty limited)

Matt

On Sat, Jan 28, 2012 at 11:32 AM, Benjamin Hall
 wrote:
> Justin A. Lemkul wrote:
>
>
> We get junk output with 4.5.4 if the box size is set to zero, for some odd
> reason, though in principle it should be ignored with "pbc = no" in the
> .mdp
> file.  Using any non-zero box results in usable results.  Our OpenMM version
> is
> the same, but Cuda is in the 3.x series (can't remember off the top of my
> head,
> sorry).
>
>
> I've tried setting the box size in the gro file but that doesn't seem to
> work (100x100x100nm). Which compiler did you use? I realise that this is an
> unlikely source of trouble but it's another variable to eliminate in
> testing.
>
> I'll update issue 568 on redmine, which has been closed but appears to be
> this problem.
>
> Thanks & best wishes
>
> Ben
>
>
> --
> Dr Benjamin A Hall
> Centre for Computational Science, Department of Chemistry, UCL
> benjamin.a.h...@ucl.ac.uk
>
>
>
>
>
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Re: [gmx-users] Gromacs on GPU

[Matthew Lardy]

Sorry for the delay, but I used gcc version 4.1.2 20080704 to compile
our version of "GPU" enabled gromacs.

Matt

On Sat, Jan 28, 2012 at 11:32 AM, Benjamin Hall
 wrote:
> Justin A. Lemkul wrote:
>
>
> We get junk output with 4.5.4 if the box size is set to zero, for some odd
> reason, though in principle it should be ignored with "pbc = no" in the
> .mdp
> file.  Using any non-zero box results in usable results.  Our OpenMM version
> is
> the same, but Cuda is in the 3.x series (can't remember off the top of my
> head,
> sorry).
>
>
> I've tried setting the box size in the gro file but that doesn't seem to
> work (100x100x100nm). Which compiler did you use? I realise that this is an
> unlikely source of trouble but it's another variable to eliminate in
> testing.
>
> I'll update issue 568 on redmine, which has been closed but appears to be
> this problem.
>
> Thanks & best wishes
>
> Ben
>
>
> --
> Dr Benjamin A Hall
> Centre for Computational Science, Department of Chemistry, UCL
> benjamin.a.h...@ucl.ac.uk
>
>
>
>
>
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Re: [gmx-users] Gromacs on GPU

[Justin A. Lemkul]

Benjamin Hall wrote:

Justin A. Lemkul wrote:


We get junk output with 4.5.4 if the box size is set to zero, for some 
odd 
reason, though in principle it should be ignored with "pbc = no" in 
the .mdp 
file.  Using any non-zero box results in usable results.  Our OpenMM 
version is 
the same, but Cuda is in the 3.x series (can't remember off the top of 
my head, 
sorry).




I've tried setting the box size in the gro file but that doesn't seem to 
work (100x100x100nm). Which compiler did you use? I realise that this is 
an unlikely source of trouble but it's another variable to eliminate in 
testing.




Ours is gcc-4.4.6 on a local machine using Cuda 3.2.  On our university's GPU 
cluster, the installation was done with gcc-4.3.4 and Cuda 3.1.  I have not 
tested Cuda 4.0, though it has recently become available to us so it might be 
worth a shot to see if this is another issue.


-Justin

I'll update issue 568 on redmine, which has been closed but appears to 
be this problem.


Thanks & best wishes

Ben


--
Dr Benjamin A Hall
Centre for Computational Science, Department of Chemistry, UCL
benjamin.a.h...@ucl.ac.uk 






--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Gromacs on GPU

[Benjamin Hall]

Justin A. Lemkul wrote:
> 
> We get junk output with 4.5.4 if the box size is set to zero, for some odd 
> reason, though in principle it should be ignored with "pbc = no" in the .mdp 
> file.  Using any non-zero box results in usable results.  Our OpenMM version 
> is 
> the same, but Cuda is in the 3.x series (can't remember off the top of my 
> head, 
> sorry).
> 

I've tried setting the box size in the gro file but that doesn't seem to work 
(100x100x100nm). Which compiler did you use? I realise that this is an unlikely 
source of trouble but it's another variable to eliminate in testing.

I'll update issue 568 on redmine, which has been closed but appears to be this 
problem.

Thanks & best wishes

Ben


--
Dr Benjamin A Hall
Centre for Computational Science, Department of Chemistry, UCL
benjamin.a.h...@ucl.ac.uk




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Re: [gmx-users] Gromacs on GPU

[Justin A. Lemkul]

Matthew Lardy wrote:

Sorry to hear that, as I have had the same problem for over four
months (OpenMM 3+, Gromacs 4.5.4+, Cuda 4, etc.).  No one ever got
back to me, and I just abandoned Gromacs for Amber (who's GPU
accelerated code base compiles and works).

I would be interested to hear if the intervening time, if a plan had
been hatched to make the GPU code production quality.  If that has
indeed happened.



I don't see a corresponding issue posted to redmine.gromacs.org - has there been 
one filed?  If not, reports often get lost on the mailing list, so the only way 
to ensure action is to post a bug report.


We get junk output with 4.5.4 if the box size is set to zero, for some odd 
reason, though in principle it should be ignored with "pbc = no" in the .mdp 
file.  Using any non-zero box results in usable results.  Our OpenMM version is 
the same, but Cuda is in the 3.x series (can't remember off the top of my head, 
sorry).


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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Re: [gmx-users] Gromacs on GPU

[Matthew Lardy]

Sorry to hear that, as I have had the same problem for over four
months (OpenMM 3+, Gromacs 4.5.4+, Cuda 4, etc.).  No one ever got
back to me, and I just abandoned Gromacs for Amber (who's GPU
accelerated code base compiles and works).

I would be interested to hear if the intervening time, if a plan had
been hatched to make the GPU code production quality.  If that has
indeed happened.

Matthew

On Fri, Jan 27, 2012 at 9:18 AM, Ben Hall  wrote:
> Hi
>
> I've been attempting to use the GPU enabled version of gromacs to run
> implicit solvent simulations, but I've run into an odd problem. I have
> downloaded and can run the benchmark simulations from the gromacs website,
> and reproduce the speeds reported there. However, when I edit the MDP
> files to write out data both the xtc and trr files contain junk data- the
> first frame is correct but every coordinate in the following frames is the
> same. These same MDP files work on the GPU disabled (default) gromacs and
> produce reasonable trajectories. As the simulations aren't crashing I
> assume that the issue relates to writing specifically; has anyone observed
> the same problem, and is there a workaround or patch?
>
> The versions of each piece of software used are
> gromacs 4.5.5
> openmm 3.1.1
> cuda 4.0
> and all compiled using intel compiler version 11.1/072
>
> Thanks in advance
>
> Ben
>
>
> --
> Dr Benjamin A Hall
> Centre for Computational Science, Department of Chemistry, UCL
> benjamin.a.h...@ucl.ac.uk
>
>
>
>
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[gmx-users] Gromacs on GPU

[Ben Hall]

Hi

I've been attempting to use the GPU enabled version of gromacs to run
implicit solvent simulations, but I've run into an odd problem. I have
downloaded and can run the benchmark simulations from the gromacs website,
and reproduce the speeds reported there. However, when I edit the MDP
files to write out data both the xtc and trr files contain junk data- the
first frame is correct but every coordinate in the following frames is the
same. These same MDP files work on the GPU disabled (default) gromacs and
produce reasonable trajectories. As the simulations aren't crashing I
assume that the issue relates to writing specifically; has anyone observed
the same problem, and is there a workaround or patch?

The versions of each piece of software used are
gromacs 4.5.5
openmm 3.1.1
cuda 4.0
and all compiled using intel compiler version 11.1/072

Thanks in advance

Ben


-- 
Dr Benjamin A Hall
Centre for Computational Science, Department of Chemistry, UCL
benjamin.a.h...@ucl.ac.uk




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Re: [gmx-users] Gromacs on GPU

[Esteban Gabriel Vega Hissi]

Hi,
It is not possible.
Any code requires a sequential section that is run on the CPU, and the
parallel section (when it is possible to parallelized) is evoqued from the
CPU to be run in the GPU.
I recommend you to read about GPU programming basics.

Greetings.


On Fri, Jan 20, 2012 at 10:16 AM,  wrote:

> Hi Users,
>
> Is it possible to run gromacs executables solely on GPU (nvidia with cuda
> libraries) without using CPU. Where can I get more information about this.
>
> Thank you,
> Aiswarya
> Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for
> it!
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>



-- 
Esteban Gabriel Vega Hissi
Área de Química Física
Departamento de Química
Universidad Nacional de San Luis
Argentina
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[gmx-users] Gromacs on GPU

[aiswarya . pawar]

Hi Users,

Is it possible to run gromacs executables solely on GPU (nvidia with cuda 
libraries) without using CPU. Where can I get more information about this.

Thank you,
Aiswarya 
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[gmx-users] Gromacs on GPU: GTX or Tesla?

[Efrat Exlrod]

Hi,



We want to start using Gromacs on GPU and we are debating whether to purchase 
GeForce GTX card or Tesla platform. Looking at the published data it seems 
GTX580 has much impressive performance compared to Tesla C2050, and of course 
it is much cheaper. Is there a reason to prefer Tesla over GTX for running 
Gromacs in the short or long term?



Thanks, Efrat
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