Hello,
I have now run a single simulation with nmropt=0 and nmropt=1 both with
amber14.13 and amber16. Everything else exactly identical. I will post
nvidia-smi outputs and I will append the two test cases.(removed the
appendix..)
Please pay attention only to the 0-th GPU as this is the one I was
using. Notice the increase in memory use even without nmr restraints
from amber14 to 16 is small while with nmr restraint it is about a
factor of 4.5.
Best,
Paul
I'll post the nvidia-smi outputs here:
amber 14 with nmropt=1:
Tue Mar 21 12:21:54 2017
+------------------------------------------------------+
| NVIDIA-SMI 352.93 Driver Version: 352.93 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile
Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util
Compute M. |
|===============================+======================+======================|
| 0 GeForce GTX TIT... Off | 0000:02:00.0 Off |
N/A |
| 30% 72C P2 177W / 250W | 292MiB / 12287MiB | 97% Default |
+-------------------------------+----------------------+----------------------+
| 1 GeForce GTX TIT... Off | 0000:03:00.0 Off |
N/A |
| 33% 73C P2 204W / 250W | 1262MiB / 12287MiB | 97% Default |
+-------------------------------+----------------------+----------------------+
| 2 GeForce GTX TIT... Off | 0000:81:00.0 Off |
N/A |
| 22% 34C P8 15W / 250W | 23MiB / 12287MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
| 3 GeForce GTX TIT... Off | 0000:82:00.0 Off |
N/A |
| 22% 29C P8 15W / 250W | 23MiB / 12287MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
| GPU PID Type Process name Usage |
|=============================================================================|
| 0 28177 C pmemd.cuda
267MiB |
| 1 25712 C /home/fzeller/amber16//bin/pmemd.cuda
1237MiB |
+-----------------------------------------------------------------------------+
amber 14 with nmropt=0:
Tue Mar 21 12:20:44 2017
+------------------------------------------------------+
| NVIDIA-SMI 352.93 Driver Version: 352.93 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile
Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util
Compute M. |
|===============================+======================+======================|
| 0 GeForce GTX TIT... Off | 0000:02:00.0 Off |
N/A |
| 22% 63C P2 188W / 250W | 292MiB / 12287MiB | 99% Default |
+-------------------------------+----------------------+----------------------+
| 1 GeForce GTX TIT... Off | 0000:03:00.0 Off |
N/A |
| 33% 73C P2 205W / 250W | 1262MiB / 12287MiB | 97% Default |
+-------------------------------+----------------------+----------------------+
| 2 GeForce GTX TIT... Off | 0000:81:00.0 Off |
N/A |
| 22% 34C P8 15W / 250W | 23MiB / 12287MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
| 3 GeForce GTX TIT... Off | 0000:82:00.0 Off |
N/A |
| 22% 29C P8 15W / 250W | 23MiB / 12287MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
| GPU PID Type Process name Usage |
|=============================================================================|
| 0 28138 C pmemd.cuda
267MiB |
| 1 25712 C /home/fzeller/amber16//bin/pmemd.cuda
1237MiB |
+-----------------------------------------------------------------------------+
amber 16 with nmropt=1:
Tue Mar 21 12:17:47 2017
+------------------------------------------------------+
| NVIDIA-SMI 352.93 Driver Version: 352.93 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile
Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util
Compute M. |
|===============================+======================+======================|
| 0 GeForce GTX TIT... Off | 0000:02:00.0 Off |
N/A |
| 23% 65C P2 194W / 250W | 1295MiB / 12287MiB | 96% Default |
+-------------------------------+----------------------+----------------------+
| 1 GeForce GTX TIT... Off | 0000:03:00.0 Off |
N/A |
| 32% 73C P2 205W / 250W | 1262MiB / 12287MiB | 97% Default |
+-------------------------------+----------------------+----------------------+
| 2 GeForce GTX TIT... Off | 0000:81:00.0 Off |
N/A |
| 22% 34C P8 15W / 250W | 23MiB / 12287MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
| 3 GeForce GTX TIT... Off | 0000:82:00.0 Off |
N/A |
| 22% 29C P8 15W / 250W | 23MiB / 12287MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
| GPU PID Type Process name Usage |
|=============================================================================|
| 0 28007 C pmemd.cuda
1270MiB |
| 1 25712 C /home/fzeller/amber16//bin/pmemd.cuda
1237MiB |
+-----------------------------------------------------------------------------+
amber 16 with nmropt=0:
Tue Mar 21 12:19:16 2017
+------------------------------------------------------+
| NVIDIA-SMI 352.93 Driver Version: 352.93 |
|-------------------------------+----------------------+----------------------+
| GPU Name Persistence-M| Bus-Id Disp.A | Volatile
Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util
Compute M. |
|===============================+======================+======================|
| 0 GeForce GTX TIT... Off | 0000:02:00.0 Off |
N/A |
| 33% 76C P2 202W / 250W | 327MiB / 12287MiB | 99% Default |
+-------------------------------+----------------------+----------------------+
| 1 GeForce GTX TIT... Off | 0000:03:00.0 Off |
N/A |
| 33% 73C P2 203W / 250W | 1262MiB / 12287MiB | 97% Default |
+-------------------------------+----------------------+----------------------+
| 2 GeForce GTX TIT... Off | 0000:81:00.0 Off |
N/A |
| 22% 34C P8 15W / 250W | 23MiB / 12287MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
| 3 GeForce GTX TIT... Off | 0000:82:00.0 Off |
N/A |
| 22% 30C P8 15W / 250W | 23MiB / 12287MiB | 0% Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU Memory |
| GPU PID Type Process name Usage |
|=============================================================================|
| 0 28048 C pmemd.cuda
302MiB |
| 1 25712 C /home/fzeller/amber16//bin/pmemd.cuda
1237MiB |
+-----------------------------------------------------------------------------+
Am 20.03.2017 um 19:24 schrieb Jason Swails:
> What happens if you set nmropt to 0? (Basically turn off the restraints altogether). This will help determine if the restraints are to blame or not.
>
> All the best,
> Jason
>
> --
> Jason M. Swails
>
>> On Mar 20, 2017, at 12:01 PM, paul <paul_westphaelinger.ewetel.net> wrote:
>>
>> hello,
>>
>> I was using just one center of mass restraint, both groups containing
>> three atoms. Both were performed with nmr restraints, and identical
>> input files. The nvidia-smi outputs I put in the email from before, were
>> created while I was trying to find out what was going on, so everything
>> is identical.
>>
>> I was using Hamiltonian replica exchange if that helps. If there is more
>> information I can give you I would be happy to do so.
>>
>> This would be an example .in file with the corresponding .disang file :
>>
>> the infile:
>>
>> &cntrl
>> ntx=5,
>> nstlim=1000,
>> restraint_wt=0.5,
>> ntr=0,
>> ntt=3,
>> temp0=300,
>> gamma_ln=5.0,
>> ntc=2,
>> ntwx=25000,
>> dt=0.004,
>> ig=-1,
>> ntf=2,
>> cut=9.0,
>> restraintmask=':1-10',
>> numexchg=25000,
>> ntpr=500,
>> irest=1,
>> imin=0,
>> ntxo=2,
>> nmropt=1,
>> ioutfm=1,
>> &end
>> &wt type='DUMPFREQ', istep1=50,/
>> &wt type='END',/
>> DUMPAVE=restart0.disang.out
>> DISANG=restart0.disang
>>
>>
>> the disang file:
>>
>> &rst
>> iat=-1,-1
>> iresid=0,irstyp=0,ifvari=0,ninc=0,imult=0,ir6=0,ifntyp=0,
>> r1=0,r2=11.4,r3=11.4,r4=999,
>> rk2=5.5,rk3=5.5,
>> igr1= 29, 62, 94, 127,
>> igr2= 189, 219, 252, 282,
>> /
>>
>>
>>> Am 20.03.2017 um 15:44 schrieb David Case:
>>>> On Mon, Mar 20, 2017, paul wrote:
>>>> My simulations started crashing and I soon realized that a dramatic
>>>> increase in memory consumption was at fault. I am using the NMR center
>>>> of mass distance restraints and after the version change a four window
>>>> replica system jumped in memory usage.
>>> Are you using the same inputs, or are you now using "nfe" or something like
>>> that? Posting your mdin input file + restraints would probably be helpful.
>>> We would also benefit by knowing how many atoms are involved in the
>>> center-of-mass calculation. Checking to see what happens if you reduce that
>>> number might be informative. And, are you using lots of COM restraints, or
>>> just a few?
>>>
>>> What you report does sound like a bug/regression, but we need information
>>> requested above to even know which routines to look at.
>>>
>>> ...thx...dac
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>
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Received on Tue Mar 21 2017 - 05:00:03 PDT
