Hello,
just wanted to ask if there has been any progress.
Best regards,
Paul Westphälinger
Am 05.04.2017 um 22:03 schrieb Paul Westphaelinger:
> Hi,
>
> thanks.
>
> Best regards,
> Paul Westphälinger
>
> Am 05.04.2017 um 21:46 schrieb Charles Lin:
>> I was able to reproduce the error. I'll take a look into it.
>>
>> Thanks,
>> Charlie
>> ________________________________________
>> From: Paul Westphaelinger [paul_westphaelinger.ewetel.net]
>> Sent: Thursday, March 30, 2017 12:46 PM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16
>>
>> yes
>>
>>
>> Am 30.03.2017 um 21:26 schrieb Charles Lin:
>>> Hi,
>>>
>>> I've been meaning to take a look at this, but as I am currently in the middle of relocating, my resources are currently very limited for another week or so. Both amber14 and amber16 being run are fully patched correct?
>>>
>>> Thanks,
>>> Charlie
>>>
>>> ________________________________________
>>> From: Paul Westphälinger [paul_westphaelinger.ewetel.net]
>>> Sent: Thursday, March 30, 2017 7:57 AM
>>> To: AMBER Mailing List
>>> Subject: [AMBER] 4.5 fold increase in memory consumption for nmr restraints going from amber14 to amber16
>>>
>>> Hello,
>>>
>>> I noticed a dramatic memory usage increase going from amber14 to amber16 when using nmr center
>>> of mass restraints. I have documented this in this email:
>>>
>>>
>>> I have run four simulations with nmropt=0 and nmropt=1 and both with
>>> amber14.13 and amber16. Everything else exactly identical. The restrained
>>> atom groups contain only three atoms each, and only one center of mass restrain is used
>>> in the simulation.
>>>
>>> I posted the nvidia-smi outputs below in this email, and I uploaded the testcase file to this file
>>> sharing service of my university:https://syncandshare.lrz.de/filestable/MkR2Qld2TDlWZXo4N3N5WXdndG1y
>>> The ex_init.sh files execute the simulations, I would appreciate to be informed if these
>>> test cases work for you or not. (If you are interested in receiving these files via mail
>>> I'll be happy to send them to you or to the whole mailing list if that is desired)
>>>
>>>
>>> To the nvidia-smi outputs:
>>>
>>> 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 Westphälinger
>>>
>>>
>>> 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 |
>>> +-----------------------------------------------------------------------------+
>>>
>>>
>>> Greetings,
>>>
>>> Paul Westphälinger
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
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Received on Tue May 09 2017 - 01:30:02 PDT
