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
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>>
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Received on Wed Apr 05 2017 - 13:30:03 PDT
