Dear Amber Developers,
I would be very glad to see this bug fixed. I am at the moment
wasting resourced due to this fivefold increase in memory that still
happens in amber 18. It means I have to use more graphics cards
for a simulation then really necessary.
The bug is probably just due to a mistake in one of the later amber 14
updates and
should not be hard to track down, I hope.
Best regards
Paul Westphälinger
Am 25.09.2018 um 18:49 schrieb James Kress:
> Did you find the same issue with Amber 18?
>
> Jim Kress
>
> -----Original Message-----
> From: Paul Westphälinger <paul_westphaelinger.ewetel.net>
> Sent: Tuesday, September 25, 2018 6:44 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] 4.5 fold increase in memory consumption for nmr
> restraints going from amber14 to amber16
>
> Dear Amber Developers,
>
> I just wanted to ask if there has been any progress on this bug. Should I
> migrate to using other
>
> amber modules? Would be happy about any update, even if it is that this will
> not be further worked on.
>
> Best regards
>
> Paul Westphälinger
>
> 09.05.2017 um 10:00 schrieb Paul Westphaelinger:
>> 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/MkR2Qld2TDlWZXo4N
>>>>> 3N5WXdndG1y 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 Oct 02 2018 - 03:00:01 PDT
