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
>>>>
>>>> _______________________________________________
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>>>>
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>>
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Received on Tue Sep 25 2018 - 10:00:03 PDT
