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
Received on Thu Mar 30 2017 - 08:00:02 PDT
