Dear AMBER users, especially GPU experts,
I am running a 432-residue protein in explicit (amber12) on GPU (installed
in a desktop Ubuntu 12.04, 64bit). What confuses me is that it runs so slow
(and I think it should not have been).
My mdinfo (equilibrium for 20ns) says:
------------------------------------------------------------------------------
| Current Timing Info
| -------------------
| Total steps : 10000000 | Completed : 50000 | Remaining : 9950000
|
| Average timings for last 50000 steps:
| Elapsed(s) = 2803.57 Per Step(ms) = 56.07
| ns/day = 3.08 seconds/ns = 28035.65
|
| Average timings for all steps:
| Elapsed(s) = 2803.57 Per Step(ms) = 56.07
| ns/day = 3.08 seconds/ns = 28035.65
|
|
| Estimated time remaining: 155.0 hours.
------------------------------------------------------------------------------
The rate of 3ns/day for GPU (pmemd.cuda) may be not right here.
When I checked "nvidia-smi" for the GPU info, it gives:
+------------------------------------------------------+
| NVIDIA-SMI 346.72 Driver Version: 346.72
|
|-------------------------------+----------------------+----------------------+
| 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 760 Off | 0000:01:00.0 N/A |
N/A |
| 80% 73C P0 N/A / N/A | 1267MiB / 2047MiB | N/A
Default |
+-------------------------------+----------------------+----------------------+
+-----------------------------------------------------------------------------+
| Processes: GPU
Memory |
| GPU PID Type Process name
Usage |
|=============================================================================|
| 0 C+G Not
Supported |
+-----------------------------------------------------------------------------+
May I ask if there is anything wrong about the card or the system?
Or if I made any mistakes during the set-up?
Attached is the results from the heating stage, and it seems ok.
Thank you. Please help.
My input file (eq.in):
&cntrl
imin=0, irest=1, ntx=7,
ntxo=2
ig=-1, ntb=2,
pres0=1.0, ntp=1, taup=2.0,
cut=10.0,
ntr=0, ntc=2, ntf=2,
tempi=300.0, temp0=300.0,
ntt=3, gamma_ln=1.0,
nstlim=10000000, dt=0.002,
ntpr=50000, ntwx=50000, ntwr=50000
/
Thanks and regards,
Chinh
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Received on Thu Jun 04 2015 - 01:30:02 PDT
