[AMBER] Fwd: GPU pmemd.cuda runs very slow (3ns/day)???

From: Chinh Su Tran To <chinh.sutranto.gmail.com>
Date: Thu, 4 Jun 2015 16:13:55 +0800

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
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