Dear all ,
I'm sorry for unclear formulation . Yes, I had patched the latest bug
fixes applied to my
AMBER 12 installation four days ago.Section of my mdout file as below:
---------------------------------------------------
| GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
| Version 12.1
|
| 08/17/2012
|
| Implementation by:
| Ross C. Walker (SDSC)
| Scott Le Grand (nVIDIA)
| Duncan Poole (nVIDIA)
|
| CAUTION: The CUDA code is currently experimental.
| You use it at your own risk. Be sure to
| check ALL results carefully.
|
| Precision model in use:
| [SPFP] - Mixed Single/Double/Fixed Point Precision.
| (Default)
|
|--------------------------------------------------------
|------------------- GPU DEVICE INFO --------------------
|
| CUDA Capable Devices Detected: 1
| CUDA Device ID in use: 0
| CUDA Device Name: GeForce GTX 680
| CUDA Device Global Mem Size: 4095 MB
| CUDA Device Num Multiprocessors: 8
| CUDA Device Core Freq: 1.06 GHz
|
|----------------------------------------------------- ---
The last two structures saved before termination
NSTEP = 9340000 TIME(PS) = 9380.000 TEMP(K) = 299.60 PRESS =
57.2
Etot = -45286.0177 EKtot = 10964.4258 EPtot =
-56250.4435
BOND = 152.4609 ANGLE = 442.1494 DIHED =
928.6754
1-4 NB = 198.6770 1-4 EEL = 2549.4139 VDWAALS =
7784.2754
EELEC = -68306.0955 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 5165.8274 VIRIAL = 4938.6230 VOLUME =
184043.5036
Density =
0.9938
------------------------------------------------------------------------------
NSTEP = 9350000 TIME(PS) = 9390.000 TEMP(K) = 297.06 PRESS =
177.7
Etot = -45372.9947 EKtot = 10871.5488 EPtot =
-56244.5436
BOND = 161.8453 ANGLE = 452.8540 DIHED =
929.1794
1-4 NB = 192.6678 1-4 EEL = 2496.1657 VDWAALS =
7883.0276
EELEC = -68360.2834 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 5140.5200 VIRIAL = 4432.4655 VOLUME =
184532.1277
Density =
0.9912
------------------------------------------------------------------------------
At last ,the exclamation mark in from of irest=1, ntx=5 in my input file
means comment line, I know it's used in restrat caculation.
Any help ? Thanks a lot.
Yours,
Tu
2013/3/8 Ross Walker <ross.rosswalker.co.uk>
> Hi Tu,
>
> Can you please make sure you have all the latest bug fixes applied to your
> AMBER 12 installation. Do:
>
> cd $AMBERHOME
> ./patch_amber.py --patch-level
>
>
> And post what it says.
>
> Could you also post your mdout file please. In particular I am interested
> in what version and date it reports for the GPU code. The section should
> look something like this:
>
> |--------------------- INFORMATION ----------------------
> | GPU (CUDA) Version of PMEMD in use: NVIDIA GPU IN USE.
> | Version 12.1
> |
> | 07/06/2012
> |
> | Implementation by:
> | Ross C. Walker (SDSC)
> | Scott Le Grand (nVIDIA)
> | Duncan Poole (nVIDIA)
> |
> | CAUTION: The CUDA code is currently experimental.
> | You use it at your own risk. Be sure to
> | check ALL results carefully.
> |
> | Precision model in use:
> | [SPFP] - Mixed Single/Double/Fixed Point Precision.
> | (Default)
> |
> |--------------------------------------------------------
>
>
> BTW, is the exclamation mark in from of irest=1, ntx=5 a typo or is that
> really in your input file?
>
> All the best
> Ross
>
>
>
> On 3/7/13 7:12 PM, "Tu Zhiping" <tuzhiping711.gmail.com> wrote:
>
> >Dear all :
> >
> >I'm using amber12 pmemd.cuda_SPFP to run MD simulation. But the running
> >process is always terminated sooner or later. There was nothing error in
> >the
> >md2.out. I don't know how to solve the question. The log.txt exports:
> >cudaMemcpy GpuBuffer::Download failed unspecified launch failure.
> >
> >My input file :
> >
> >!irest=1, ntx=5,
> >
> >imin=0,
> >
> >ntb=2, ntp=1, pres0=1.0, taup=2.0,
> >
> >ntpr=10000, ntwr=10000, ntwx=10000,
> >
> >ntt=3, gamma_ln=1.0, tempi = 300.0, temp0 = 300.0,
> >
> >ig=9999, ! rand number
> >
> >ntf=2, ntc=2, ! SHAKE
> >
> >nstlim=50000000, dt=0.001, ! steptime
> >
> >cut=12.0,
> >
> >iwrap=1
> >
> >/
> >
> >Another question:
> >
> >when I tleap ,there was a waring : The unperturbed charge of the unit:
> >1.000000 is not zero. I use the solvateBox TIP3PBOX, I didn't add Na+ to
> >neutralize the system. Did it influence the simulation?
> >
> >Any help will be appreciate. Thanks a lot.
> >
> >
> >
> >Yours
> >
> >
> >
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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>
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Received on Thu Mar 07 2013 - 21:00:02 PST
