Hi Tu,
The version 12.1 means you do NOT have all the latest bug fixes. In
particular bugfix.14 which updated it to v12.2. It should be:
Version 12.2
01/10/2013
I suggest going to your AMBERHOME directory. Running 'make clean' then:
./configure -cuda gnu
Say yes when it asks to apply patches. Then keep rerunning configure until
it no longer asks you if you want to apply any patches. Then run 'make
install' and then try repeating your calculation (checking that Version
12.2 is reported int he output file) and see if that fixes it.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
---------------------------------------------------------
Note: Electronic Mail is not secure, has no guarantee of delivery, may not
be read every day, and should not be used for urgent or sensitive issues.
On 3/7/13 8:51 PM, "Ò\§ÓµÓ" <tuzhiping711.gmail.com> wrote:
>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
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 07 2013 - 21:30:02 PST
