No wonder it doesn't work.
Use the AMBER 14 release - with the updates please.
Otherwise all bets are off.
All the best
Ross
> On Mar 26, 2015, at 10:08 AM, Brian Radak <brian.radak.accts.gmail.com> wrote:
>
> Yes, all of the tests gave an error.
>
> I'm actually using a release made from the developer tree last September (I
> am not part of git at the moment). The revert command that Jason mentioned
> says that I have Amber15/0 and thus cannot undo updates.
>
> Did I inadvertently grab updates that I didn't want? I could maybe try to
> obtain a more official release from our site license?
>
> Brian
>
> On Thu, Mar 26, 2015 at 11:46 AM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> On Thu, Mar 26, 2015 at 11:49 AM, Ross Walker <ross.rosswalker.co.uk>
>> wrote:
>>
>>> Hi Brian,
>>>
>>> Can you try one thing for me quickly. Delete your amber14 directory. Then
>>> untar things from the original .tar.bz2 files and cd $AMBERHOME;
>>> ./configure cuda gnu
>>>
>>> But in this case when it asks you about applying updates - say NO. Then
>>> compile everything and see what happens. I am wondering if there might
>> be a
>>> bug introduced with one of the latest updates.
>>>
>>
>> You can always use "./update_amber --revert-to Amber/0" to revert all of
>> the updates instead of deleting everything...
>>
>>
>>
>>
>>>
>>> All the best
>>> Ross
>>>
>>>> On Mar 26, 2015, at 7:41 AM, Brian Radak <brian.radak.accts.gmail.com>
>>> wrote:
>>>>
>>>> The nvidia install seems to differentiate those as 32/64 bit libraries.
>>>> Anyway, I've been including both now.
>>>>
>>>> Noting how obnoxious things can be with stray library files, etc. I
>> just
>>>> re-installed /everything/ from a clean install. There are now no signs
>>>> of different driver or cuda toolkit versions on my computer.
>>>>
>>>> I installed both the driver and cuda 6.5 with the run script from the
>>>> nvidia website (this was a slightly nuanced affair on Ubuntu 14.04
>> given
>>>> my hardware). However, I still get the same error:
>>>>
>>>> cudaMemcpyToSymbol: SetSim copy to cSim failed invalid device symbol
>>>>
>>>> I also tried manually running the cuda/4096wat test; unfortunately
>> there
>>>> wasn't much more helpful output than that above:
>>>>
>>>> |------------------- GPU DEVICE INFO --------------------
>>>> |
>>>> | CUDA_VISIBLE_DEVICES: not set
>>>> | CUDA Capable Devices Detected: 1
>>>> | CUDA Device ID in use: 0
>>>> | CUDA Device Name: Quadro K2200
>>>> | CUDA Device Global Mem Size: 4095 MB
>>>> | CUDA Device Num Multiprocessors: 5
>>>> | CUDA Device Core Freq: 1.12 GHz
>>>> |
>>>> |--------------------------------------------------------
>>>>
>>>>
>>>> | Conditional Compilation Defines Used:
>>>> | PUBFFT
>>>> | BINTRAJ
>>>> | CUDA
>>>> | EMIL
>>>>
>>>> | Largest sphere to fit in unit cell has radius = 24.800
>>>>
>>>>
>>>>
>>>>
>>>> On 03/25/2015 01:49 PM, Jason Swails wrote:
>>>>>> On Mar 25, 2015, at 2:46 PM, Brian Radak <
>> brian.radak.accts.gmail.com>
>>> wrote:
>>>>>>
>>>>>> Ah yes, the compiling equivalent of "turning it off and on again."
>>>>>> Unfortunately it looks like the result is the same.
>>>>>>
>>>>>> Double checking my CUDA_HOME, etc. settings:
>>>>>>
>>>>>>>> nvcc -V
>>>>>> nvcc: NVIDIA (R) Cuda compiler driver
>>>>>> Copyright (c) 2005-2014 NVIDIA Corporation
>>>>>> Built on Thu_Jul_17_21:41:27_CDT_2014
>>>>>> Cuda compilation tools, release 6.5, V6.5.12
>>>>>>>> echo $CUDA_HOME
>>>>>> /usr/local/cuda-6.5
>>>>>>>> echo $LD_LIBRARY_PATH
>>>>>>
>>>
>> /home/radak/software/amber14/lib:/usr/local/cuda-6.5/lib64:/usr/local/cuda-6.5/lib
>>>>>>
>>>>>> The CUDA install instructions I found suggested the "lib64" addition
>>> above,
>>>>>> but the AMBER install msg only suggests "lib". Is that all cool?
>>>>> Both is probably better (my LD_LIBRARY_PATH is
>>> ...:/opt/cuda/6.5/lib:/opt/cuda/6.5/lib64:...). $CUDA_HOME/lib on my
>>> machine only contains the runtime libraries -- all of the other libraries
>>> (like libcufft and libcublas) are in lib64, and at least cufft is needed
>>> for pmemd.cuda...
>>>>>
>>>>> HTH,
>>>>> Jason
>>>>>
>>>>> --
>>>>> Jason M. Swails
>>>>> BioMaPS,
>>>>> Rutgers University
>>>>> Postdoctoral Researcher
>>>>>
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>> --
>>>> Brian Radak
>>>> Postdoctoral Scholar
>>>> Gordon Center for Integrative Science, W323A
>>>> Department of Biochemistry & Molecular Biology
>>>> University of Chicago
>>>> 929 E. 57th St.
>>>> Chicago, IL 60637-1454
>>>> Tel: 773/834-2812
>>>> email: radak.uchicago.edu
>>>> _______________________________________________
>>>> 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
>>>
>>
>>
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Brian Radak
> Postdoctoral Scholar
> University of Chicago
> Department of Biochemistry & Molecular Biology
> Gordon Center for Integrative Science, W323A
> 929 E. 57th St.
> Chicago, IL 60637-1454
> Tel: 773/834-2812
> e-mail: radak.uchicago.edu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Thu Mar 26 2015 - 10:30:08 PDT
