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
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Mar 26 2015 - 10:00:09 PDT
