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
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Received on Thu Mar 26 2015 - 10:30:07 PDT
