Is the development branch really that bleeding edge? Goodness, I wish I had
known that in year 3 of my PhD!
Using a fully patched release of 14 everything now runs without error. I
get some "possible failures" with energy differences in the 4th decimal
place - I expect these can be safely ignored.
On Thu, Mar 26, 2015 at 12:17 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> 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
>
>
> _______________________________________________
> 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
Received on Thu Mar 26 2015 - 11:30:03 PDT
