Thanks Mohd, I've tried CUDA toolkit 4.0 and it works well with GTX480 and
GTX580 but not GTX670 (the error with GTX670 is: cudaMemcpyToSymbol: SetSim
copy to cSim failed invalid device symbol).
Thanks for your information Ryan, it sounds good (y)
Best,
Khuong
On Fri, Jan 16, 2015 at 1:48 PM, Novosielski, Ryan <novosirj.ca.rutgers.edu>
wrote:
> The good news is that Amber14 is easy to install and performs really well.
> You can have a new installation in probably 30 mins with little hassle.
>
> ____ *Note: UMDNJ is now Rutgers-Biomedical and Health Sciences*
> || \\UTGERS |---------------------*O*---------------------
> ||_// Biomedical | Ryan Novosielski - Senior Technologist
> || \\ and Health | novosirj.rutgers.edu<mailto:novosirj.rutgers.edu>-
> 973/972.0922 (2x0922)
> || \\ Sciences | OIRT/High Perf & Res Comp - MSB C630, Newark
> `'
>
> On Jan 15, 2015, at 21:24, Khuong Truong Gia <khuongtg.gmail.com<mailto:
> khuongtg.gmail.com>> wrote:
>
> Hi Jason,
>
> Thank you very much for your sharing, you're very kind.
> About installation, I've already applied all bug fixes. But it still
> doesn't work. So, it's time to retire Amber11.
>
> Thanks again,
> Khuong
>
> On Thu, Jan 15, 2015 at 9:11 PM, Jason Swails <jason.swails.gmail.com
> <mailto:jason.swails.gmail.com>>
> wrote:
>
> On Thu, 2015-01-15 at 17:24 +0900, Khuong Truong Gia wrote:
> Hi David,
>
> This is result when I run "test_amber_cuda.sh":
>
> ./test_amber_cuda.sh
> Using default GPU_ID = -1
> Using default PREC_MODEL = SPDP
> make[1]: Entering directory `/opt/amber11/test'
> cd cuda && make -k test.pmemd.cuda GPU_ID=-1 PREC_MODEL=SPDP
> make[2]: Entering directory `/opt/amber11/test/cuda'
> ------------------------------------
> Running CUDA Implicit solvent tests.
> Precision Model = SPDP
> GPU_ID = -1
> ------------------------------------
> cd trpcage/ && ./Run_md_trpcage -1 SPDP netcdf.mod
> diffing trpcage_md.out.GPU_SPDP with trpcage_md.out
> PASSED
> ==============================================================
> cd myoglobin/ && ./Run_md_myoglobin -1 SPDP netcdf.mod
> diffing myoglobin_md.out.GPU_SPDP with myoglobin_md.out
> PASSED
>
> *.....(all Implicit solvent tests PASSED),Then, it stood still (no update
> for long time) at line "cd 4096wat/ && ./Run.pure_wat -1 SPDP
> netcdf.mod"*
>
> cd gb_ala3/ && ./Run.irest1_ntt1_igb1_ntc2 -1 SPDP netcdf.mod
> diffing irest1_ntt1_igb1_ntc2.out.GPU_SPDP with irest1_ntt1_igb1_ntc2.out
> PASSED
> ==============================================================
> ------------------------------------
> Running CUDA Explicit solvent tests.
> Precision Model = SPDP
> GPU_ID = -1
> ------------------------------------
> cd 4096wat/ && ./Run.pure_wat -1 SPDP netcdf.mod
>
> Is that my installation's mistake?
>
> It is hard to tell. Your symptoms look a lot like problems that were
> addressed by bugfix.12 for Amber 11 (see
> http://ambermd.org/bugfixes11.html) If you have not already applied all
> of the bug fixes, you need to. If you have and it still doesn't work,
> you probably need to upgrade to Amber 14 to use pmemd.cuda.
>
> As Dave pointed out, Amber 11 is 5 years old at this point and
> represents pmemd.cuda in its infancy. Amber 11 was the first release
> that featured a production-ready GPU code. Support for that version
> ended not too long after Amber 12 was released (almost 3 years ago now).
>
> Since that time, GPU hardware has changed dramatically (Amber 11 was
> released alongside the Tesla architecture, like the Tesla 1060 and 1070
> cards and the GTX 2xx series). NVidia has gone through several
> different generations of architectures (and CUDA toolkits) since then --
> through Fermi, Kepler, and now on to Maxwell. Each architecture
> necessitated changes to pmemd.cuda's internals in order to take better
> advantage of the new hardware. As a result, Amber 11 won't run (or
> won't run well) on Kepler or Maxwell cards. Furthermore, numerous bugs
> have been found and fixed since Amber 11 has been released, and those
> fixes will most certainly not be ported back to Amber 11. Performance
> has also improved *dramatically* since the days of Amber 11.
>
> Long story short, it is probably time to retire Amber 11 if you are
> having problems with it. You are unlikely to find anybody on this list
> that can help out that has used Amber 11 within the last 3 to 5 years. I
> don't think Amber 11 is something we actively support anymore.
>
> Hope this helps,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
>
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Received on Fri Jan 16 2015 - 18:30:02 PST
