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>
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 Thu Jan 15 2015 - 18:30:03 PST
