Hi Hai,
Can you create a bug reports (with repros) for the problems you see. Specifically things you change that are valid simulations in the CPU code that do not give the correct answer in the GPU code? - Without this feedback, and careful repros it is impossible for us to keep the GPU code in check with the CPU code. Plus there are changes that people modify that we never even knew people would want to change in a simulation. At the least I can put in warnings / errors for combinations that don't work and in the better we can address this. Without it being logged in bugzilla though it's hard to keep track (or even know).
Thanks,
All the best
Ross
> On Jan 30, 2015, at 11:35 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> On Fri, Jan 30, 2015 at 2:22 PM, Ilyas Yildirim <iy222.cam.ac.uk> wrote:
>
>> It seems that when new atom types are used in amber14 and prmtop/inpcrd
>> files are created with amber14's Leap, pmemd.cuda_DPFP gives the same
>> energies. When, however, the prmtop/inpcrd files are created with amber12's
>> Leap, this is not the case. If ff12SB by itself was used to create
>> prmtop/inpcrd files, the energies come out to be the same at each run.
>
> I think the golden standard is to use sander/pmemd CPU code to
> validate GPU code. I found that lots of GB parameters are hard coded
> in CUDA version and users can still change their values (like
> `offset`) without getting proper warning.
>
> Hai Nguyen
> Simmerling lab
>
>>> the specific igb value (GB model). Are there specific sets of frcmod/atom
>>> type that don't mix well with particular intrinsic radii set and specific
>>> gb model?
>>> Thanks
>>> Carlos
>>> On Jan 30, 2015 10:11 AM, "Ilyas Yildirim" <iy222.cam.ac.uk> wrote:
>>>
>>>> To MODERATOR: I've sent the same email today early morning with some
>>>> attachments, but the size of the attachments were too big, which required
>>>> the moderator to decide to post or not. I am re-sending the email without
>>>> the attachments; thus, please discard and do not send the previous email
>>>> to
>>>> the list.
>>>>
>>>> Dear Jason, Scott, Dave, and Ross,
>>>>
>>>> I have been reading this thread since Rosie described the problem with
>>>> the
>>>> energies coming out different at each new calculation. Scott and Jason
>>>> were
>>>> talking about the problem arising due to the GB model, or the method it
>>>> is
>>>> being used by cuda. So, I provided Rosie with a new prmtop/inpcrd input
>>>> set
>>>> directly created with ff12SB force field. The new set seems to work fine.
>>>> The previous one was created with new frcmod/lib files loaded over
>>>> ff12SB.
>>>> The new frcmod has new atom types in it, and it seems that those are the
>>>> ones causing the problem (though it is not clear yet to me why energies
>>>> are
>>>> different at the end). You can check out the prmtop.notworking and
>>>> prmtop.working from the following address:
>>>>
>>>> http://www-wales.ch.cam.ac.uk/rosie/new_input/
>>>>
>>>> While creating the prmtop.notworking file, I used the following leap
>>>> script to create it.
>>>>
>>>> ---------- xleap.in -----------
>>>> source leaprc.ff12SB
>>>> addPdbAtomMap {
>>>> { "OP1" "O1P" } { "OP2" "O2P" }
>>>> { "HO5'" "H5T" } { "HO3'" "H3T" }
>>>> { "H5'" "H5'1" } { "H5''" "H5'2" }
>>>> { "H2'" "H2'1" } { "H2''" "H2'2" }
>>>> }
>>>> addAtomTypes {
>>>> { "DH" "H" "sp3" }
>>>> { "C1" "C" "sp2" }
>>>> { "C2" "C" "sp2" }
>>>> { "C3" "C" "sp2" }
>>>> { "C4" "C" "sp2" }
>>>> { "C5" "C" "sp2" }
>>>> { "C6" "C" "sp2" }
>>>> { "C7" "C" "sp2" }
>>>> { "C8" "C" "sp2" }
>>>> { "CI" "C" "sp3" }
>>>> { "OZ" "O" "sp3" }
>>>> }
>>>> loadamberparams ./libraries/frcmod.parmCHI
>>>> loadamberparams ./libraries/frcmod.ionsjc_tip3p
>>>> loadoff ./libraries/dna.parm99chi.parmbsc.off
>>>> loadoff ./libraries/ions08.lib
>>>> set default PBradii mbondi2
>>>> mol = loadpdb model.pdb
>>>> saveAmberParm mol prmtop.notworking inpcrd
>>>> quit
>>>> ------------------------------------------------
>>>>
>>>> If someone wants to use a GB model on a modified system (or let's say a
>>>> model with revised force field) I am not sure what else needs to be
>>>> defined
>>>> in the leap input file. In the cuda version of pmemd, is there a specific
>>>> file that has info on the GB model which needs to be modified in order
>>>> make
>>>> sure that the new atom types are recognized by AMBER 14 DPFP runs (so
>>>> that
>>>> the GB model won't complain about it)? It seems that usage of new atoms
>>>> types somehow creates this whole problem. Thanks.
>>>>
>>>> Best regards,
>>>>
>>>> Ilyas Yildirim, Ph.D.
>>>> -----------------------------------------------------------
>>>> = Department of Chemistry | University of Cambridge =
>>>> = Lensfield Road (Room # 380) | Cambridge, UK CB2 1EW =
>>>> = Ph.: +44-1223-336-353 | E-mail: iy222.cam.ac.uk =
>>>> = Website: http://ilyasyildirim.wordpress.com =
>>>> = ------------------------------------------------------- =
>>>> = http://www.linkedin.com/in/yildirimilyas =
>>>> = http://scholar.google.com/citations?user=O6RQCcwAAAAJ =
>>>> -----------------------------------------------------------
>>>>
>>>>
>>>> On Thu, 29 Jan 2015, Jason Swails wrote:
>>>>
>>>> On Thu, Jan 29, 2015 at 9:14 PM, Scott Le Grand <varelse2005.gmail.com>
>>>>>
>>>>> wrote:
>>>>>
>>>>> Hey Jason, I found the root cause and checked in a fix.
>>>>>>
>>>>>>
>>>>>> If I put a printf into any CUDA kernel, that's the end of its
>>>>>> performance.
>>>>>> Printf is a hog. It's only useful for debugging purposes.
>>>>>>
>>>>>
>>>>>
>>>>> That's what I was suggesting it be used for. Basically what I was
>>>>> curious
>>>>> about was whether or not any of the GB tests in our test suite hit the
>>>>> code
>>>>> path where dr didn't get initialized. If it did, that would seem (to
>>>>> me)
>>>>> to be clear evidence that that code path is not illegal/unusual (i.e.,
>>>>> indicative of bad parameters). If that printf is never triggered during
>>>>> the test suite, the parameters may be unusual. I certainly wasn't
>>>>> suggesting it be left in permanently. I'll take a look if I have time.
>>>>>
>>>>>
>>>>>
>>>>> The beginning
>>>>>>
>>>>>> of this thread has links to the data to repro this behavior. It's
>>>>>> weird
>>>>>> that we never saw this before.
>>>>>>
>>>>>> Just initialializing PMEFloat dr does the trick. The bug is fixed.
>>>>>>
>>>>>>
>>>>> I saw the commit log :).
>>>>>
>>>>> Thanks,
>>>>> Jason
>>>>>
>>>>> --
>>>>> Jason M. Swails
>>>>> BioMaPS,
>>>>> Rutgers University
>>>>> Postdoctoral Researcher
>>>>> _______________________________________________
>>>>> AMBER mailing list
>>>>> AMBER.ambermd.org
>>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>>
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Received on Fri Jan 30 2015 - 12:30:04 PST
