Re: [AMBER] Running Explicit pH MD

From: Pacheco, Sayuri <sayuri.pacheco.987.my.csun.edu>
Date: Fri, 10 Nov 2017 10:56:28 -0800

Hello,

Since the last email exceeded the size limit I have attached only the input
files for the simulation.

Best,
Sayuri

On Fri, Nov 10, 2017 at 10:53 AM, Pacheco, Sayuri <
sayuri.pacheco.987.my.csun.edu> wrote:

> Hi Vinicius,
>
> I have attached the input files let me know if you are able to view them.
> Thank you for your help!
>
> Best,
> Sayuri
>
> On Fri, Nov 10, 2017 at 8:00 AM, Cruzeiro,Vinicius Wilian D <
> vwcruzeiro.ufl.edu> wrote:
>
>> Hi Sayuri,
>>
>>
>> May you please email me your input files off the list so I can take a
>> better look at this issue?
>>
>>
>> Regards,
>>
>>
>> Vinícius Wilian D Cruzeiro
>>
>> PhD Candidate
>> Department of Chemistry, Physical Chemistry Division
>> University of Florida, United States
>>
>> Voice: +1(352)846-1633
>>
>> ________________________________
>> From: Pacheco, Sayuri <sayuri.pacheco.987.my.csun.edu>
>> Sent: Friday, November 10, 2017 1:56:59 AM
>> To: AMBER Mailing List
>> Subject: Re: [AMBER] Running Explicit pH MD
>>
>> Hi Wilian,
>> I was able to run the constant pH simulation in explicit solvent without
>> any issues using pmemd. The problem only arises when I try to run the
>> simulation using pmemd.cuda. The production step does not run and I
>> immediately get an error saying "cudaMemcpy** GpuBuffer:: Upload failed an
>> illegal memory access was
>> encountered*"
>>
>> Sayuri Pacheco
>>
>> On Mon, Oct 30, 2017 at 8:24 AM, Cruzeiro,Vinicius Wilian D <
>> vwcruzeiro.ufl.edu> wrote:
>>
>> > This is a pmemd.cuda error, but you said the simulation also crashes
>> when
>> > you use pmemd serial, correct? What is the error printed in this case?
>> >
>> >
>> > Vinícius Wilian D Cruzeiro
>> >
>> > PhD Candidate
>> > Department of Chemistry, Physical Chemistry Division
>> > University of Florida, United States
>> >
>> > Voice: +1(352)846-1633<tel:+1(352)846-1633>
>> >
>> > On Oct 30, 2017, at 11:21 AM, Pacheco, Sayuri
>> <sayuri.pacheco.987.my.csun.
>> > edu<mailto:sayuri.pacheco.987.my.csun.edu>> wrote:
>> >
>> > This is the error I'm getting
>> >
>> > "cudaMemcpy GpuBuffer::Upload failed an illegal memory access was
>> > encountered"
>> >
>> >
>> > On Mon, Oct 30, 2017 at 8:14 AM, Cruzeiro,Vinicius Wilian D <
>> > vwcruzeiro.ufl.edu<mailto:vwcruzeiro.ufl.edu>> wrote:
>> >
>> > Dear Sayuri,
>> >
>> > We need more information so we can try to help you. What is the error
>> you
>> > are getting when you run pmemd serial?
>> >
>> > Thanks,
>> >
>> >
>> > Vinícius Wilian D Cruzeiro
>> >
>> > PhD Candidate
>> > Department of Chemistry, Physical Chemistry Division
>> > University of Florida, United States
>> >
>> > Voice: +1(352)846-1633<tel:+1(352)846-1633>
>> >
>> > On Oct 30, 2017, at 10:32 AM, Pacheco, Sayuri
>> <sayuri.pacheco.987.my.csun<
>> > mailto:sayuri.pacheco.987.my.csun>.
>> > edu<mailto:sayuri.pacheco.987.my.csun.edu>> wrote:
>> >
>> > ---------- Forwarded message ----------
>> > From: "Pacheco, Sayuri" <sayuri.pacheco.987.my.csun.edu<mailto:
>> > sayuri.pacheco.987.my.csun.edu><mailto:
>> > sayuri.pacheco.987.my.csun.edu<mailto:sayuri.pacheco.987.my.csun.edu>>>
>> > Date: Oct 16, 2017 8:26 AM
>> > Subject: Running Explicit pH MD
>> > To: "AMBER Mailing List" <amber.ambermd.org<mailto:amber.ambermd.org>
>> ><mailto:amber.ambermd.org>>
>> > Cc:
>> >
>> > Dear All,
>> >
>> > I have been trying to run a constant pH explicit solvent MD using
>> > pmemd.cuda and while running the production step I get the following
>> error
>> > c*udaMemcpy** GpuBuffer:: Upload failed an illegal memory access was
>> > encountered*. When I tried running the MD with pmemd the simulation ran
>> > without a problem for a few minutes and then it crashed (icnstph=2) . Do
>> > you know what might cause this error message?
>> >
>> > P.S I ran the simulation with no problem when I set icnstph= 0 with
>> pmemd
>> > and pmemd.cuda. When I changed icnstph to 2 the simulations crashed with
>> > both pmemd and pmemd.cuda.
>> >
>> > Sincerely,
>> > Sayuri Pacheco
>> > _______________________________________________
>> > AMBER mailing list
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>> > DrdQBJXyFyocKAWXc&m=46datliKQ4xTiNjFEhwmdF0rI98dFdHgKzKZ-pUad5g&s=
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>> >
>> >
>> > --
>> > Sayuri Pacheco
>> > California State University, Northridge
>> > Biochemistry Major
>> > Undergraduate Biomedical Researcher
>> > _______________________________________________
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>>
>>
>> --
>> Sayuri Pacheco
>> California State University, Northridge
>> Biochemistry Major
>> Undergraduate Biomedical Researcher
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>> AMBER mailing list
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>
>
>
> --
> Sayuri Pacheco
> California State University, Northridge
> Biochemistry Major
> Undergraduate Biomedical Researcher
>



-- 
Sayuri Pacheco
California State University, Northridge
Biochemistry Major
Undergraduate Biomedical Researcher






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Received on Fri Nov 10 2017 - 11:00:02 PST
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