Sayuri,
These files are not very helpful. In order to try to reproduce your error, I need all the input files of your production simulation. I don't need any input files for your minimization, heating and equilibration runs.
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 1:56:28 PM
To: AMBER Mailing List
Cc: Abrol, Ravinder (Ravi)
Subject: Re: [AMBER] Running Explicit pH MD
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
>> > AMBER.ambermd.org<mailto:AMBER.ambermd.org><mailto:AMBER.ambermd.org>
>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
>> > ambermd.org_mailman_listinfo_amber&d=DwICAg&c=
>> > pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfb
>> Mg9_5FnKrt9-
>> > DrdQBJXyFyocKAWXc&m=0CzOuk-2YLh1F6uUAFND6WOjwV7GcNk39lYXolp9Hv4&s=
>> > zK4HAG10w8rXNdJ7QSX1RdykLqqoPJ13oLUF96YMio8&e=
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org<mailto:AMBER.ambermd.org>
>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
>> > ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=
>> > pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfb
>> Mg9_5FnKrt9-
>> > DrdQBJXyFyocKAWXc&m=46datliKQ4xTiNjFEhwmdF0rI98dFdHgKzKZ-pUad5g&s=
>> > auAQnhI5MpiGOk8f60XWS5-drYUCQDXLp4HwDfCDUYY&e=
>> >
>> >
>> >
>> >
>> > --
>> > Sayuri Pacheco
>> > California State University, Northridge
>> > Biochemistry Major
>> > Undergraduate Biomedical Researcher
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org<mailto:AMBER.ambermd.org>
>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.
>> > ambermd.org_mailman_listinfo_amber&d=DwIGaQ&c=
>> > pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfb
>> Mg9_5FnKrt9-
>> > DrdQBJXyFyocKAWXc&m=46datliKQ4xTiNjFEhwmdF0rI98dFdHgKzKZ-pUad5g&s=
>> > auAQnhI5MpiGOk8f60XWS5-drYUCQDXLp4HwDfCDUYY&e=
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.am
>> bermd.org_mailman_listinfo_amber&d=DwIGaQ&c=pZJPUDQ3SB9JplYb
>> ifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-DrdQ
>> BJXyFyocKAWXc&m=Ga6oBW7o1d_DtDGpAo8AmSlaQc_jyeKo_
>> WUAXrTBISo&s=3cf1q4Lvo6GrLDPLWu43QwkjdIqF0tFsBth1LwWXdIc&e=
>> >
>>
>>
>>
>> --
>> Sayuri Pacheco
>> California State University, Northridge
>> Biochemistry Major
>> Undergraduate Biomedical Researcher
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.am
>> bermd.org_mailman_listinfo_amber&d=DwIGaQ&c=pZJPUDQ3SB9JplYb
>> ifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-DrdQ
>> BJXyFyocKAWXc&m=Ga6oBW7o1d_DtDGpAo8AmSlaQc_jyeKo_
>> WUAXrTBISo&s=3cf1q4Lvo6GrLDPLWu43QwkjdIqF0tFsBth1LwWXdIc&e=
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwIFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=LIQu8OlVNKmzfbMg9_5FnKrt9-DrdQBJXyFyocKAWXc&m=FdC6XEqQP_-DDjLLnqQJzvk4rHHdXk1vRCZsSb6cNs8&s=uMT6bgyRZe5QVmU0_aGxVv2HY1fuYZsrKnCy-AAXx3U&e=
>>
>
>
>
> --
> 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 - 13:00:03 PST
