Hi Vinicius,
I will send you all my production files to your personal email. Is there
anyway to remove the files from the AMBER forum?
Sayuri
On Fri, Nov 10, 2017 at 12:54 PM, Cruzeiro,Vinicius Wilian D <
vwcruzeiro.ufl.edu> wrote:
> 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_-DDjLLnqQJzvk4rHHdXk1vRCZsSb6cN
> s8&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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Sayuri Pacheco
California State University, Northridge
Biochemistry Major
Undergraduate Biomedical Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 10 2017 - 13:30:03 PST
