Dear Sayuri,
After inspecting your input files, I concluded your CUDA error is caused by the fact that you are using a CPIN file corresponding to an implicit solvent simulation into an explicit solvent simulation! Even though your serial calculation is not printing any errors, the results generated are obviously wrong because of this. You have to generate your CPIN file again using the correct explicit solvent prmtop file. You should have no problems to run your simulation with the correct CPIN file.
Regards,
Vinícius Wilian D Cruzeiro
PhD Candidate
Department of Chemistry, Physical Chemistry Division
University of Florida, United States
Voice: +1(352)846-1633
________________________________
From: Cruzeiro,Vinicius Wilian D <vwcruzeiro.ufl.edu>
Sent: Friday, November 10, 2017 3:54:10 PM
To: AMBER Mailing List
Cc: Abrol, Ravinder (Ravi)
Subject: Re: [AMBER] Running Explicit pH MD
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
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>> > 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
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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 Thu Nov 16 2017 - 12:30:02 PST
