Dave and Stephan
Thank you for your suggestions.
I shall try to use the same seed number to check about the randomness.
Dave i shall send you the files asked.
I missed to tell you that all equilibration steps were run on CPU
without errors or warnings, and only Hold steps 1-10 and production was
run on GPU.
Sice i follow the tutorial, on all hold steps i use the skinnb=5 command.
George
Στις 22/3/20 1:44 π.μ., ο Stephan Schott έγραψε:
> Hi George,
> Indeed those errors are not very informative, but also farily common with
> membrane systems. Maybe David can find something wrong there, but some tips
> that usually help is to minimize using CPU code, rather than GPU. Sometimes
> and rather randomly an atom could get "lost". Also increasing the number of
> atoms included in the nonbonded pairlist with skinnb in the first
> equilibrations steps helps in some cases. For the you can add something
> like this at the end of your input file (default is 2A):
> &ewald
> skinnb = 5
> &end
>
>
> El sáb., 21 mar. 2020 a las 23:58, David Cerutti (<dscerutti.gmail.com>)
> escribió:
>
>> If your random seed is set to -1, that is one possible source of the
>> randomness (bases the PRNG on wall clock time). But I suspect that there
>> is something else amiss with your system. Perhaps a strained bond or clash
>> that is giving SHAKE problems. Can you reply (just to me) with your
>> topology and inpcrd?
>>
>> Dave
>>
>>
>> On Sat, Mar 21, 2020 at 3:43 PM Giorgos Lambrinidis <
>> lambrinidis.pharm.uoa.gr> wrote:
>>
>>> Dear Amber Users
>>>
>>> I am facing a strange problem, regarding MSI RTX 2080 Super GPU.
>>>
>>> I am working on a transmembrane GPCR protein with 69385 atoms including
>>> the Lipids and water molecules. I have created the system using the
>>> Amber Tutorial 16 for Lipid14 ForceField.
>>>
>>> I run the equilibration protocol + the production simulation on a
>>> computer with the following characteristics:
>>>
>>> AMD Ryzen 7 2700 Eight-Core Processor, 24GB RAM, GeForce GTX 1060 with
>>> 6GB, and nvidia driver 418,43, GNU compilers and cuda 10.1. I am using
>>> Amber 18 with Ambertools19.
>>>
>>> Few days ago, I bought a new GPU, MSI RTX 2080 Super 8GB and I installed
>>> on the following system:
>>>
>>> Intel(R) Core(TM) i7-3770 CPU @ 3.40GHz, 16GB RAM, with nvidia driver
>>> 435,21, GNU compilers and cuda 10.1 . I am using Amber 18 with
>>> Ambertools19.
>>>
>>> When I run the same GPCR protein with 69385 on the new GPU I get
>>> randomly the following error:
>>>
>>> “cudamemcpy gpubuffer::download failed an illegal memory access was
>>> encounterer”
>>>
>>> The job terminates but the next steps (hold or production based on Amber
>>> Tutorial 16) are running normally until the next error etc.
>>>
>>> I know that this kind of error is very general. I am open to suggestions
>>> how to determine if the error is because of the hardware, or in the
>>> compilation process.
>>>
>>> I tried a bigger system produced by CHARMM-GUI for amber, and the
>>> equilibration + production was run without any error.
>>>
>>> As I said the error is generating randomly. If I repeat the same job
>>> with the same parameters I will get the error in a different step (on
>>> hold or production step)
>>>
>>> I can share input files if necessary.
>>>
>>> Thank you in advance
>>>
>>> Dr. George Lamprinidis
>>>
>>> --
>>> ---------------------------------------------
>>> Dr George Lambrinidis
>>> Researcher & Laboratory Assistant Staff
>>> School of Health Sciences
>>> Faculty of Pharmacy
>>> National & Kapodistrian University of Athens
>>> Greece
>>> tel: +30 2107274304
>>> +30 2107274521
>>> fax: +30 2107274747
>>> e-mail: lambrinidis.pharm.uoa.gr
>>> geolampr.gmail.com
>>> ---------------------------------------------
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>> _______________________________________________
>> AMBER mailing list
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>>
>
--
---------------------------------------------
Dr George Lambrinidis
Researcher & Laboratory Assistant Staff
School of Health Sciences
Faculty of Pharmacy
National & Kapodistrian University of Athens
Greece
tel: +30 2107274304
+30 2107274521
fax: +30 2107274747
e-mail: lambrinidis.pharm.uoa.gr
geolampr.gmail.com
---------------------------------------------
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Received on Sun Mar 22 2020 - 03:00:02 PDT
