Hello to everyone,.
Some updates,
I tried my simulation with specific seed number and the simulation crashes
on the sime step everytime. So there must be a problem with my system,
although it seems pretty normal when i check it with vmd. Anyway i am glad
that there is no problem with my card.
However i am supprised that my old GPU (GTX 1060) does not produce such
error whatever seed number i use.
Best Regards
George
> 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
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
> --
> ---------------------------------------------
> 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
>
--
---------------------------------------------
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
Received on Wed Apr 01 2020 - 00:30:02 PDT
