Hi Darrin,
I tried uploading my files to the list but I got a message back that
it was too big to post directly and that the message is awaiting
approval. I will email you and taisung the files I was mentioning in
this post.
Thanks,
Max
On Mon, Jun 25, 2018 at 2:00 PM, Darrin York <york.chem.rutgers.edu> wrote:
> Hi Max,
>
> Thanks for pointing out the problem. I think you have
> sent us (Tai-Sung) the full input files we will use to reproduce the
> symptoms - but feel free to send them, or anything additional that might
> help, also to me (Darrin.York.rutgers.edu), and we will get back to you
> soon. We are working on it, and will talk with you directly and post to
> the list when we have it sorted out.
>
> thanks again!
>
> Darrin
>
> On 06/24/2018 10:58 AM, Maximilian Ebert wrote:
>> Oh and I also tried the system with NVT in each window to rule out the
>> barostat. We see the same error in an NVT ensemble. (mail with files
>> awaits approval, do you have another mean to transfer the files?)
>>
>> On Sat, Jun 23, 2018 at 6:10 PM, David Cerutti <dscerutti.gmail.com> wrote:
>>> This error message "an illegal memory access was encountered launching
>>> kernel kNLSkinTest" is not one of the code's most helpful error messages.
>>> It's kind of like saying that the patient died from lack of oxygen reaching
>>> the brain. (But WHY--what started the sequence of events leading to that
>>> condition?) In the GPU code, if something goes wrong, the ultimate symptom
>>> is often that a particle gets moving too fast and flies off into the
>>> stratosphere, which creates the kNLSkinTest problem. But if you can post
>>> your inputs we can take a look. For some very large systems we have been
>>> seeing occasional issues like this in standard MD and I have made some
>>> progress tracking down the problem.
>>>
>>> Dave
>>>
>>>
>>> On Sat, Jun 23, 2018 at 10:53 AM Maximilian Ebert <mebert.chemcomp.com>
>>> wrote:
>>>
>>>> Hi,
>>>>
>>>> we are running the following TI protocol using AMBER18 pmemd.cuda:
>>>>
>>>> Full dual topology one step TI transformation. 2fs time step and full
>>>> shake.
>>>>
>>>> Common equilibration at lambda 0.5 and scalpha = scbeta = 0
>>>> 1. minimization on cpu
>>>> 2. heating to 300k 200ps
>>>> 3. nvt 300k 200ps
>>>> 4. npt (Monte Carlo) 1bar 300k 1600ps
>>>>
>>>> TI with 14 lambda windows (values from chebyshev integration) and
>>>> scalpha = 0.5 scbeta=12
>>>> 1. start with new velocities from common equilibration NPT 1000ps
>>>> 2. production NPT 1000ps
>>>>
>>>> each trajectory is segmented in a max length of 250ps and restarted.
>>>>
>>>> The above protocol works without any crash for small ligands like the
>>>> lysozyme + bnz/phn but using larger systems like kinase + Imatinib
>>>> (gleevec) causes for edge lambdas (lambda > 0.8 or lambda < 0.2) the
>>>> system to crash.
>>>>
>>>> Nothing in the stdout indicates a reason for the Error: an illegal
>>>> memory access was encountered launching kernel kNLSkinTest. Also
>>>> restarting the segment often recovers and runs just fine. The message
>>>> comes most of the times in the beginning of the run after a couple of
>>>> steps but not always. The Skin appears to have something to do with
>>>> the barostat and the box size.
>>>>
>>>> Therefore, we also tried the berendsen barostat but this resulted
>>>> mainly in distorted ligand conformations (forming a pile of atoms in
>>>> space). There might also be a bug in the berendsen barostat when using
>>>> TI GPU code. We also tried 1fs with tishakemask for the ligand but
>>>> didn't help.
>>>>
>>>> We are currently running a test with full NVT in each lambda
>>>> production window. However, if anybody can give us some insight what
>>>> is going on it would help us greatly.
>>>>
>>>> Thanks,
>>>> Max
>>>>
>>>> --
>>>> Maximilian Ebert, PhD | Applications Scientist
>>>> +1 (514) 393-1055 x136 | support.chemcomp.com
>>>>
>>>> --
>>>> Chemical Computing Group | https://na01.safelinks.protection.outlook.com/?url=www.chemcomp.com&data=02%7C01%7Cyork%40chem.rutgers.edu%7C9673ca29a50440c7efe508d5d9e309b0%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636654491503927766&sdata=rb%2FlIHrPIRyWXkKePFBGBD6b0C2zR9ttCCgi76syyBA%3D&reserved=0 <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.chemcomp.com&data=02%7C01%7Cyork%40chem.rutgers.edu%7C9673ca29a50440c7efe508d5d9e309b0%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636654491503927766&sdata=xsoojuHqHltlpprTnFWxWiEgpM3OfSGedv7LySVR5FI%3D&reserved=0> |
>>>> 910-1010 Sherbrooke W., Montreal QC H3A 2R7, Canada | +1 514 393 1055
>>>>
>>>> Manage Communications: https://na01.safelinks.protection.outlook.com/?url=www.chemcomp.com%2FManage_Subscription.htm&data=02%7C01%7Cyork%40chem.rutgers.edu%7C9673ca29a50440c7efe508d5d9e309b0%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636654491503927766&sdata=9H2HrUzF6Ic1K6QxL40hzNguZIPGg6eoJPy2zRVsE8s%3D&reserved=0
>>>> <https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.chemcomp.com%2FManage_Subscription.htm&data=02%7C01%7Cyork%40chem.rutgers.edu%7C9673ca29a50440c7efe508d5d9e309b0%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636654491503927766&sdata=udGBUnq8c4zZOxv3UG%2BdSDwrcqnZfGaq7dVUvIVutKE%3D&reserved=0>
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%7Cyork%40chem.rutgers.edu%7C9673ca29a50440c7efe508d5d9e309b0%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636654491503927766&sdata=x%2FZkDLm1RiZNNY4Ofp9LHB639pVyq0PTe4aE08wuvHI%3D&reserved=0
>>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.ambermd.org%2Fmailman%2Flistinfo%2Famber&data=02%7C01%7Cyork%40chem.rutgers.edu%7C9673ca29a50440c7efe508d5d9e309b0%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636654491503927766&sdata=x%2FZkDLm1RiZNNY4Ofp9LHB639pVyq0PTe4aE08wuvHI%3D&reserved=0
>>
>>
>
> --
> --
> ======================================================================
> Darrin M. York : Henry Rutgers University Professor
> : Director, Cyberlearning
> Center for Integrative Proteomics : Innovation & Research Center
> Research and Department of : Director, Laboratory for
> Chemistry & Chemical Biology : Biomolecular Simulation Research
> :
> Rutgers, the State University : Darrin.York.rutgers.edu
> of New Jersey : fax: +1-732-445-4320
> 174 Frelinghuysen Road : phone: +1-848-445-5199
> Piscataway, NJ 08854 USA : http://theory.rutgers.edu
> ======================================================================
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Maximilian Ebert, PhD | Applications Scientist
+1 (514) 393-1055 x136 | support.chemcomp.com
--
Chemical Computing Group | www.chemcomp.com <http://www.chemcomp.com> |
910-1010 Sherbrooke W., Montreal QC H3A 2R7, Canada | +1 514 393 1055
Manage Communications: www.chemcomp.com/Manage_Subscription.htm
<http://www.chemcomp.com/Manage_Subscription.htm>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 26 2018 - 14:00:03 PDT
