From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Tue Jun 05 2018 - 22:39:41 CDT

Behind the scenes NAMD is just running and many succsessive MM energy minimizations, which likely won’t benefit from running in parallel. Further, the Tcl code which performs the optimization isn’t parallelized at all — something I was hoping to address once the issues with comping VMD with Tcl8.6 (which includes the threads package as part of the Tcl core) were addressed; I wouldn’t hold my breath for this though.

Regards,
Christopher Mayne

> On Jun 5, 2018, at 7:38 PM, Timothy Click <tclick_at_nctu.edu.tw> wrote:
>
> Thanks for the replies. They are most helpful.
>
> On a side note, is it possible to have NAMD run in parallel? I’ve noticed that, on my 4-core iMac (27-in., late 2012, macOS High Sierra 10.13.5), NAMD occasionally runs two processes with 2 threads/process, but I was wondering whether I could specify the number of cores for bond or dihedral optimization?
>
> --
> Cordially,
> Timothy H. Click, Ph.D.
> Department of Biological Science and Technology
> Institute of Bioinformatics and Systems Biology
> National Chiao Tung University
> Dong District, Hsinchu, Taiwan 30062
>
>> On Jun 4, 2018, at 11:26, JC Gumbart <gumbart_at_physics.gatech.edu> wrote:
>>
>> Glad it worked!
>>
>> There’s a NAMD pair interaction bug that seems to only crop up in 2.12 for Macs. I’m waiting for the official 2.13 release to test again.
>>
>> Best,
>> JC
>>
>>> On Jun 3, 2018, at 11:20 PM, Timothy Click <tclick_at_nctu.edu.tw> wrote:
>>>
>>> This seems to work. Thanks.
>>>
>>> Yet, I am curious as to why NAMD 2.12 doesn’t play nicely (although I can run an independent job successfully)?
>>>
>>> --
>>> Cordially,
>>> 柯明 Timothy H. Click, Ph.D.
>>> Department of Biological Science and Technology
>>> Institute of Bioinformatics and Systems Biology
>>> National Chiao Tung University
>>> 208 Lab Building 1, 75 Bo-Ai St.
>>> Dong District, Hsinchu, Taiwan 30062
>>> (R.O.C.)
>>> +886-3-5712121 x56997
>>> tclick_at_nctu.edu.tw
>>>
>>>> On Jun 3, 2018, at 09:07, JC Gumbart <gumbart_at_physics.gatech.edu> wrote:
>>>>
>>>> Can you try NAMD 2.11?
>>>>
>>>> Best,
>>>> JC
>>>>
>>>>> On Jun 1, 2018, at 8:24 AM, <tclick_at_nctu.edu.tw> <tclick_at_nctu.edu.tw> wrote:
>>>>>
>>>>> I am attempting to run FFTK on a Mac (macOS 10.13.4, 32 Gb). Charge optimization works well, but when I attempt to perform bond optimization, it hangs on me. I start with a round of simulated annealing (T: 25, Tsteps: 25, Iter: 40). Initially, NAMD runs but after a couple of iterations [e.g., Optimizing(Iter:2)], it hangs and doesn’t advance any further. I have encountered this problem with a different molecules, but I am successful in my endeavors if I run in Linux. I am using VMD 1.9.4a 2017-12-21 and NAMD 2.12 on both the Mac and on Linux.
>>>>>
>>>>> Any suggestions on how to correct this?
>>>>>
>>>>> --
>>>>> Timothy H. Click, Ph.D.
>>>>> Dept. of Biological Sciences and Technology
>>>>> National Chiao Tung University
>>>>>
>>>>>
>>>>> <Mail Attachment>
>>>>
>>>>
>>>
>>
>>
>
>


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