Hi,
> Is there anything in AmberTools that benefits much from -openmp
The OpenMP build of cpptraj (cpptraj.OMP) has several time-consuming
actions that speed up nicely (radial, closest, the pairwise distance
calc in clustering etc). Full details are in the manual. NAB also has
certain functions that use OpenMP.
-Dan
On Fri, Oct 16, 2015 at 2:14 PM, Novosielski, Ryan
<novosirj.ca.rutgers.edu> wrote:
>> On Oct 16, 2015, at 16:03, Jason Swails <jason.swails.gmail.com> wrote:
>>
>> On Fri, Oct 16, 2015 at 3:55 PM, Novosielski, Ryan <novosirj.ca.rutgers.edu>
>> wrote:
>>
>>>> From: David A Case [dacase.scarletmail.rutgers.edu]
>>>> Sent: Friday, October 16, 2015 3:55 PM
>>>> To: AMBER Mailing List
>>>> Subject: Re: [AMBER] sander missing from AmberTools15?
>>>>
>>>>> On Fri, Oct 16, 2015, Novosielski, Ryan wrote:
>>>>>
>>>>> ...or did something go wrong with my installation if a sander binary
>>>>> wasn't built? Anyplace in particular I should look?
>>>>
>>>> Yes, something went wrong. Clues are presumably in the output of the
>>> "make
>>>> install" step. One idea: save that output to a file, e.g.
>>>>
>>>> make install | tee install.log
>>>
>>>> so you won't lose things as the scroll off the screen. But I'm a little
>>>> surprised that such a failure didn't halt the install process and leave
>>> the
>>>> error starting at you on the terminal....
>>>
>>> I was surprised too, that's why I was pretty sure I should at least ask! I
>>> just recalled -- I did -openmp, presuming that to be the right thing to on
>>> a multi-core/non-MPI environment. Maybe that was the wrong thing to dod?
>>
>> sander doesn't have an OpenMP build, so it won't get built with that
>> configure option. Using the -openmp flag *only* installs OpenMP-enabled
>> programs (if memory serves, that would be cpptraj.OMP, nab, and paramfit...
>> maybe others, but I don't remember).
>>
>> You need to configure in serial to get sander and with -mpi to get
>> sander.MPI.
>
> OK; thanks. Thought that might explain it. Is there anything in AmberTools that benefits much from -openmp much to the point that one would bother two configures to get the serial stuff and then OpenMP build, or no? I don't use the software, just maintain it, so I'm a little low on information like that. Thanks again, Jason. You are always a help.
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Oct 16 2015 - 14:00:03 PDT
