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.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Oct 16 2015 - 13:30:07 PDT
