Hi Jason,
Okay, so untar that and then just run ./configure and everything should
work out? Shouldn't it already be using the python2.7 in my miniconda
directory?
Thanks again,
Joe
Joe
------
Joseph Baker, PhD
Assistant Professor
Department of Chemistry
C101 Science Complex
The College of New Jersey
Ewing, NJ 08628
Phone: (609) 771-3173
Web: http://bakerj.pages.tcnj.edu/
On Fri, Apr 21, 2017 at 4:48 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> Untar the tar file you found in the directory after the upgrade finished.
> That will finish the upgrade.
>
> I will fix the upgrade script to work with python 2.4-2.6.
>
> Thanks,
> Jason
>
> --
> Jason M. Swails
>
> > On Apr 21, 2017, at 4:23 PM, Baker, Joseph <bakerj.tcnj.edu> wrote:
> >
> > Okay, will wait for Jason to weigh in. Thanks, Hai.
> >
> > Joe
> >
> >
> > ------
> > Joseph Baker, PhD
> > Assistant Professor
> > Department of Chemistry
> > C101 Science Complex
> > The College of New Jersey
> > Ewing, NJ 08628
> > Phone: (609) 771-3173
> > Web: http://bakerj.pages.tcnj.edu/
> >
> >
> >> On Fri, Apr 21, 2017 at 3:46 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >>
> >>> On Fri, Apr 21, 2017 at 3:43 PM, Baker, Joseph <bakerj.tcnj.edu>
> wrote:
> >>> Hi Hai,
> >>>
> >>> Thanks. So looking in the AmberTools/src directory, I see a number of
> >>> directories that are updated to today's date actually, so it does seem
> >> that
> >>> something must have been extracted? For example, paramfit, parmed,
> >> cpptraj,
> >>> etc., are updated to today's date. There are a few that are not, for
> >>> example sebomd directory, ucpp-1.3 directory, include directory lapack
> >>> directory, lib directory, and some others. I am not sure if they are
> all
> >>> supposed to be Apr21 in there now?
> >>
> >>> So perhaps some directories got
> >>> extracted okay but not others?
> >>
> >> yeah
> >>
> >> Hai
> >>
> >>>
> >>> Joe
> >>>
> >>>
> >>> ------
> >>> Joseph Baker, PhD
> >>> Assistant Professor
> >>> Department of Chemistry
> >>> C101 Science Complex
> >>> The College of New Jersey
> >>> Ewing, NJ 08628
> >>> Phone: (609) 771-3173
> >>> Web: http://bakerj.pages.tcnj.edu/
> >>>
> >>>
> >>>> On Fri, Apr 21, 2017 at 3:39 PM, Hai Nguyen <nhai.qn.gmail.com>
> wrote:
> >>>>
> >>>>> On Fri, Apr 21, 2017 at 3:36 PM, Baker, Joseph <bakerj.tcnj.edu>
> wrote:
> >>>>> Perhaps that warning at the end of my original email about __exit__
> >> does
> >>>>> not matter, and I can just run ./configure now manually without any
> >>>> trouble?
> >>>>
> >>>> I don't think so. The error meant that the tarfile was not
> >>>> successfully extracted.
> >>>>
> >>>> Let's wait for Jason (who wrote that script) to give feedback.
> >>>>
> >>>> Meanwhile, may be playing with the tarfile downloaded from amber
> >> website?
> >>>>
> >>>> thanks.
> >>>> Hai
> >>>>
> >>>>>
> >>>>>
> >>>>> ------
> >>>>> Joseph Baker, PhD
> >>>>> Assistant Professor
> >>>>> Department of Chemistry
> >>>>> C101 Science Complex
> >>>>> The College of New Jersey
> >>>>> Ewing, NJ 08628
> >>>>> Phone: (609) 771-3173
> >>>>> Web: http://bakerj.pages.tcnj.edu/
> >>>>>
> >>>>>
> >>>>> On Fri, Apr 21, 2017 at 3:30 PM, Baker, Joseph <bakerj.tcnj.edu>
> >> wrote:
> >>>>>
> >>>>>> Hi Hai,
> >>>>>>
> >>>>>> I just tried that and get the following output
> >>>>>>
> >>>>>> [root.neon amber16]# miniconda/bin/python update_amber --upgrade
> >>>>>> No major upgrade available.
> >>>>>> [root.neon amber16]#
> >>>>>>
> >>>>>>
> >>>>>> ------
> >>>>>> Joseph Baker, PhD
> >>>>>> Assistant Professor
> >>>>>> Department of Chemistry
> >>>>>> C101 Science Complex
> >>>>>> The College of New Jersey
> >>>>>> Ewing, NJ 08628
> >>>>>> Phone: (609) 771-3173
> >>>>>> Web: http://bakerj.pages.tcnj.edu/
> >>>>>>
> >>>>>>
> >>>>>>> On Fri, Apr 21, 2017 at 3:27 PM, Nhai <nhai.qn.gmail.com> wrote:
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>>> On Apr 21, 2017, at 3:23 PM, Baker, Joseph <bakerj.tcnj.edu>
> >> wrote:
> >>>>>>>>
> >>>>>>>> $AMBERHOME/miniconda/bin
> >>>>>>>
> >>>>>>> Uhm, python 2.6 does not have context manger for tarfile. Can you
> >> use
> >>>>>>> miniconda python
> >>>>>>>
> >>>>>>> $AMBERHOME/miniconda/bin/python update_amber --upgrade
> >>>>>>>
> >>>>>>> (Or use amber.python which is alias of miniconda python).
> >>>>>>>
> >>>>>>> Hai
> >>>>>>> _______________________________________________
> >>>>>>> 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
> >>>>>>
> >>>>> _______________________________________________
> >>>>> 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
> >>>>
> >>> _______________________________________________
> >>> 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
> >>
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 21 2017 - 14:00:03 PDT
