On Fri, Apr 21, 2017 at 4:53 PM, Baker, Joseph <bakerj.tcnj.edu> wrote:
> 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?
>
If you look at the header of update_amber, you will see
#!/usr/bin/env python
so the script will use whatever python version in your environment.
(and some users prefer not using Miniconda python).
cheers
Hai
> 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
>> >>>>>>>
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Received on Fri Apr 21 2017 - 21:00:02 PDT
