Hi all,
Jason, I untarred the file and ran the ./configure script in $AMBERHOME,
and the installation was running fine for a bit until this set of messages
Installing
/share/apps/amber16/lib/perl/share/man/man3/Chemistry::Pattern.3pm
Installing /share/apps/amber16/lib/perl/share/man/man3/Math::VectorReal.3pm
Installing /share/apps/amber16/lib/perl/share/man/man3/Chemistry::File.3pm
Installing
/share/apps/amber16/lib/perl/share/man/man3/Chemistry::3DBuilder.3pm
Installing /share/apps/amber16/lib/perl/share/man/man3/Chemistry::Ring.3pm
Installing
/share/apps/amber16/lib/perl/share/man/man3/Chemistry::File::MDLMol.3pm
Installing /share/apps/amber16/lib/perl/bin/yapp
Installing /share/apps/amber16/lib/perl/bin/mok
Appending installation info to
/share/apps/amber16/lib/perl//lib64/perl5/perllocal.pod
make[3]: Leaving directory
`/share/apps/amber16/AmberTools/src/FEW/additional_libs/PerlMol-0.3500'
cp -f /share/apps/amber16/AmberTools/src/FEW/FEW.pl /share/apps/amber16/bin
cp: `/share/apps/amber16/AmberTools/src/FEW/FEW.pl' and
`/share/apps/amber16/bin/FEW.pl' are the same file
make[2]: *** [install] Error 1
make[2]: Leaving directory `/share/apps/amber16/AmberTools/src/FEW'
make[1]: *** [serial] Error 2
make[1]: Leaving directory `/share/apps/amber16/AmberTools/src'
make: *** [install] Error 2
And then it stopped. What should I do to fix this?
Thanks,
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 11:49 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> 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
> >> >>>>>>>
> >> >>>>>> _______________________________________________
> >> >>>>>> 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
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
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> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Apr 24 2017 - 10:00:02 PDT
