Thanks, Hai. That worked out fine.
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 Mon, Apr 24, 2017 at 12:54 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> in AT16, the bin/FEW.pl program is symlinked to AmberTools/src/FEW/FEW.pl
> but in AT17, that file is copied.
>
> You can just remove bin/FEW.pl and "make install" again.
> PS: We did this change to FEW.pl can go to binary distribution
> (without source code).
>
> cheers
> Hai
>
> On Mon, Apr 24, 2017 at 12:41 PM, Baker, Joseph <bakerj.tcnj.edu> wrote:
> > 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
> >> >> _______________________________________________
> >> >> 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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Received on Mon Apr 24 2017 - 12:00:02 PDT
