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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 24 2017 - 10:00:03 PDT
