On Mon, Jun 17, 2013 at 12:46 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> If you just re-run configure it will automatically initiate the update
> process. Running the steps I listed and the recompiling should work.
>
> Let us know if you encounter issues.
>
This should also work ;).
>
> -Dan
>
> On Mon, Jun 17, 2013 at 10:44 AM, Hunter Brown
> <bassoongoon.earthlink.net> wrote:
> > Okay thank you. I have successfully compiled and installed amber WITHOUT
> the patches. How can I get the patches after the installation? Do I just
> run update amber?
> >
> > Correct me if I am wrong: I need to (1) look for the patch files (2)
> delete the dos endings (3) run update amber.
> >
> > I really appreciate your help.
> >
> > -Hunter
> >
> > -----Original Message-----
> >>From: Daniel Roe <daniel.r.roe.gmail.com>
> >>Sent: Jun 17, 2013 10:10 AM
> >>To: Hunter Brown <bassoongoon.earthlink.net>, AMBER Mailing List <
> amber.ambermd.org>
> >>Subject: Re: [AMBER] Difficulty compiling amber12/ambertools13
> >>
> >>Hi,
> >>
> >>This is actually an issue with dos line endings in the patch file
> >>confusing 'patch' under cygwin. If you remove the dos line endings
> >>from the patch, updating should occur successfully:
> >>
> >>$> cd $AMBERHOME
> >>$> ./configure -cygwin gnu
> >>...
> >>Applying AmberTools 13/update.4
> >>PatchingError: .patches/AmberTools13_Unapplied_Patches/update.4 failed
> >>to apply. No changes made from this patch
> >>Automatic patching failed! Check the errors before re-configuring
> >>$> dos2unix.exe .patches/AmberTools13_Unapplied_Patches/update.4
> >>dos2unix: converting file
> >>.patches/AmberTools13_Unapplied_Patches/update.4 to Unix format ...
> >>$> ./configure -cygwin gnu
> >>...
> >>
> >>A fix to update_amber is also in the works to correct this.
> >>
> >>-Dan
> >>
> >>On Fri, Jun 14, 2013 at 4:41 PM, Hunter Brown <bassoongoon.earthlink.net>
> wrote:
> >>> Hello, I am having difficulty compiling amber12 and ambertools 13. I
> am a windows user, so I am working via Cygwin.
> >>>
> >>> When I try to apply patches I get this message:
> >>>
> >>>
> >>>
> >>> PatchingError: .patches/AmberTools13_Unapplied_Patches/update.4 failed
> to apply. No changes made from this patch
> >>> Automatic patching failed! Check the errors before re-configuring
> >>>
> >>>
> >>>
> >>>
> >>> When I try to skip the patches using './configure cygwin' I get this
> message:
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> NOT updating your tree and continuing anyway.
> >>> Could not find the X11 libraries; you may need to edit config.h
> >>> to set the XHOME and XLIBS variables.
> >>> Searching for python2... Found python2.7: /usr/bin/python2.7
> >>> Error: Architecture/compiler 'cygwin' is not supported!
> >>> Type './configure -help' for options.
> >>> Configure failed due to the errors above!
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> I have tried using './configure gnu -cygwin' as well. The patches
> still fail to apply. If I try to skip the patches with './configure gnu
> -cygwin' I get this message (by the way, the single quotes are to make the
> commands I enter stand out from the rest of my text. I did not actually put
> single quotes into my Cygwin bash) :
> >>>
> >>>
> >>>
> >>>
> >>> NOT updating your tree and continuing anyway.
> >>> Error: unknown compiler: gnu
> >>> Type './configure -help' for options.
> >>> Configure failed due to the errors above!
> >>>
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> If somebody could help me get that sorted out I would really
> appreciate it. I need to learn Amber/Ambertools so that I can start running
> simulations. Because I have had difficulty configuring/compiling Amber, I
> cannot even reach the stage where I can begin learning how to use it; its
> frustrating!
> >>>
> >>>
> >>>
> >>>
> >>>
> >>> Anyways, thanks for reading and I hope that someone can be of
> assistance to me.
> >>>
> >>>
> >>> -Hunter
> >>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >>--
> >>-------------------------
> >>Daniel R. Roe, PhD
> >>Department of Medicinal Chemistry
> >>University of Utah
> >>30 South 2000 East, Room 201
> >>Salt Lake City, UT 84112-5820
> >>http://home.chpc.utah.edu/~cheatham/
> >>(801) 587-9652
> >>(801) 585-9119 (Fax)
> >>
> >>_______________________________________________
> >>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
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jun 17 2013 - 10:00:04 PDT
