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.
-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
Received on Mon Jun 17 2013 - 10:00:03 PDT
