This is OK. I think this has to do with line endings (DOS and Unix do
theirs differently). IMO, you can safely ignore this failure. Just re-run
patch_amber.py with the --ignore-fails flag. i.e.:
cd $AMBERHOME
./patch_amber.py --update-tree --ignore-fails
Then you should be good to run configure and build Amber.
Out of curiosity, which packages had you forgotten?
All the best,
Jason
On Wed, Jul 18, 2012 at 10:38 PM, 钟舜 <zhongshun0643.gmail.com> wrote:
> Dear jason，
>
> First， I feel very upset for my OS is Win7.
> But I still try to check the Cygwin setup back up as you
> advise. There are indeed two little items remained "skip". After
> reinstallation of the Cygwin, the error is gone.
> I have learnt the lesson again: "Be careful whatever you do."
> But unfortunately I encounter a new error:
> Applying AmberTools12 patches
> Error or warning during patching process for
> .patches/AmberTools_Unapplied_Patches/bugfix.4:
> 4 out of 4 hunks FAILED -- saving rejects to file
> AmberTools/test/mmpbsa_py/08_Stability/FINAL_DECOMP_MMPBSA2.csv.save.rej
> I am approaching breakdown, maybe I should give up now.
>
> Shun Zhong
> 2012/7/19 Jason Swails <jason.swails.gmail.com>
>
>> You should keep these replies on the Amber mailing list so others stay
>> generally informed and so you can benefit from others' experiences and
>> advice.
>>
>> Your error suggests something has gone awry with the mechanism that the
>> patch_amber.py Python script uses to try to access the web. I'm not
>> sure why the first message is coming about (the one about address space) --
>> I don't know if it's a memory issue (seems unlikely), or if some later
>> version of Windows has broken this part of Cygwin.
>>
>> I don't think it's possible for me (or anybody else, most likely) to help
>> fix this behavior unless we can reproduce the issue. So please follow
>> these steps:
>>
>> Open the Cygwin setup back up and go through carefully to make sure that
>> every package listed on http://jswails.wikidot.com/windows-cygwin is
>> selected and installed. If it is, and you are still getting these errors,
>> then respond back (to the list) with the OS you are using (is it Windows 7,
>> XP, Vista, ...?)
>>
>> I've only tested the Cygwin install on Windows XP, and it's worked fine
>> for me. It's always possible that Windows 7 (or some upgrade therein) has
>> broken Cygwin's urllib module in its Python.
>>
>> You can always download the patches one-by-one and apply them using
>> "./patch_amber.py --apply <patch_file>" (it never attempts to go online to
>> find it at that point).
>>
>> You can also set up a guest Linux OS in a virtual machine (google for
>> VirtualBox) and operate with Amber in there (this is probably the easiest
>> route, since Linux/Mac are the best-tested platforms by the developers).
>>
>> HTH,
>> Jason
>>
>> On Wed, Jul 18, 2012 at 2:15 AM, 钟舜 <zhongshun0643.gmail.com> wrote:
>>
>>> Dear jason，
>>>
>>> Thank for your answer and it's very helpful. But I receive
>>> a new error after reinstallation of cygwin as you advised. The error is as
>>> follows:
>>>
>>>
>>> Applying AmberTools12 patches
>>> 1 [main] python2.6 8624 child_info_fork::abort: address space
>>> needed by 'fcntl.dll' (0x3D0000) is already occupied
>>> Traceback (most recent call last):
>>> File "./patch_amber.py", line 958, in <module>
>>> if ipatch.apply_patch() and not opt.ignore_fails: sys.exit(1)
>>> File "./patch_amber.py", line 271, in apply_patch
>>> process = Popen(args, stdin=patch_file, stdout=PIPE, stderr=PIPE)
>>> File "/usr/lib/python2.6/subprocess.py", line 623, in __init__
>>> errread, errwrite)
>>> File "/usr/lib/python2.6/subprocess.py", line 1051, in _execute_child
>>> self.pid = os.fork()
>>> OSError: [Errno 11] Resource temporarily unavailable
>>> Automatic patching failed! Check the errors before re-configuring
>>>
>>>
>>> I have tried many times, but it still gives this error. I don't know how
>>> long the "temporarily" means, or I must do something to solve this error.
>>>
>>> Best regards!
>>> Shun Zhong
>>>
>>> ---------------
>>> shun zhong
>>> Graduate Student of Technical Institute of Physcis and Chemistry, CAS
>>> Beijing, P.R.China, 100190
>>> Web: htthttp://www.ipc.ac.cn/
>>>
>>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>>
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jul 18 2012 - 20:00:04 PDT
