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
>
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Received on Wed Jul 18 2012 - 20:00:03 PDT
