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 - 13:00:02 PDT
