When you run configure, use the "-nomtkpp" flag. MTK++ has had plenty of
issues in the past with Cygwin. If you don't need MTK++, then this does
not matter. If you do, perhaps Dan can provide advice about getting it
working on Win7 if he was able to, but a better idea would be to get ahold
of some kind of Unix system somehow.
HTH,
Jason
On Thu, Jul 19, 2012 at 3:36 AM, 钟舜 <zhongshun0643.gmail.com> wrote:
> Dear Jason,
> It is some patches of "netcdf" "hdf5" and "_autorebase". But
> I'm sorry to forget the exact name of these small patches. I didn't
> remember to write their name down when reinstallation.
> But I still get a warning after I typed "make install" and the
> installation failed at last.
>
> 警告： (1)处的 DO 循环会被执行零次
> netcdf_text_variables.f90:60.93:
> 包含于 netcdf.f90:51：
> numDims ) = (/ 1, (product(localCount(:counter)), counter = 1, numDims -
> 1) /)
>
> 1
> 警告： (1)处的 DO 循环会被执行零次
> /bin/sh ../libtool --mode=link gfortran -I../libsrc -I. -O3 -o
> libnetcdff90.la typeSizes.lo netcdf.lo
> See any operating system documentation about shared libraries for
> more information, such as the ld(1) and ld.so(8) manual pages.
> ----------------------------------------------------------------------
> test -z "/home/administrator/amber12/lib/pkgconfig" || /usr/bin/mkdir -p
> "/home/administrator/amber12/lib/pkgconfig"
> /usr/bin/install -c -m 644 fftw3.pc
> '/home/administrator/amber12/lib/pkgconfig'
> make[4]: 离开目录“/home/administrator/amber12/AmberTools/src/fftw-3.3”
> make[3]: 离开目录“/home/administrator/amber12/AmberTools/src/fftw-3.3”
> Making install in tests
> make[3]: 进入目录“/home/administrator/amber12/AmberTools/src/fftw-3.3/tests”
> make[4]: 进入目录“/home/administrator/amber12/AmberTools/src/fftw-3.3/tests”
> make[4]: 对“install-exec-am”无需做任何事。
> make[4]: 对“install-data-am”无需做任何事。
>
> ~
> ~
> ~
> ~
>
> Starting installation of MTK++ at 2012年07月19日 15:20:52.
> (cd mtkpp && make && make -j 1 install )
> make[2]: 进入目录“/home/administrator/amber12/AmberTools/src/mtkpp”
> make[2]: *** 没有指明目标并且找不到 makefile。 停止。
> make[2]: 离开目录“/home/administrator/amber12/AmberTools/src/mtkpp”
> Makefile:106: recipe for target `install_mtkpp' failed
> make[1]: *** [install_mtkpp] Error 2
> make[1]: 离开目录“/home/administrator/amber12/AmberTools/src”
> Makefile:7: recipe for target `install' failed
> make: *** [install] Error 2
>
> I really don't know what should I do now.
>
> Shun Zhong
>
> 2012/7/19 Jason Swails
>>
>> <jason.swails.gmail.com>
>
>
>
>> 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
>>
>>
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jul 19 2012 - 06:00:03 PDT
